--- _id: '1041' abstract: - lang: eng text: We demonstrate efficient transfer of ultracold molecules into a deeply bound rovibrational level of the singlet ground state potential in the presence of an optical lattice. The overall molecule creation efficiency is 25%, and the transfer efficiency to the rovibrational level |v = 73, J = 2) is above 80%. We find that the molecules in |v = 73, J = 2) are trapped in the optical lattice, and that the lifetime in the lattice is limited by optical excitation by the lattice light. The molecule trapping time for a lattice depth of 15 atomic recoil energies is about 20 ms. We determine the trapping frequency by the lattice phase and amplitude modulation technique. It will now be possible to transfer the molecules to the rovibrational ground state |v = 0, J = 0) in the presence of the optical lattice. acknowledgement: We are indebted to R Grimm for generous support and we thank S Knoop, N Boloufa, and O Dulieu for valuable discussions. We gratefully acknowledge funding by the Austrian Ministry of Science and Research (BMWF) and the Austrian Science Fund (FWF) in the form of a START prize grant. RH acknowledges support by the European Union in the form of a Marie-Curie International Incoming Fellowship (IIF). article_processing_charge: No author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Manfred full_name: Mark, Manfred last_name: Mark - first_name: Elmar full_name: Haller, Elmar last_name: Haller - first_name: Mattias full_name: Gustavsson, Mattias last_name: Gustavsson - first_name: Russell full_name: Hart, Russell last_name: Hart - first_name: Andreas full_name: Liem, Andreas last_name: Liem - first_name: Holger full_name: Zellmer, Holger last_name: Zellmer - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl citation: ama: Danzl JG, Mark M, Haller E, et al. Deeply bound ultracold molecules in an optical lattice. New Journal of Physics. 2009;11. doi:10.1088/1367-2630/11/5/055036 apa: Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., Liem, A., … Nägerl, H. (2009). Deeply bound ultracold molecules in an optical lattice. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/11/5/055036 chicago: Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, Andreas Liem, Holger Zellmer, and Hanns Nägerl. “Deeply Bound Ultracold Molecules in an Optical Lattice.” New Journal of Physics. IOP Publishing Ltd., 2009. https://doi.org/10.1088/1367-2630/11/5/055036. ieee: J. G. Danzl et al., “Deeply bound ultracold molecules in an optical lattice,” New Journal of Physics, vol. 11. IOP Publishing Ltd., 2009. ista: Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Liem A, Zellmer H, Nägerl H. 2009. Deeply bound ultracold molecules in an optical lattice. New Journal of Physics. 11. mla: Danzl, Johann G., et al. “Deeply Bound Ultracold Molecules in an Optical Lattice.” New Journal of Physics, vol. 11, IOP Publishing Ltd., 2009, doi:10.1088/1367-2630/11/5/055036. short: J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, A. Liem, H. Zellmer, H. Nägerl, New Journal of Physics 11 (2009). date_created: 2018-12-11T11:49:50Z date_published: 2009-03-14T00:00:00Z date_updated: 2021-01-12T06:47:51Z day: '14' doi: 10.1088/1367-2630/11/5/055036 extern: '1' external_id: arxiv: - '0812.5070' intvolume: ' 11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/0812.5070 month: '03' oa: 1 oa_version: None publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '6349' status: public title: Deeply bound ultracold molecules in an optical lattice type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2009' ... --- _id: '1043' abstract: - lang: eng text: One possibility for the creation of ultracold, high phase space density quantum gases of molecules in the rovibronic ground state relies on first associating weakly-bound molecules from quantum-degenerate atomic gases on a Feshbach resonance and then transferring the molecules via several steps of coherent two-photon stimulated Raman adiabatic passage (STIRAP) into the rovibronic ground state. Here, in ultracold samples of Cs2 Feshbach molecules produced out of ultracold samples of Cs atoms, we observe several optical transitions to deeply-bound rovibrational levels of the excited 0 u+ molecular potentials with high resolution. At least one of these transitions, although rather weak, allows efficient STIRAP transfer into the deeply-bound vibrational level v = 73> of the singlet X 1Σg+ ground state potential, as recently demonstrated (J. G. Danzl, E. Haller, M. Gustavsson, M. J. Mark, R. Hart, N. Bouloufa, O. Dulieu, H. Ritsch, and H.-C. Nägerl, Science, 2008, 321, 1062). From this level, the rovibrational ground state v = 0, J = 0> can be reached with one more transfer step. In total, our results show that coherent ground state transfer for Cs2 is possible using a maximum of two successive two-photon STIRAP processes or one single four-photon STIRAP process. acknowledgement: "We are indebted to R. Grimm for generous support and we thank T. Bergeman, H.\r\nSalami, J. Hutson, J. Aldegunde, and E. Tiemann for valuable discussions. We\r\ngratefully acknowledge funding by the Austrian Ministry of Science and Research\r\n(BMWF) and the Austrian Science Fund (FWF) in the form of a START prize grant\r\nand by the European Science Foundation (ESF) in the framework of the EuroQUAM collective research project QuDipMol. R. H. acknowledges support by\r\nthe European Union in form of a Marie Curie International Incoming Fellowship\r\n(IIF)." article_processing_charge: No author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Manfred full_name: Mark, Manfred last_name: Mark - first_name: Elmar full_name: Haller, Elmar last_name: Haller - first_name: Mattias full_name: Gustavsson, Mattias last_name: Gustavsson - first_name: Nadia full_name: Bouloufa, Nadia last_name: Bouloufa - first_name: Olivier full_name: Dulieu, Olivier last_name: Dulieu - first_name: Helmut full_name: Ritsch, Helmut last_name: Ritsch - first_name: Russell full_name: Hart, Russell last_name: Hart - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl citation: ama: Danzl JG, Mark M, Haller E, et al. Precision molecular spectroscopy for ground state transfer of molecular quantum gases. Faraday Discussions. 2009;142:283-295. doi:10.1039/b820542f apa: Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Bouloufa, N., Dulieu, O., … Nägerl, H. (2009). Precision molecular spectroscopy for ground state transfer of molecular quantum gases. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/b820542f chicago: Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Nadia Bouloufa, Olivier Dulieu, Helmut Ritsch, Russell Hart, and Hanns Nägerl. “Precision Molecular Spectroscopy for Ground State Transfer of Molecular Quantum Gases.” Faraday Discussions. Royal Society of Chemistry, 2009. https://doi.org/10.1039/b820542f. ieee: J. G. Danzl et al., “Precision molecular spectroscopy for ground state transfer of molecular quantum gases,” Faraday Discussions, vol. 142. Royal Society of Chemistry, pp. 283–295, 2009. ista: Danzl JG, Mark M, Haller E, Gustavsson M, Bouloufa N, Dulieu O, Ritsch H, Hart R, Nägerl H. 2009. Precision molecular spectroscopy for ground state transfer of molecular quantum gases. Faraday Discussions. 142, 283–295. mla: Danzl, Johann G., et al. “Precision Molecular Spectroscopy for Ground State Transfer of Molecular Quantum Gases.” Faraday Discussions, vol. 142, Royal Society of Chemistry, 2009, pp. 283–95, doi:10.1039/b820542f. short: J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, N. Bouloufa, O. Dulieu, H. Ritsch, R. Hart, H. Nägerl, Faraday Discussions 142 (2009) 283–295. date_created: 2018-12-11T11:49:51Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T06:47:52Z day: '01' doi: 10.1039/b820542f extern: '1' external_id: arxiv: - '0811.2374' intvolume: ' 142' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/0811.2374 month: '01' oa: 1 oa_version: Preprint page: 283 - 295 publication: Faraday Discussions publication_status: published publisher: Royal Society of Chemistry publist_id: '6347' status: public title: Precision molecular spectroscopy for ground state transfer of molecular quantum gases type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 142 year: '2009' ... --- _id: '110' abstract: - lang: eng text: In order to better understand magnetic reconnection and particle acceleration in solar flares, we compare the RHESSI hard X-ray (HXR) footpoint motions of three flares with a detailed study of the corresponding topology given by a Magnetic Charge Topology model. We analyze the relationship between the footpoint motions and topological spine lines and find that the examined footpoint sources move along spine lines. We present a three-dimensional topological model in which this movement can be understood. As reconnection proceeds, flux is transferred between the reconnecting domains, causing the separator to move. The movement of the separator\'s chromospheric ends, identified with the HXR footpoints, is along those spine lines on which the separator ends. acknowledgement: This work was supported by RHESSI funds from the University of California at Berkeley through a contract, SA1868-26308PG, with Montana State University. Funding for our Research Experience for Undergraduates (REU) students was provided by NSF grant ATM-0243923. author: - first_name: Angela full_name: Des Jardins, Angela last_name: Des Jardins - first_name: Richard full_name: Canfield, Richard last_name: Canfield - first_name: Dana full_name: Longcope, Dana last_name: Longcope - first_name: Crystal full_name: Fordyce, Crystal last_name: Fordyce - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: 'Des Jardins A, Canfield R, Longcope D, Fordyce C, Waitukaitis SR. Reconnection in three dimensions: The role of spines in three eruptive flares. The Astrophysical Journal. 2009;693(2):1628-1636. doi:10.1088/0004-637X/693/2/1628' apa: 'Des Jardins, A., Canfield, R., Longcope, D., Fordyce, C., & Waitukaitis, S. R. (2009). Reconnection in three dimensions: The role of spines in three eruptive flares. The Astrophysical Journal. IOP Publishing Ltd. https://doi.org/10.1088/0004-637X/693/2/1628' chicago: 'Des Jardins, Angela, Richard Canfield, Dana Longcope, Crystal Fordyce, and Scott R Waitukaitis. “Reconnection in Three Dimensions: The Role of Spines in Three Eruptive Flares.” The Astrophysical Journal. IOP Publishing Ltd., 2009. https://doi.org/10.1088/0004-637X/693/2/1628.' ieee: 'A. Des Jardins, R. Canfield, D. Longcope, C. Fordyce, and S. R. Waitukaitis, “Reconnection in three dimensions: The role of spines in three eruptive flares,” The Astrophysical Journal, vol. 693, no. 2. IOP Publishing Ltd., pp. 1628–1636, 2009.' ista: 'Des Jardins A, Canfield R, Longcope D, Fordyce C, Waitukaitis SR. 2009. Reconnection in three dimensions: The role of spines in three eruptive flares. The Astrophysical Journal. 693(2), 1628–1636.' mla: 'Des Jardins, Angela, et al. “Reconnection in Three Dimensions: The Role of Spines in Three Eruptive Flares.” The Astrophysical Journal, vol. 693, no. 2, IOP Publishing Ltd., 2009, pp. 1628–36, doi:10.1088/0004-637X/693/2/1628.' short: A. Des Jardins, R. Canfield, D. Longcope, C. Fordyce, S.R. Waitukaitis, The Astrophysical Journal 693 (2009) 1628–1636. date_created: 2018-12-11T11:44:41Z date_published: 2009-03-10T00:00:00Z date_updated: 2021-01-12T06:48:16Z day: '10' doi: 10.1088/0004-637X/693/2/1628 extern: '1' intvolume: ' 693' issue: '2' language: - iso: eng month: '03' oa_version: None page: 1628 - 1636 publication: The Astrophysical Journal publication_status: published publisher: IOP Publishing Ltd. publist_id: '7944' quality_controlled: '1' status: public title: 'Reconnection in three dimensions: The role of spines in three eruptive flares' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 693 year: '2009' ... --- _id: '111' abstract: - lang: eng text: Thin streams of liquid commonly break up into characteristic droplet patterns owing to the surface-tension-driven PlateauRayleigh instability 1-3. Very similar patterns are observed when initially uniform streams of dry granular material break up into clusters of grains4-6, even though flows of macroscopic particles are considered to lack surface tension7,8. Recent studies on freely falling granular streams tracked fluctuations in the stream profile9, but the clustering mechanism remained unresolved because the full evolution of the instability could not be observed. Here we demonstrate that the cluster formation is driven by minute, nanoNewton cohesive forces that arise from a combination of van der Waals interactions and capillary bridges between nanometre-scale surface asperities. Our experiments involve high-speed video imaging of the granular stream in the co-moving frame, control over the properties of the grain surfaces and the use of atomic force microscopy to measure grain-grain interactions. The cohesive forces that we measure correspond to an equivalent surface tension five orders of magnitude below that, of ordinary liquids. We find that, the shapes of these weakly cohesive, non-thermal clusters of macroscopic particles closely resemble droplets resulting from thermally induced rupture of liquid nanojets 10-12. acknowledgement: This work was supported by NSF through its MRSEC programme and the Inter-American Materials Collaboration Chicago-Chile, and by the Keck Initiative for Ultrafast Imaging at the University of Chicago. author: - first_name: John full_name: Royer, John last_name: Royer - first_name: Daniel full_name: Evans, Daniel last_name: Evans - first_name: Loreto full_name: Oyarte, Loreto last_name: Oyarte - first_name: Qiti full_name: Guo, Qiti last_name: Guo - first_name: Eliot full_name: Kapit, Eliot last_name: Kapit - first_name: Matthias full_name: Möbius, Matthias last_name: Möbius - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Heinrich full_name: Jaeger, Heinrich last_name: Jaeger citation: ama: Royer J, Evans D, Oyarte L, et al. High-speed tracking of rupture and clustering in freely falling granular streams. Nature. 2009;459(7250):1110-1113. doi:10.1038/nature08115 apa: Royer, J., Evans, D., Oyarte, L., Guo, Q., Kapit, E., Möbius, M., … Jaeger, H. (2009). High-speed tracking of rupture and clustering in freely falling granular streams. Nature. Nature Publishing Group. https://doi.org/10.1038/nature08115 chicago: Royer, John, Daniel Evans, Loreto Oyarte, Qiti Guo, Eliot Kapit, Matthias Möbius, Scott R Waitukaitis, and Heinrich Jaeger. “High-Speed Tracking of Rupture and Clustering in Freely Falling Granular Streams.” Nature. Nature Publishing Group, 2009. https://doi.org/10.1038/nature08115. ieee: J. Royer et al., “High-speed tracking of rupture and clustering in freely falling granular streams,” Nature, vol. 459, no. 7250. Nature Publishing Group, pp. 1110–1113, 2009. ista: Royer J, Evans D, Oyarte L, Guo Q, Kapit E, Möbius M, Waitukaitis SR, Jaeger H. 2009. High-speed tracking of rupture and clustering in freely falling granular streams. Nature. 459(7250), 1110–1113. mla: Royer, John, et al. “High-Speed Tracking of Rupture and Clustering in Freely Falling Granular Streams.” Nature, vol. 459, no. 7250, Nature Publishing Group, 2009, pp. 1110–13, doi:10.1038/nature08115. short: J. Royer, D. Evans, L. Oyarte, Q. Guo, E. Kapit, M. Möbius, S.R. Waitukaitis, H. Jaeger, Nature 459 (2009) 1110–1113. date_created: 2018-12-11T11:44:41Z date_published: 2009-06-25T00:00:00Z date_updated: 2021-01-12T06:48:21Z day: '25' doi: 10.1038/nature08115 extern: '1' intvolume: ' 459' issue: '7250' language: - iso: eng month: '06' oa_version: None page: 1110 - 1113 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '7943' quality_controlled: '1' status: public title: High-speed tracking of rupture and clustering in freely falling granular streams type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 459 year: '2009' ... --- _id: '11103' abstract: - lang: eng text: Over the last decade, the nuclear envelope (NE) has emerged as a key component in the organization and function of the nuclear genome. As many as 100 different proteins are thought to specifically localize to this double membrane that separates the cytoplasm and the nucleoplasm of eukaryotic cells. Selective portals through the NE are formed at sites where the inner and outer nuclear membranes are fused, and the coincident assembly of ∼30 proteins into nuclear pore complexes occurs. These nuclear pore complexes are essential for the control of nucleocytoplasmic exchange. Many of the NE and nuclear pore proteins are thought to play crucial roles in gene regulation and thus are increasingly linked to human diseases. article_processing_charge: No article_type: review author: - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X - first_name: Susan R. full_name: Wente, Susan R. last_name: Wente citation: ama: 'Hetzer M, Wente SR. Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes. Developmental Cell. 2009;17(5):606-616. doi:10.1016/j.devcel.2009.10.007' apa: 'Hetzer, M., & Wente, S. R. (2009). Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2009.10.007' chicago: 'Hetzer, Martin, and Susan R. Wente. “Border Control at the Nucleus: Biogenesis and Organization of the Nuclear Membrane and Pore Complexes.” Developmental Cell. Elsevier, 2009. https://doi.org/10.1016/j.devcel.2009.10.007.' ieee: 'M. Hetzer and S. R. Wente, “Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes,” Developmental Cell, vol. 17, no. 5. Elsevier, pp. 606–616, 2009.' ista: 'Hetzer M, Wente SR. 2009. Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes. Developmental Cell. 17(5), 606–616.' mla: 'Hetzer, Martin, and Susan R. Wente. “Border Control at the Nucleus: Biogenesis and Organization of the Nuclear Membrane and Pore Complexes.” Developmental Cell, vol. 17, no. 5, Elsevier, 2009, pp. 606–16, doi:10.1016/j.devcel.2009.10.007.' short: M. Hetzer, S.R. Wente, Developmental Cell 17 (2009) 606–616. date_created: 2022-04-07T07:53:45Z date_published: 2009-11-17T00:00:00Z date_updated: 2022-07-18T08:55:01Z day: '17' doi: 10.1016/j.devcel.2009.10.007 extern: '1' external_id: pmid: - '19922866' intvolume: ' 17' issue: '5' keyword: - Developmental Biology - Cell Biology - General Biochemistry - Genetics and Molecular Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2009.10.007 month: '11' oa: 1 oa_version: Published Version page: 606-616 pmid: 1 publication: Developmental Cell publication_identifier: issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes' type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 17 year: '2009' ... --- _id: '11106' abstract: - lang: eng text: Formation of the nuclear envelope (NE) around segregated chromosomes occurs by the reshaping of the endoplasmic reticulum (ER), a reservoir for disassembled nuclear membrane components during mitosis. In this study, we show that inner nuclear membrane proteins such as lamin B receptor (LBR), MAN1, Lap2β, and the trans-membrane nucleoporins Ndc1 and POM121 drive the spreading of ER membranes into the emerging NE via their capacity to bind chromatin in a collaborative manner. Despite their redundant functions, decreasing the levels of any of these trans-membrane proteins by RNAi-mediated knockdown delayed NE formation, whereas increasing the levels of any of them had the opposite effect. Furthermore, acceleration of NE formation interferes with chromosome separation during mitosis, indicating that the time frame over which chromatin becomes membrane enclosed is physiologically relevant and regulated. These data suggest that functionally distinct classes of chromatin-interacting membrane proteins, which are present at nonsaturating levels, collaborate to rapidly reestablish the nuclear compartment at the end of mitosis. article_processing_charge: No article_type: original author: - first_name: Daniel J. full_name: Anderson, Daniel J. last_name: Anderson - first_name: Jesse D. full_name: Vargas, Jesse D. last_name: Vargas - first_name: Joshua P. full_name: Hsiao, Joshua P. last_name: Hsiao - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Anderson DJ, Vargas JD, Hsiao JP, Hetzer M. Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo. Journal of Cell Biology. 2009;186(2):183-191. doi:10.1083/jcb.200901106 apa: Anderson, D. J., Vargas, J. D., Hsiao, J. P., & Hetzer, M. (2009). Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.200901106 chicago: Anderson, Daniel J., Jesse D. Vargas, Joshua P. Hsiao, and Martin Hetzer. “Recruitment of Functionally Distinct Membrane Proteins to Chromatin Mediates Nuclear Envelope Formation in Vivo.” Journal of Cell Biology. Rockefeller University Press, 2009. https://doi.org/10.1083/jcb.200901106. ieee: D. J. Anderson, J. D. Vargas, J. P. Hsiao, and M. Hetzer, “Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo,” Journal of Cell Biology, vol. 186, no. 2. Rockefeller University Press, pp. 183–191, 2009. ista: Anderson DJ, Vargas JD, Hsiao JP, Hetzer M. 2009. Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo. Journal of Cell Biology. 186(2), 183–191. mla: Anderson, Daniel J., et al. “Recruitment of Functionally Distinct Membrane Proteins to Chromatin Mediates Nuclear Envelope Formation in Vivo.” Journal of Cell Biology, vol. 186, no. 2, Rockefeller University Press, 2009, pp. 183–91, doi:10.1083/jcb.200901106. short: D.J. Anderson, J.D. Vargas, J.P. Hsiao, M. Hetzer, Journal of Cell Biology 186 (2009) 183–191. date_created: 2022-04-07T07:54:18Z date_published: 2009-07-20T00:00:00Z date_updated: 2022-07-18T08:58:35Z day: '20' doi: 10.1083/jcb.200901106 extern: '1' external_id: pmid: - '19620630' intvolume: ' 186' issue: '2' keyword: - Cell Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1083/jcb.200901106 month: '07' oa: 1 oa_version: Published Version page: 183-191 pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1083/jcb.20090110620090903c scopus_import: '1' status: public title: Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 186 year: '2009' ... --- _id: '11107' abstract: - lang: eng text: Nucleocytoplasmic transport occurs exclusively through nuclear pore complexes (NPCs) embedded in pores formed by inner and outer nuclear membrane fusion. The mechanism for de novo pore and NPC biogenesis remains unclear. Reticulons (RTNs) and Yop1/DP1 are conserved membrane protein families required to form and maintain the tubular endoplasmic reticulum (ER) and the postmitotic nuclear envelope. In this study, we report that members of the RTN and Yop1/DP1 families are required for nuclear pore formation. Analysis of Saccharomyces cerevisiae prp20-G282S and nup133Δ NPC assembly mutants revealed perturbations in Rtn1–green fluorescent protein (GFP) and Yop1-GFP ER distribution and colocalization to NPC clusters. Combined deletion of RTN1 and YOP1 resulted in NPC clustering, nuclear import defects, and synthetic lethality with the additional absence of Pom34, Pom152, and Nup84 subcomplex members. We tested for a direct role in NPC biogenesis using Xenopus laevis in vitro assays and found that anti-Rtn4a antibodies specifically inhibited de novo nuclear pore formation. We hypothesize that these ER membrane–bending proteins mediate early NPC assembly steps. article_processing_charge: No article_type: original author: - first_name: T. Renee full_name: Dawson, T. Renee last_name: Dawson - first_name: Michelle D. full_name: Lazarus, Michelle D. last_name: Lazarus - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X - first_name: Susan R. full_name: Wente, Susan R. last_name: Wente citation: ama: Dawson TR, Lazarus MD, Hetzer M, Wente SR. ER membrane–bending proteins are necessary for de novo nuclear pore formation. Journal of Cell Biology. 2009;184(5):659-675. doi:10.1083/jcb.200806174 apa: Dawson, T. R., Lazarus, M. D., Hetzer, M., & Wente, S. R. (2009). ER membrane–bending proteins are necessary for de novo nuclear pore formation. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.200806174 chicago: Dawson, T. Renee, Michelle D. Lazarus, Martin Hetzer, and Susan R. Wente. “ER Membrane–Bending Proteins Are Necessary for de Novo Nuclear Pore Formation.” Journal of Cell Biology. Rockefeller University Press, 2009. https://doi.org/10.1083/jcb.200806174. ieee: T. R. Dawson, M. D. Lazarus, M. Hetzer, and S. R. Wente, “ER membrane–bending proteins are necessary for de novo nuclear pore formation,” Journal of Cell Biology, vol. 184, no. 5. Rockefeller University Press, pp. 659–675, 2009. ista: Dawson TR, Lazarus MD, Hetzer M, Wente SR. 2009. ER membrane–bending proteins are necessary for de novo nuclear pore formation. Journal of Cell Biology. 184(5), 659–675. mla: Dawson, T. Renee, et al. “ER Membrane–Bending Proteins Are Necessary for de Novo Nuclear Pore Formation.” Journal of Cell Biology, vol. 184, no. 5, Rockefeller University Press, 2009, pp. 659–75, doi:10.1083/jcb.200806174. short: T.R. Dawson, M.D. Lazarus, M. Hetzer, S.R. Wente, Journal of Cell Biology 184 (2009) 659–675. date_created: 2022-04-07T07:54:44Z date_published: 2009-03-09T00:00:00Z date_updated: 2022-07-18T08:55:05Z day: '09' doi: 10.1083/jcb.200806174 extern: '1' external_id: pmid: - '19273614' intvolume: ' 184' issue: '5' keyword: - Cell Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1083/jcb.200806174 month: '03' oa: 1 oa_version: Published Version page: 659-675 pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: ER membrane–bending proteins are necessary for de novo nuclear pore formation type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 184 year: '2009' ... --- _id: '11108' abstract: - lang: eng text: In dividing cells, nuclear pore complexes (NPCs) disassemble during mitosis and reassemble into the newly forming nuclei. However, the fate of nuclear pores in postmitotic cells is unknown. Here, we show that NPCs, unlike other nuclear structures, do not turn over in differentiated cells. While a subset of NPC components, like Nup153 and Nup50, are continuously exchanged, scaffold nucleoporins, like the Nup107/160 complex, are extremely long-lived and remain incorporated in the nuclear membrane during the entire cellular life span. Besides the lack of nucleoporin expression and NPC turnover, we discovered an age-related deterioration of NPCs, leading to an increase in nuclear permeability and the leaking of cytoplasmic proteins into the nucleus. Our finding that nuclear “leakiness” is dramatically accelerated during aging and that a subset of nucleoporins is oxidatively damaged in old cells suggests that the accumulation of damage at the NPC might be a crucial aging event. article_processing_charge: No article_type: original author: - first_name: Maximiliano A. full_name: D'Angelo, Maximiliano A. last_name: D'Angelo - first_name: Marcela full_name: Raices, Marcela last_name: Raices - first_name: Siler H. full_name: Panowski, Siler H. last_name: Panowski - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: D’Angelo MA, Raices M, Panowski SH, Hetzer M. Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. Cell. 2009;136(2):284-295. doi:10.1016/j.cell.2008.11.037 apa: D’Angelo, M. A., Raices, M., Panowski, S. H., & Hetzer, M. (2009). Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. Cell. Elsevier. https://doi.org/10.1016/j.cell.2008.11.037 chicago: D’Angelo, Maximiliano A., Marcela Raices, Siler H. Panowski, and Martin Hetzer. “Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells.” Cell. Elsevier, 2009. https://doi.org/10.1016/j.cell.2008.11.037. ieee: M. A. D’Angelo, M. Raices, S. H. Panowski, and M. Hetzer, “Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells,” Cell, vol. 136, no. 2. Elsevier, pp. 284–295, 2009. ista: D’Angelo MA, Raices M, Panowski SH, Hetzer M. 2009. Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. Cell. 136(2), 284–295. mla: D’Angelo, Maximiliano A., et al. “Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells.” Cell, vol. 136, no. 2, Elsevier, 2009, pp. 284–95, doi:10.1016/j.cell.2008.11.037. short: M.A. D’Angelo, M. Raices, S.H. Panowski, M. Hetzer, Cell 136 (2009) 284–295. date_created: 2022-04-07T07:54:52Z date_published: 2009-01-23T00:00:00Z date_updated: 2022-07-18T08:55:29Z day: '23' doi: 10.1016/j.cell.2008.11.037 extern: '1' external_id: pmid: - '19167330' intvolume: ' 136' issue: '2' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2008.11.037 month: '01' oa: 1 oa_version: Published Version page: 284-295 pmid: 1 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 136 year: '2009' ... --- _id: '11105' abstract: - lang: eng text: Nuclear-pore complexes (NPCs) are large protein channels that span the nuclear envelope (NE), which is a double membrane that encloses the nuclear genome of eukaryotes. Each of the typically 2,000–4,000 pores in the NE of vertebrate cells is composed of multiple copies of 30 different proteins known as nucleoporins. The evolutionarily conserved NPC proteins have the well-characterized function of mediating the transport of molecules between the nucleoplasm and the cytoplasm. Mutations in nucleoporins are often linked to specific developmental defects and disease, and the resulting phenotypes are usually interpreted as the consequences of perturbed nuclear transport activity. However, recent evidence suggests that NPCs have additional functions in chromatin organization and gene regulation, some of which might be independent of nuclear transport. Here, we review the transport-dependent and transport-independent roles of NPCs in the regulation of nuclear function and gene expression. article_processing_charge: No article_type: original author: - first_name: Maya full_name: Capelson, Maya last_name: Capelson - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Capelson M, Hetzer M. The role of nuclear pores in gene regulation, development and disease. EMBO reports. 2009;10(7):697-705. doi:10.1038/embor.2009.147 apa: Capelson, M., & Hetzer, M. (2009). The role of nuclear pores in gene regulation, development and disease. EMBO Reports. EMBO. https://doi.org/10.1038/embor.2009.147 chicago: Capelson, Maya, and Martin Hetzer. “The Role of Nuclear Pores in Gene Regulation, Development and Disease.” EMBO Reports. EMBO, 2009. https://doi.org/10.1038/embor.2009.147. ieee: M. Capelson and M. Hetzer, “The role of nuclear pores in gene regulation, development and disease,” EMBO reports, vol. 10, no. 7. EMBO, pp. 697–705, 2009. ista: Capelson M, Hetzer M. 2009. The role of nuclear pores in gene regulation, development and disease. EMBO reports. 10(7), 697–705. mla: Capelson, Maya, and Martin Hetzer. “The Role of Nuclear Pores in Gene Regulation, Development and Disease.” EMBO Reports, vol. 10, no. 7, EMBO, 2009, pp. 697–705, doi:10.1038/embor.2009.147. short: M. Capelson, M. Hetzer, EMBO Reports 10 (2009) 697–705. date_created: 2022-04-07T07:54:06Z date_published: 2009-07-01T00:00:00Z date_updated: 2022-07-18T08:42:44Z day: '01' doi: 10.1038/embor.2009.147 extern: '1' external_id: pmid: - '19543230' intvolume: ' 10' issue: '7' keyword: - Genetics - Molecular Biology - Biochemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/embor.2009.147 month: '07' oa: 1 oa_version: Published Version page: 697-705 pmid: 1 publication: EMBO reports publication_identifier: eissn: - 1469-3178 issn: - 1469-221X publication_status: published publisher: EMBO quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/embor.2009.176 scopus_import: '1' status: public title: The role of nuclear pores in gene regulation, development and disease type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 10 year: '2009' ... --- _id: '11799' abstract: - lang: eng text: We study the problem of matching bidders to items where each bidder i has general, strictly monotonic utility functions u i,j (p j ) expressing her utility of being matched to item j at price p j . For this setting we prove that a bidder optimal outcome always exists, even when the utility functions are non-linear and non-continuous. Furthermore, we give an algorithm to find such a solution. Although the running time of this algorithm is exponential in the number of items, it is polynomial in the number of bidders. alternative_title: - LNCS article_processing_charge: No author: - first_name: Paul full_name: Dütting, Paul last_name: Dütting - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Ingmar full_name: Weber, Ingmar last_name: Weber citation: ama: 'Dütting P, Henzinger MH, Weber I. Bidder optimal assignments for general utilities. In: 5th International Workshop on Internet and Network Economics. Vol 5929. Springer Nature; 2009:575-582. doi:10.1007/978-3-642-10841-9_58' apa: 'Dütting, P., Henzinger, M. H., & Weber, I. (2009). Bidder optimal assignments for general utilities. In 5th International Workshop on Internet and Network Economics (Vol. 5929, pp. 575–582). Rome, Italy: Springer Nature. https://doi.org/10.1007/978-3-642-10841-9_58' chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Bidder Optimal Assignments for General Utilities.” In 5th International Workshop on Internet and Network Economics, 5929:575–82. Springer Nature, 2009. https://doi.org/10.1007/978-3-642-10841-9_58. ieee: P. Dütting, M. H. Henzinger, and I. Weber, “Bidder optimal assignments for general utilities,” in 5th International Workshop on Internet and Network Economics, Rome, Italy, 2009, vol. 5929, pp. 575–582. ista: 'Dütting P, Henzinger MH, Weber I. 2009. Bidder optimal assignments for general utilities. 5th International Workshop on Internet and Network Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 5929, 575–582.' mla: Dütting, Paul, et al. “Bidder Optimal Assignments for General Utilities.” 5th International Workshop on Internet and Network Economics, vol. 5929, Springer Nature, 2009, pp. 575–82, doi:10.1007/978-3-642-10841-9_58. short: P. Dütting, M.H. Henzinger, I. Weber, in:, 5th International Workshop on Internet and Network Economics, Springer Nature, 2009, pp. 575–582. conference: end_date: 2009-12-18 location: Rome, Italy name: 'WINE: International Conference on Web and Internet Economics' start_date: 2009-12-14 date_created: 2022-08-11T12:33:38Z date_published: 2009-12-01T00:00:00Z date_updated: 2023-02-21T16:32:35Z day: '01' doi: 10.1007/978-3-642-10841-9_58 extern: '1' intvolume: ' 5929' language: - iso: eng month: '12' oa_version: None page: 575-582 publication: 5th International Workshop on Internet and Network Economics publication_identifier: isbn: - '9783642108402' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '11902' relation: later_version status: public scopus_import: '1' status: public title: Bidder optimal assignments for general utilities type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5929 year: '2009' ... --- _id: '11912' abstract: - lang: eng text: As the World Wide Web is growing rapidly, it is getting increasingly challenging to gather representative information about it. Instead of crawling the web exhaustively one has to resort to other techniques like sampling to determine the properties of the web. A uniform random sample of the web would be useful to determine the percentage of web pages in a specific language, on a topic or in a top level domain. Unfortunately, no approach has been shown to sample the web pages in an unbiased way. Three promising web sampling algorithms are based on random walks. They each have been evaluated individually, but making a comparison on different data sets is not possible. We directly compare these algorithms in this paper. We performed three random walks on the web under the same conditions and analyzed their outcomes in detail. We discuss the strengths and the weaknesses of each algorithm and propose improvements based on experimental results. alternative_title: - LIPIcs article_processing_charge: No author: - first_name: ' Eda' full_name: Baykan, Eda last_name: Baykan - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Stefan F. full_name: Keller, Stefan F. last_name: Keller - first_name: Sebastian full_name: de Castelberg, Sebastian last_name: de Castelberg - first_name: Markus full_name: Kinzler, Markus last_name: Kinzler citation: ama: 'Baykan Eda, Henzinger MH, Keller SF, de Castelberg S, Kinzler M. A comparison of techniques for sampling web pages. In: 26th International Symposium on Theoretical Aspects of Computer Science. Vol 3. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2009:13-30. doi:10.4230/LIPICS.STACS.2009.1809' apa: 'Baykan, Eda, Henzinger, M. H., Keller, S. F., de Castelberg, S., & Kinzler, M. (2009). A comparison of techniques for sampling web pages. In 26th International Symposium on Theoretical Aspects of Computer Science (Vol. 3, pp. 13–30). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2009.1809' chicago: Baykan, Eda, Monika H Henzinger, Stefan F. Keller, Sebastian de Castelberg, and Markus Kinzler. “A Comparison of Techniques for Sampling Web Pages.” In 26th International Symposium on Theoretical Aspects of Computer Science, 3:13–30. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009. https://doi.org/10.4230/LIPICS.STACS.2009.1809. ieee: Eda Baykan, M. H. Henzinger, S. F. Keller, S. de Castelberg, and M. Kinzler, “A comparison of techniques for sampling web pages,” in 26th International Symposium on Theoretical Aspects of Computer Science, Freiburg, Germany, 2009, vol. 3, pp. 13–30. ista: 'Baykan Eda, Henzinger MH, Keller SF, de Castelberg S, Kinzler M. 2009. A comparison of techniques for sampling web pages. 26th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 3, 13–30.' mla: Baykan, Eda, et al. “A Comparison of Techniques for Sampling Web Pages.” 26th International Symposium on Theoretical Aspects of Computer Science, vol. 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009, pp. 13–30, doi:10.4230/LIPICS.STACS.2009.1809. short: Eda Baykan, M.H. Henzinger, S.F. Keller, S. de Castelberg, M. Kinzler, in:, 26th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2009, pp. 13–30. conference: end_date: 2009-02-28 location: Freiburg, Germany name: 'STACS: Symposium on Theoretical Aspects of Computer Science' start_date: 2009-02-26 date_created: 2022-08-18T06:57:25Z date_published: 2009-02-01T00:00:00Z date_updated: 2023-02-17T08:57:16Z day: '01' doi: 10.4230/LIPICS.STACS.2009.1809 extern: '1' external_id: arxiv: - '0902.1604' intvolume: ' 3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.STACS.2009.1809 month: '02' oa: 1 oa_version: Published Version page: 13-30 publication: 26th International Symposium on Theoretical Aspects of Computer Science publication_identifier: isbn: - 978-3-939897-09-5 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: A comparison of techniques for sampling web pages type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2009' ... --- _id: '11905' abstract: - lang: eng text: Given only the URL of a web page, can we identify its topic? This is the question that we examine in this paper. Usually, web pages are classified using their content, but a URL-only classifier is preferable, (i) when speed is crucial, (ii) to enable content filtering before an (objection-able) web page is downloaded, (iii) when a page's content is hidden in images, (iv) to annotate hyperlinks in a personalized web browser, without fetching the target page, and (v) when a focused crawler wants to infer the topic of a target page before devoting bandwidth to download it. We apply a machine learning approach to the topic identification task and evaluate its performance in extensive experiments on categorized web pages from the Open Directory Project (ODP). When training separate binary classifiers for each topic, we achieve typical F-measure values between 80 and 85, and a typical precision of around 85. We also ran experiments on a small data set of university web pages. For the task of classifying these pages into faculty, student, course and project pages, our methods improve over previous approaches by 13.8 points of F-measure. article_processing_charge: No author: - first_name: Eda full_name: Baykan, Eda last_name: Baykan - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Ludmila full_name: Marian, Ludmila last_name: Marian - first_name: Ingmar full_name: Weber, Ingmar last_name: Weber citation: ama: 'Baykan E, Henzinger MH, Marian L, Weber I. Purely URL-based topic classification. In: 18th International World Wide Web Conference. Association for Computing Machinery; 2009:1109-1110. doi:10.1145/1526709.1526880' apa: 'Baykan, E., Henzinger, M. H., Marian, L., & Weber, I. (2009). Purely URL-based topic classification. In 18th International World Wide Web Conference (pp. 1109–1110). New York, NY, United States: Association for Computing Machinery. https://doi.org/10.1145/1526709.1526880' chicago: Baykan, Eda, Monika H Henzinger, Ludmila Marian, and Ingmar Weber. “Purely URL-Based Topic Classification.” In 18th International World Wide Web Conference, 1109–10. Association for Computing Machinery, 2009. https://doi.org/10.1145/1526709.1526880. ieee: E. Baykan, M. H. Henzinger, L. Marian, and I. Weber, “Purely URL-based topic classification,” in 18th International World Wide Web Conference, New York, NY, United States, 2009, pp. 1109–1110. ista: 'Baykan E, Henzinger MH, Marian L, Weber I. 2009. Purely URL-based topic classification. 18th International World Wide Web Conference. WWW: Conference on World Wide Web, 1109–1110.' mla: Baykan, Eda, et al. “Purely URL-Based Topic Classification.” 18th International World Wide Web Conference, Association for Computing Machinery, 2009, pp. 1109–10, doi:10.1145/1526709.1526880. short: E. Baykan, M.H. Henzinger, L. Marian, I. Weber, in:, 18th International World Wide Web Conference, Association for Computing Machinery, 2009, pp. 1109–1110. conference: end_date: 2009-04-24 location: New York, NY, United States name: 'WWW: Conference on World Wide Web' start_date: 2009-04-20 date_created: 2022-08-17T11:49:53Z date_published: 2009-04-01T00:00:00Z date_updated: 2023-02-17T14:54:56Z day: '01' doi: 10.1145/1526709.1526880 extern: '1' language: - iso: eng month: '04' oa_version: None page: 1109-1110 publication: 18th International World Wide Web Conference publication_identifier: isbn: - 978-1-60558-487-4 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Purely URL-based topic classification type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2009' ... --- _id: '11906' abstract: - lang: eng text: In the origin detection problem an algorithm is given a set S of documents, ordered by creation time, and a query document D. It needs to output for every consecutive sequence of k alphanumeric terms in D the earliest document in $S$ in which the sequence appeared (if such a document exists). Algorithms for the origin detection problem can, for example, be used to detect the "origin" of text segments in D and thus to detect novel content in D. They can also find the document from which the author of D has copied the most (or show that D is mostly original.) We concentrate on solutions that use only a fixed amount of memory. We propose novel algorithms for this problem and evaluate them together with a large number of previously published algorithms. Our results show that (1) detecting the origin of text segments efficiently can be done with very high accuracy even when the space used is less than 1% of the size of the documents in $S$, (2) the precision degrades smoothly with the amount of available space, (3) various estimation techniques can be used to increase the performance of the algorithms. article_processing_charge: No author: - first_name: Ossama full_name: Abdel Hamid, Ossama last_name: Abdel Hamid - first_name: Behshad full_name: Behzadi, Behshad last_name: Behzadi - first_name: Stefan full_name: Christoph, Stefan last_name: Christoph - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: 'Abdel Hamid O, Behzadi B, Christoph S, Henzinger MH. Detecting the origin of text segments efficiently. In: 18th International World Wide Web Conference. Association for Computing Machinery; 2009:61-70. doi:10.1145/1526709.1526719' apa: 'Abdel Hamid, O., Behzadi, B., Christoph, S., & Henzinger, M. H. (2009). Detecting the origin of text segments efficiently. In 18th International World Wide Web Conference (pp. 61–70). Madrid, Spain: Association for Computing Machinery. https://doi.org/10.1145/1526709.1526719' chicago: Abdel Hamid, Ossama, Behshad Behzadi, Stefan Christoph, and Monika H Henzinger. “Detecting the Origin of Text Segments Efficiently.” In 18th International World Wide Web Conference, 61–70. Association for Computing Machinery, 2009. https://doi.org/10.1145/1526709.1526719. ieee: O. Abdel Hamid, B. Behzadi, S. Christoph, and M. H. Henzinger, “Detecting the origin of text segments efficiently,” in 18th International World Wide Web Conference, Madrid, Spain, 2009, pp. 61–70. ista: 'Abdel Hamid O, Behzadi B, Christoph S, Henzinger MH. 2009. Detecting the origin of text segments efficiently. 18th International World Wide Web Conference. WWW: International Conference on World Wide Web, 61–70.' mla: Abdel Hamid, Ossama, et al. “Detecting the Origin of Text Segments Efficiently.” 18th International World Wide Web Conference, Association for Computing Machinery, 2009, pp. 61–70, doi:10.1145/1526709.1526719. short: O. Abdel Hamid, B. Behzadi, S. Christoph, M.H. Henzinger, in:, 18th International World Wide Web Conference, Association for Computing Machinery, 2009, pp. 61–70. conference: end_date: 2009-04-24 location: Madrid, Spain name: 'WWW: International Conference on World Wide Web' start_date: 2009-04-20 date_created: 2022-08-17T11:54:30Z date_published: 2009-04-01T00:00:00Z date_updated: 2023-02-17T14:56:47Z day: '01' doi: 10.1145/1526709.1526719 extern: '1' language: - iso: eng month: '04' oa_version: None page: 61-70 publication: 18th International World Wide Web Conference publication_identifier: isbn: - 978-160558487-4 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Detecting the origin of text segments efficiently type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2009' ... --- _id: '12654' abstract: - lang: eng text: 'We investigate the transferability of an enhanced temperature-index melt model that was developed and tested on Haut Glacier d’Arolla, Switzerland, in the 2001 season. The model’s empirical parameters (temperature factor, TF, and shortwave radiation factor, SRF) are recalibrated for: (1) other locations on Haut Glacier d’Arolla; (2) subperiods of distinct meteorological conditions; (3) different years on Haut Glacier d’Arolla; and (4) other glaciers in different years. The model parameters are optimized against simulations of an energy-balance model validated against ablation observations. Results are compared with those obtained with the original parameters. The model works very well when applied to other sites, seasons and glaciers, with the exception of overcast conditions. Differences are due to underestimation of high melt rates. The parameter values are associated with the prevailing energy-balance conditions, showing that high SRF are obtained on clear-sky days, whereas higher TF are typical of locations where glacier winds prevail and turbulent fluxes are high. We also provide a range of parameters clearly associated with the site’s location and its meteorological characteristics that could help to assign parameter values to sites where few data are available.' article_processing_charge: No article_type: original author: - first_name: Marco full_name: Carenzo, Marco last_name: Carenzo - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Stefan full_name: Rimkus, Stefan last_name: Rimkus - first_name: Paolo full_name: Burlando, Paolo last_name: Burlando citation: ama: Carenzo M, Pellicciotti F, Rimkus S, Burlando P. Assessing the transferability and robustness of an enhanced temperature-index glacier-melt model. Journal of Glaciology. 2009;55(190):258-274. doi:10.3189/002214309788608804 apa: Carenzo, M., Pellicciotti, F., Rimkus, S., & Burlando, P. (2009). Assessing the transferability and robustness of an enhanced temperature-index glacier-melt model. Journal of Glaciology. Cambridge University Press. https://doi.org/10.3189/002214309788608804 chicago: Carenzo, Marco, Francesca Pellicciotti, Stefan Rimkus, and Paolo Burlando. “Assessing the Transferability and Robustness of an Enhanced Temperature-Index Glacier-Melt Model.” Journal of Glaciology. Cambridge University Press, 2009. https://doi.org/10.3189/002214309788608804. ieee: M. Carenzo, F. Pellicciotti, S. Rimkus, and P. Burlando, “Assessing the transferability and robustness of an enhanced temperature-index glacier-melt model,” Journal of Glaciology, vol. 55, no. 190. Cambridge University Press, pp. 258–274, 2009. ista: Carenzo M, Pellicciotti F, Rimkus S, Burlando P. 2009. Assessing the transferability and robustness of an enhanced temperature-index glacier-melt model. Journal of Glaciology. 55(190), 258–274. mla: Carenzo, Marco, et al. “Assessing the Transferability and Robustness of an Enhanced Temperature-Index Glacier-Melt Model.” Journal of Glaciology, vol. 55, no. 190, Cambridge University Press, 2009, pp. 258–74, doi:10.3189/002214309788608804. short: M. Carenzo, F. Pellicciotti, S. Rimkus, P. Burlando, Journal of Glaciology 55 (2009) 258–274. date_created: 2023-02-20T08:18:34Z date_published: 2009-03-01T00:00:00Z date_updated: 2023-02-20T09:06:27Z day: '01' doi: 10.3189/002214309788608804 extern: '1' intvolume: ' 55' issue: '190' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3189/002214309788608804 month: '03' oa: 1 oa_version: Published Version page: 258-274 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Assessing the transferability and robustness of an enhanced temperature-index glacier-melt model type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2009' ... --- _id: '12655' abstract: - lang: eng text: We discuss the inclusion of the subsurface heat-conduction flux into the calculation of the energy balance and ablation at the glacier–atmosphere interface. Data from automatic weather stations are used to force an energy-balance model at several locations on alpine glaciers and at one site in the dry Andes of central Chile. The heat-conduction flux is computed using a two-layer scheme, assuming that 36% of the net shortwave radiation is absorbed by the surface layer and that the rest penetrates into the snowpack. We compare simulations conducted with and without subsurface heat flux. Results show that assuming a surface temperature of zero degrees leads to a larger overestimation of melt at the sites in the accumulation area (10.4–13.3%) than in the ablation area (0.5–2.8%), due to lower air temperatures and the presence of snow. The difference between simulations with and without heat conduction is also high at the beginning and end of the ablation season (up to 29% for the first 15 days of the season), when air temperatures are lower and snow covers the glacier surface, while they are of little importance during periods of sustained melt at all the locations investigated. article_processing_charge: No article_type: original author: - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Marco full_name: Carenzo, Marco last_name: Carenzo - first_name: Jakob full_name: Helbing, Jakob last_name: Helbing - first_name: Stefan full_name: Rimkus, Stefan last_name: Rimkus - first_name: Paolo full_name: Burlando, Paolo last_name: Burlando citation: ama: Pellicciotti F, Carenzo M, Helbing J, Rimkus S, Burlando P. On the role of subsurface heat conduction in glacier energy-balance modelling. Annals of Glaciology. 2009;50(50):16-24. doi:10.3189/172756409787769555 apa: Pellicciotti, F., Carenzo, M., Helbing, J., Rimkus, S., & Burlando, P. (2009). On the role of subsurface heat conduction in glacier energy-balance modelling. Annals of Glaciology. International Glaciological Society. https://doi.org/10.3189/172756409787769555 chicago: Pellicciotti, Francesca, Marco Carenzo, Jakob Helbing, Stefan Rimkus, and Paolo Burlando. “On the Role of Subsurface Heat Conduction in Glacier Energy-Balance Modelling.” Annals of Glaciology. International Glaciological Society, 2009. https://doi.org/10.3189/172756409787769555. ieee: F. Pellicciotti, M. Carenzo, J. Helbing, S. Rimkus, and P. Burlando, “On the role of subsurface heat conduction in glacier energy-balance modelling,” Annals of Glaciology, vol. 50, no. 50. International Glaciological Society, pp. 16–24, 2009. ista: Pellicciotti F, Carenzo M, Helbing J, Rimkus S, Burlando P. 2009. On the role of subsurface heat conduction in glacier energy-balance modelling. Annals of Glaciology. 50(50), 16–24. mla: Pellicciotti, Francesca, et al. “On the Role of Subsurface Heat Conduction in Glacier Energy-Balance Modelling.” Annals of Glaciology, vol. 50, no. 50, International Glaciological Society, 2009, pp. 16–24, doi:10.3189/172756409787769555. short: F. Pellicciotti, M. Carenzo, J. Helbing, S. Rimkus, P. Burlando, Annals of Glaciology 50 (2009) 16–24. date_created: 2023-02-20T08:18:40Z date_published: 2009-01-01T00:00:00Z date_updated: 2023-02-20T09:00:53Z day: '01' doi: 10.3189/172756409787769555 extern: '1' intvolume: ' 50' issue: '50' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3189/172756409787769555 month: '01' oa: 1 oa_version: Published Version page: 16-24 publication: Annals of Glaciology publication_identifier: eissn: - 1727-5644 issn: - 0260-3055 publication_status: published publisher: International Glaciological Society quality_controlled: '1' scopus_import: '1' status: public title: On the role of subsurface heat conduction in glacier energy-balance modelling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2009' ... --- _id: '1302' abstract: - lang: eng text: 'The nervous system of seeing animals derives information about optic flow in two subsequent steps. First, local motion vectors are calculated from moving retinal images, and second, the spatial distribution of these vectors is analyzed on the dendrites of large downstream neurons. In dipteran flies, this second step relies on a set of motion-sensitive lobula plate tangential cells (LPTCs), which have been studied in great detail in large fly species. Yet, studies on neurons that convey information to LPTCs and neuroanatomical investigations that enable a mechanistic understanding of the underlying dendritic computations in LPTCs are rare. We investigated the subcellular distribution of nicotinic acetylcholine receptors (nAChRs) on two sets of LPTCs: vertical system (VS) and horizontal system (HS) cells in Drosophila melanogaster. In this paper, we describe that both cell types express Dα7-type nAChR subunits specifically on higher order dendritic branches, similar to the expression of gamma aminobutyric acid (GABA) receptors. These findings support a model in which directional selectivity of LPTCs is achieved by the dendritic integration of excitatory, cholinergic, and inhibitory GABA-ergic input from local motion detectors with opposite preferred direction. Nonetheless, whole-cell recordings in mutant flies without Dα7 nAChRs revealed that direction selectivity of VS and HS cells is largely retained. In addition, mutant LPTCs were responsive to acetylcholine and remaining nAChR receptors were labeled by α-bungarotoxin. These results in LPTCs with genetically manipulated excitatory input synapses suggest a robust cellular implementation of dendritic processing that warrants direction selectivity. The underlying mechanism that ensures appropriate nAChR-mediated synaptic currents and the functional implications of separate sets or heteromultimeric nAChRs can now be addressed in this system.' author: - first_name: Shamprasad full_name: Raghu, Shamprasad V last_name: Raghu - first_name: Maximilian A full_name: Maximilian Jösch id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 - first_name: Stephan full_name: Sigrist, Stephan J last_name: Sigrist - first_name: Alexander full_name: Borst, Alexander last_name: Borst - first_name: Dierk full_name: Reiff, Dierk F last_name: Reiff citation: ama: 'Raghu S, Jösch MA, Sigrist S, Borst A, Reiff D. Synaptic organization of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors. Journal of Neurogenetics. 2009;23(1-2):200-209. doi:10.1080/01677060802471684' apa: 'Raghu, S., Jösch, M. A., Sigrist, S., Borst, A., & Reiff, D. (2009). Synaptic organization of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors. Journal of Neurogenetics. Informa Healthcare. https://doi.org/10.1080/01677060802471684' chicago: 'Raghu, Shamprasad, Maximilian A Jösch, Stephan Sigrist, Alexander Borst, and Dierk Reiff. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: Dα7 Cholinergic Receptors.” Journal of Neurogenetics. Informa Healthcare, 2009. https://doi.org/10.1080/01677060802471684.' ieee: 'S. Raghu, M. A. Jösch, S. Sigrist, A. Borst, and D. Reiff, “Synaptic organization of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors,” Journal of Neurogenetics, vol. 23, no. 1–2. Informa Healthcare, pp. 200–209, 2009.' ista: 'Raghu S, Jösch MA, Sigrist S, Borst A, Reiff D. 2009. Synaptic organization of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors. Journal of Neurogenetics. 23(1–2), 200–209.' mla: 'Raghu, Shamprasad, et al. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: Dα7 Cholinergic Receptors.” Journal of Neurogenetics, vol. 23, no. 1–2, Informa Healthcare, 2009, pp. 200–09, doi:10.1080/01677060802471684.' short: S. Raghu, M.A. Jösch, S. Sigrist, A. Borst, D. Reiff, Journal of Neurogenetics 23 (2009) 200–209. date_created: 2018-12-11T11:51:15Z date_published: 2009-03-01T00:00:00Z date_updated: 2021-01-12T06:49:44Z day: '01' doi: 10.1080/01677060802471684 extern: 1 intvolume: ' 23' issue: 1-2 month: '03' page: 200 - 209 publication: Journal of Neurogenetics publication_status: published publisher: Informa Healthcare publist_id: '5972' quality_controlled: 0 status: public title: 'Synaptic organization of lobula plate tangential cells in Drosophila: Dα7 cholinergic receptors' type: journal_article volume: 23 year: '2009' ... --- _id: '164' abstract: - lang: eng text: Let g be a cubic polynomial with integer coefficients and n>9 variables, and assume that the congruence g=0 modulo p^k is soluble for all prime powers p^k. We show that the equation g=0 has infinitely many integer solutions when the cubic part of g defines a projective hypersurface with singular locus of dimension <n-10. The proof is based on the Hardy-Littlewood circle method. article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Roger full_name: Heath Brown, Roger last_name: Heath Brown citation: ama: 'Browning TD, Heath Brown R. Integral points on cubic hypersurfaces. In: Analytic Number Theory: Essays in Honour of Klaus Roth. Cambridge University Press; 2009:75-90.' apa: 'Browning, T. D., & Heath Brown, R. (2009). Integral points on cubic hypersurfaces. In Analytic Number Theory: Essays in honour of Klaus Roth (pp. 75–90). Cambridge University Press.' chicago: 'Browning, Timothy D, and Roger Heath Brown. “Integral Points on Cubic Hypersurfaces.” In Analytic Number Theory: Essays in Honour of Klaus Roth, 75–90. Cambridge University Press, 2009.' ieee: 'T. D. Browning and R. Heath Brown, “Integral points on cubic hypersurfaces,” in Analytic Number Theory: Essays in honour of Klaus Roth, Cambridge University Press, 2009, pp. 75–90.' ista: 'Browning TD, Heath Brown R. 2009.Integral points on cubic hypersurfaces. In: Analytic Number Theory: Essays in honour of Klaus Roth. , 75–90.' mla: 'Browning, Timothy D., and Roger Heath Brown. “Integral Points on Cubic Hypersurfaces.” Analytic Number Theory: Essays in Honour of Klaus Roth, Cambridge University Press, 2009, pp. 75–90.' short: 'T.D. Browning, R. Heath Brown, in:, Analytic Number Theory: Essays in Honour of Klaus Roth, Cambridge University Press, 2009, pp. 75–90.' date_created: 2018-12-11T11:44:58Z date_published: 2009-01-31T00:00:00Z date_updated: 2021-01-12T06:52:11Z day: '31' extern: '1' external_id: arxiv: - '0611086' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/math/0611086 month: '01' oa: 1 oa_version: Preprint page: 75 - 90 publication: 'Analytic Number Theory: Essays in honour of Klaus Roth' publication_status: published publisher: Cambridge University Press publist_id: '7757' quality_controlled: '1' status: public title: Integral points on cubic hypersurfaces type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2009' ... --- _id: '165' abstract: - lang: eng text: We survey the state of affairs for the distribution of ℚ-rational points on non-singular del Pezzo surfaces of low degree, highlighting the recent resolution of Manin's conjecture for a non-singular del Pezzo surface of degree 4 by la Bretèche and Browning. acknowledgement: Proceedings of the 5th China-Japan Seminar alternative_title: - Series on number theory and its application author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: 'Browning TD. Resent progress on the quantitative arithmetic of del Pezzo surfaces. In: Aoki T, Kanemitsu S, Liu J, eds. Vol 6. World Scientific Publishing; 2009:1-18. doi:https://doi.org/10.1142/9789814289924_0001' apa: 'Browning, T. D. (2009). Resent progress on the quantitative arithmetic of del Pezzo surfaces. In T. Aoki, S. Kanemitsu, & J. Liu (Eds.) (Vol. 6, pp. 1–18). Presented at the Number Theory: Dreaming in dreams, World Scientific Publishing. https://doi.org/10.1142/9789814289924_0001' chicago: Browning, Timothy D. “Resent Progress on the Quantitative Arithmetic of Del Pezzo Surfaces.” edited by Takashi Aoki, Shigeru Kanemitsu, and Jianya Liu, 6:1–18. World Scientific Publishing, 2009. https://doi.org/10.1142/9789814289924_0001. ieee: 'T. D. Browning, “Resent progress on the quantitative arithmetic of del Pezzo surfaces,” presented at the Number Theory: Dreaming in dreams, 2009, vol. 6, pp. 1–18.' ista: 'Browning TD. 2009. Resent progress on the quantitative arithmetic of del Pezzo surfaces. Number Theory: Dreaming in dreams, Series on number theory and its application, vol. 6, 1–18.' mla: Browning, Timothy D. Resent Progress on the Quantitative Arithmetic of Del Pezzo Surfaces. Edited by Takashi Aoki et al., vol. 6, World Scientific Publishing, 2009, pp. 1–18, doi:https://doi.org/10.1142/9789814289924_0001. short: T.D. Browning, in:, T. Aoki, S. Kanemitsu, J. Liu (Eds.), World Scientific Publishing, 2009, pp. 1–18. conference: name: 'Number Theory: Dreaming in dreams' date_created: 2018-12-11T11:44:58Z date_published: 2009-08-24T00:00:00Z date_updated: 2021-01-12T06:52:15Z day: '24' doi: https://doi.org/10.1142/9789814289924_0001 editor: - first_name: Takashi full_name: Aoki, Takashi last_name: Aoki - first_name: Shigeru full_name: Kanemitsu, Shigeru last_name: Kanemitsu - first_name: Jianya full_name: Liu, Jianya last_name: Liu extern: 1 intvolume: ' 6' month: '08' page: 1 - 18 publication_status: published publisher: World Scientific Publishing publist_id: '7756' quality_controlled: 0 status: public title: Resent progress on the quantitative arithmetic of del Pezzo surfaces type: conference volume: 6 year: '2009' ... --- _id: '168' abstract: - lang: eng text: The arithmetic of ternary diagonal equation is considered for degree d >1, with the outcome that the set of coefficients for which the equation admits a non-zero integer solution is shown to have density zero. alternative_title: - Contemporary Mathematics author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Rainer full_name: Dietmann, Rainer last_name: Dietmann citation: ama: 'Browning TD, Dietmann R. Solubility of Fermat equations. In: Quadratic Forms - Algebra, Arithmetic and Geometry. Vol 493. American Mathematical Society; 2009:99-106. doi:http://dx.doi.org/10.1090/conm/493' apa: Browning, T. D., & Dietmann, R. (2009). Solubility of Fermat equations. In Quadratic Forms - algebra, arithmetic and geometry (Vol. 493, pp. 99–106). American Mathematical Society. http://dx.doi.org/10.1090/conm/493 chicago: Browning, Timothy D, and Rainer Dietmann. “Solubility of Fermat Equations.” In Quadratic Forms - Algebra, Arithmetic and Geometry, 493:99–106. American Mathematical Society, 2009. http://dx.doi.org/10.1090/conm/493. ieee: T. D. Browning and R. Dietmann, “Solubility of Fermat equations,” in Quadratic Forms - algebra, arithmetic and geometry, vol. 493, American Mathematical Society, 2009, pp. 99–106. ista: 'Browning TD, Dietmann R. 2009.Solubility of Fermat equations. In: Quadratic Forms - algebra, arithmetic and geometry. Contemporary Mathematics, vol. 493, 99–106.' mla: Browning, Timothy D., and Rainer Dietmann. “Solubility of Fermat Equations.” Quadratic Forms - Algebra, Arithmetic and Geometry, vol. 493, American Mathematical Society, 2009, pp. 99–106, doi:http://dx.doi.org/10.1090/conm/493. short: T.D. Browning, R. Dietmann, in:, Quadratic Forms - Algebra, Arithmetic and Geometry, American Mathematical Society, 2009, pp. 99–106. date_created: 2018-12-11T11:44:59Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T06:52:29Z day: '01' doi: http://dx.doi.org/10.1090/conm/493 extern: 1 intvolume: ' 493' main_file_link: - open_access: '0' url: https://arxiv.org/abs/0805.3354 month: '01' page: 99 - 106 publication: Quadratic Forms - algebra, arithmetic and geometry publication_status: published publisher: American Mathematical Society publist_id: '7753' quality_controlled: 0 status: public title: Solubility of Fermat equations type: book_chapter volume: 493 year: '2009' ... --- _id: '1718' abstract: - lang: eng text: Morphogens act as graded positional cues to control cell fate specification in many developing tissues. This concept, in which a signaling gradient regulates differential gene expression in a concentration-dependent manner, has received considerable experimental support. Nevertheless, several recent studies have challenged the straightforward model of morphogen activity. In particular, the observation that pattern formation is a dynamic process has raised questions about the influence of time on morphogen activity. Here we propose that the spatiotemporal dynamics of the cellular response to a morphogen gradient depend on a combination of temporal alterations to the morphogen gradient itself, the dynamics of its signal transduction and downstream interactions between target genes. acknowledgement: EK is supported by an EMBO LTF, AK by a FEBS fellowship, and JB by MRC (UK) and the Wellcome Trust author: - first_name: Eva full_name: Kutějová, Eva last_name: Kutějová - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Kutějová E, Briscoe J, Kicheva A. Temporal dynamics of patterning by morphogen gradients. Current Opinion in Genetics & Development. 2009;19(4):315-322. doi:10.1016/j.gde.2009.05.004 apa: Kutějová, E., Briscoe, J., & Kicheva, A. (2009). Temporal dynamics of patterning by morphogen gradients. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2009.05.004 chicago: Kutějová, Eva, James Briscoe, and Anna Kicheva. “Temporal Dynamics of Patterning by Morphogen Gradients.” Current Opinion in Genetics & Development. Elsevier, 2009. https://doi.org/10.1016/j.gde.2009.05.004. ieee: E. Kutějová, J. Briscoe, and A. Kicheva, “Temporal dynamics of patterning by morphogen gradients,” Current Opinion in Genetics & Development, vol. 19, no. 4. Elsevier, pp. 315–322, 2009. ista: Kutějová E, Briscoe J, Kicheva A. 2009. Temporal dynamics of patterning by morphogen gradients. Current Opinion in Genetics & Development. 19(4), 315–322. mla: Kutějová, Eva, et al. “Temporal Dynamics of Patterning by Morphogen Gradients.” Current Opinion in Genetics & Development, vol. 19, no. 4, Elsevier, 2009, pp. 315–22, doi:10.1016/j.gde.2009.05.004. short: E. Kutějová, J. Briscoe, A. Kicheva, Current Opinion in Genetics & Development 19 (2009) 315–322. date_created: 2018-12-11T11:53:38Z date_published: 2009-08-01T00:00:00Z date_updated: 2021-01-12T06:52:44Z day: '01' doi: 10.1016/j.gde.2009.05.004 extern: 1 intvolume: ' 19' issue: '4' month: '08' page: 315 - 322 publication: Current Opinion in Genetics & Development publication_status: published publisher: Elsevier publist_id: '5410' quality_controlled: 0 status: public title: Temporal dynamics of patterning by morphogen gradients type: journal_article volume: 19 year: '2009' ... --- _id: '1720' abstract: - lang: eng text: How morphogen gradients are formed in target tissues is a key question for understanding the mechanisms of morphological patterning. Here, we review different mechanisms of morphogen gradient formation from theoretical and experimental points of view. First, a simple, comprehensive overview of the underlying biophysical principles of several mechanisms of gradient formation is provided. We then discuss the advantages and limitations of different experimental approaches to gradient formation analysis. author: - first_name: Ortrud full_name: Wartlick, Ortrud last_name: Wartlick - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Marcos full_name: González-Gaitán, Marcos A last_name: González Gaitán citation: ama: Wartlick O, Kicheva A, González Gaitán M. Morphogen gradient formation . Cold Spring Harbor perspectives in biology. 2009;1(3). doi:10.1101/cshperspect.a001255 apa: Wartlick, O., Kicheva, A., & González Gaitán, M. (2009). Morphogen gradient formation . Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a001255 chicago: Wartlick, Ortrud, Anna Kicheva, and Marcos González Gaitán. “Morphogen Gradient Formation .” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press, 2009. https://doi.org/10.1101/cshperspect.a001255. ieee: O. Wartlick, A. Kicheva, and M. González Gaitán, “Morphogen gradient formation ,” Cold Spring Harbor perspectives in biology, vol. 1, no. 3. Cold Spring Harbor Laboratory Press, 2009. ista: Wartlick O, Kicheva A, González Gaitán M. 2009. Morphogen gradient formation . Cold Spring Harbor perspectives in biology. 1(3). mla: Wartlick, Ortrud, et al. “Morphogen Gradient Formation .” Cold Spring Harbor Perspectives in Biology, vol. 1, no. 3, Cold Spring Harbor Laboratory Press, 2009, doi:10.1101/cshperspect.a001255. short: O. Wartlick, A. Kicheva, M. González Gaitán, Cold Spring Harbor Perspectives in Biology 1 (2009). date_created: 2018-12-11T11:53:39Z date_published: 2009-09-01T00:00:00Z date_updated: 2021-01-12T06:52:45Z day: '01' doi: 10.1101/cshperspect.a001255 extern: 1 intvolume: ' 1' issue: '3' month: '09' publication: Cold Spring Harbor perspectives in biology publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '5409' quality_controlled: 0 status: public title: 'Morphogen gradient formation ' type: journal_article volume: 1 year: '2009' ... --- _id: '1769' abstract: - lang: eng text: We present an ideal realization of the Tavis-Cummings model in the absence of atom number and coupling fluctuations by embedding a discrete number of fully controllable superconducting qubits at fixed positions into a transmission line resonator. Measuring the vacuum Rabi mode splitting with one, two, and three qubits strongly coupled to the cavity field, we explore both bright and dark dressed collective multiqubit states and observe the discrete N scaling of the collective dipole coupling strength. Our experiments demonstrate a novel approach to explore collective states, such as the W state, in a fully globally and locally controllable quantum system. Our scalable approach is interesting for solid-state quantum information processing and for fundamental multiatom quantum optics experiments with fixed atom numbers. acknowledgement: This work was supported by SNF Grant No. 200021-111899 and ETHZ. P. J. L. was supported by the EU with a MC-EIF. A. B. was supported by NSERC, CIFAR, and the Alfred P. Sloan Foundation author: - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: M full_name: Göppl, M last_name: Göppl - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Peter full_name: Leek, Peter J last_name: Leek - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Fink JM, Bianchetti R, Baur M, et al. Dressed collective qubit states and the Tavis-Cummings model in circuit QED. Physical Review Letters. 2009;103(8). doi:10.1103/PhysRevLett.103.083601 apa: Fink, J. M., Bianchetti, R., Baur, M., Göppl, M., Steffen, L., Filipp, S., … Wallraff, A. (2009). Dressed collective qubit states and the Tavis-Cummings model in circuit QED. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.103.083601 chicago: Fink, Johannes M, R Bianchetti, Matthias Baur, M Göppl, L. Steffen, Stefan Filipp, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Dressed Collective Qubit States and the Tavis-Cummings Model in Circuit QED.” Physical Review Letters. American Physical Society, 2009. https://doi.org/10.1103/PhysRevLett.103.083601. ieee: J. M. Fink et al., “Dressed collective qubit states and the Tavis-Cummings model in circuit QED,” Physical Review Letters, vol. 103, no. 8. American Physical Society, 2009. ista: Fink JM, Bianchetti R, Baur M, Göppl M, Steffen L, Filipp S, Leek P, Blais A, Wallraff A. 2009. Dressed collective qubit states and the Tavis-Cummings model in circuit QED. Physical Review Letters. 103(8). mla: Fink, Johannes M., et al. “Dressed Collective Qubit States and the Tavis-Cummings Model in Circuit QED.” Physical Review Letters, vol. 103, no. 8, American Physical Society, 2009, doi:10.1103/PhysRevLett.103.083601. short: J.M. Fink, R. Bianchetti, M. Baur, M. Göppl, L. Steffen, S. Filipp, P. Leek, A. Blais, A. Wallraff, Physical Review Letters 103 (2009). date_created: 2018-12-11T11:53:55Z date_published: 2009-08-17T00:00:00Z date_updated: 2021-01-12T06:53:05Z day: '17' doi: 10.1103/PhysRevLett.103.083601 extern: 1 intvolume: ' 103' issue: '8' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0812.2651 month: '08' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5350' quality_controlled: 0 status: public title: Dressed collective qubit states and the Tavis-Cummings model in circuit QED type: journal_article volume: 103 year: '2009' ... --- _id: '1767' abstract: - lang: eng text: We present spectroscopic measurements of the Autler-Townes doublet and the sidebands of the Mollow triplet in a driven superconducting qubit. The ground to first excited state transition of the qubit is strongly pumped while the resulting dressed qubit spectrum is probed with a weak tone. The corresponding transitions are detected using dispersive readout of the qubit coupled off resonantly to a microwave transmission line resonator. The observed frequencies of the Autler-Townes and Mollow spectral lines are in good agreement with a dispersive Jaynes-Cummings model taking into account higher excited qubit states and dispersive level shifts due to off-resonant drives. acknowledgement: This work was supported by the Swiss National Science Foundation and by ETH Zürich. P. J. L. acknowledges support from the EC via an Intra-European Marie-Curie Fellowship. A. B. was supported by NSERC, CIFAR, FQRNT, and Alfred P. Sloan Foundation author: - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: M full_name: Göppl, M last_name: Göppl - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Peter full_name: Leek, Peter J last_name: Leek - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Baur M, Filipp S, Bianchetti R, et al. Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. Physical Review Letters. 2009;102(24). doi:10.1103/PhysRevLett.102.243602 apa: Baur, M., Filipp, S., Bianchetti, R., Fink, J. M., Göppl, M., Steffen, L., … Wallraff, A. (2009). Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.102.243602 chicago: Baur, Matthias, Stefan Filipp, R Bianchetti, Johannes M Fink, M Göppl, L. Steffen, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Measurement of Autler-Townes and Mollow Transitions in a Strongly Driven Superconducting Qubit.” Physical Review Letters. American Physical Society, 2009. https://doi.org/10.1103/PhysRevLett.102.243602. ieee: M. Baur et al., “Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit,” Physical Review Letters, vol. 102, no. 24. American Physical Society, 2009. ista: Baur M, Filipp S, Bianchetti R, Fink JM, Göppl M, Steffen L, Leek P, Blais A, Wallraff A. 2009. Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. Physical Review Letters. 102(24). mla: Baur, Matthias, et al. “Measurement of Autler-Townes and Mollow Transitions in a Strongly Driven Superconducting Qubit.” Physical Review Letters, vol. 102, no. 24, American Physical Society, 2009, doi:10.1103/PhysRevLett.102.243602. short: M. Baur, S. Filipp, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, P. Leek, A. Blais, A. Wallraff, Physical Review Letters 102 (2009). date_created: 2018-12-11T11:53:54Z date_published: 2009-06-19T00:00:00Z date_updated: 2021-01-12T06:53:04Z day: '19' doi: 10.1103/PhysRevLett.102.243602 extern: 1 intvolume: ' 102' issue: '24' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0812.4384 month: '06' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5352' quality_controlled: 0 status: public title: Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit type: journal_article volume: 102 year: '2009' ... --- _id: '1766' abstract: - lang: eng text: We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation. acknowledgement: This work was supported by ETH Zurich, the Swiss National Science Foundation, and by the EC via the EuroSQIP project and the Marie-Curie program (P. J. L.) author: - first_name: Peter full_name: Leek, Peter J last_name: Leek - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Patrick full_name: Maurer, Patrick last_name: Maurer - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: M full_name: Göppl, M last_name: Göppl - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Leek P, Filipp S, Maurer P, et al. Using sideband transitions for two-qubit operations in superconducting circuits. Physical Review B - Condensed Matter and Materials Physics. 2009;79(18). doi:10.1103/PhysRevB.79.180511 apa: Leek, P., Filipp, S., Maurer, P., Baur, M., Bianchetti, R., Fink, J. M., … Wallraff, A. (2009). Using sideband transitions for two-qubit operations in superconducting circuits. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.79.180511 chicago: Leek, Peter, Stefan Filipp, Patrick Maurer, Matthias Baur, R Bianchetti, Johannes M Fink, M Göppl, L. Steffen, and Andreas Wallraff. “Using Sideband Transitions for Two-Qubit Operations in Superconducting Circuits.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2009. https://doi.org/10.1103/PhysRevB.79.180511. ieee: P. Leek et al., “Using sideband transitions for two-qubit operations in superconducting circuits,” Physical Review B - Condensed Matter and Materials Physics, vol. 79, no. 18. American Physical Society, 2009. ista: Leek P, Filipp S, Maurer P, Baur M, Bianchetti R, Fink JM, Göppl M, Steffen L, Wallraff A. 2009. Using sideband transitions for two-qubit operations in superconducting circuits. Physical Review B - Condensed Matter and Materials Physics. 79(18). mla: Leek, Peter, et al. “Using Sideband Transitions for Two-Qubit Operations in Superconducting Circuits.” Physical Review B - Condensed Matter and Materials Physics, vol. 79, no. 18, American Physical Society, 2009, doi:10.1103/PhysRevB.79.180511. short: P. Leek, S. Filipp, P. Maurer, M. Baur, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, A. Wallraff, Physical Review B - Condensed Matter and Materials Physics 79 (2009). date_created: 2018-12-11T11:53:54Z date_published: 2009-05-01T00:00:00Z date_updated: 2021-01-12T06:53:04Z day: '01' doi: 10.1103/PhysRevB.79.180511 extern: 1 intvolume: ' 79' issue: '18' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0812.2678 month: '05' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '5354' quality_controlled: 0 status: public title: Using sideband transitions for two-qubit operations in superconducting circuits type: journal_article volume: 79 year: '2009' ... --- _id: '1768' abstract: - lang: eng text: Quantum state tomography is an important tool in quantum information science for complete characterization of multiqubit states and their correlations. Here we report a method to perform a joint simultaneous readout of two superconducting qubits dispersively coupled to the same mode of a microwave transmission line resonator. The nonlinear dependence of the resonator transmission on the qubit state dependent cavity frequency allows us to extract the full two-qubit correlations without the need for single-shot readout of individual qubits. We employ standard tomographic techniques to reconstruct the density matrix of two-qubit quantum states. acknowledgement: This work was supported by Swiss National Science Foundation (SNF) and ETH Zurich. P. J. L. was supported by the EC with a MC-EIF, J. M. G. by CIFAR, MRI, MITACS, and NSERC, and A. B. by NSERC and CIFAR author: - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Patrick full_name: Maurer, Patrick last_name: Maurer - first_name: Peter full_name: Leek, Peter J last_name: Leek - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: M full_name: Göppl, M last_name: Göppl - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Jay full_name: Gambetta, Jay M last_name: Gambetta - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Filipp S, Maurer P, Leek P, et al. Two-qubit state tomography using a joint dispersive readout. Physical Review Letters. 2009;102(20). doi:10.1103/PhysRevLett.102.200402 apa: Filipp, S., Maurer, P., Leek, P., Baur, M., Bianchetti, R., Fink, J. M., … Wallraff, A. (2009). Two-qubit state tomography using a joint dispersive readout. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.102.200402 chicago: Filipp, Stefan, Patrick Maurer, Peter Leek, Matthias Baur, R Bianchetti, Johannes M Fink, M Göppl, et al. “Two-Qubit State Tomography Using a Joint Dispersive Readout.” Physical Review Letters. American Physical Society, 2009. https://doi.org/10.1103/PhysRevLett.102.200402. ieee: S. Filipp et al., “Two-qubit state tomography using a joint dispersive readout,” Physical Review Letters, vol. 102, no. 20. American Physical Society, 2009. ista: Filipp S, Maurer P, Leek P, Baur M, Bianchetti R, Fink JM, Göppl M, Steffen L, Gambetta J, Blais A, Wallraff A. 2009. Two-qubit state tomography using a joint dispersive readout. Physical Review Letters. 102(20). mla: Filipp, Stefan, et al. “Two-Qubit State Tomography Using a Joint Dispersive Readout.” Physical Review Letters, vol. 102, no. 20, American Physical Society, 2009, doi:10.1103/PhysRevLett.102.200402. short: S. Filipp, P. Maurer, P. Leek, M. Baur, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, J. Gambetta, A. Blais, A. Wallraff, Physical Review Letters 102 (2009). date_created: 2018-12-11T11:53:54Z date_published: 2009-05-18T00:00:00Z date_updated: 2021-01-12T06:53:04Z day: '18' doi: 10.1103/PhysRevLett.102.200402 extern: 1 intvolume: ' 102' issue: '20' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0812.2485 month: '05' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5353' quality_controlled: 0 status: public title: Two-qubit state tomography using a joint dispersive readout type: journal_article volume: 102 year: '2009' ... --- _id: '1770' abstract: - lang: eng text: The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements. acknowledgement: This work was supported by the SNF Project No. 111899 and ETH Zurich. A.B. was supported by NSERC, CIFAR, and the Alfred P. Sloan Foundation author: - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: M full_name: Göppl, M last_name: Göppl - first_name: Peter full_name: Leek, Peter J last_name: Leek - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Bianchetti R, Filipp S, Baur M, et al. Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 2009;80(4). doi:10.1103/PhysRevA.80.043840 apa: Bianchetti, R., Filipp, S., Baur, M., Fink, J. M., Göppl, M., Leek, P., … Wallraff, A. (2009). Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.80.043840 chicago: Bianchetti, R, Stefan Filipp, Matthias Baur, Johannes M Fink, M Göppl, Peter Leek, L. Steffen, Alexandre Blais, and Andreas Wallraff. “Dynamics of Dispersive Single-Qubit Readout in Circuit Quantum Electrodynamics.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2009. https://doi.org/10.1103/PhysRevA.80.043840. ieee: R. Bianchetti et al., “Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 80, no. 4. American Physical Society, 2009. ista: Bianchetti R, Filipp S, Baur M, Fink JM, Göppl M, Leek P, Steffen L, Blais A, Wallraff A. 2009. Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 80(4). mla: Bianchetti, R., et al. “Dynamics of Dispersive Single-Qubit Readout in Circuit Quantum Electrodynamics.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 80, no. 4, American Physical Society, 2009, doi:10.1103/PhysRevA.80.043840. short: R. Bianchetti, S. Filipp, M. Baur, J.M. Fink, M. Göppl, P. Leek, L. Steffen, A. Blais, A. Wallraff, Physical Review A - Atomic, Molecular, and Optical Physics 80 (2009). date_created: 2018-12-11T11:53:55Z date_published: 2009-10-30T00:00:00Z date_updated: 2021-01-12T06:53:05Z day: '30' doi: 10.1103/PhysRevA.80.043840 extern: 1 intvolume: ' 80' issue: '4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0907.2549 month: '10' oa: 1 publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '5349' quality_controlled: 0 status: public title: Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics type: journal_article volume: 80 year: '2009' ... --- _id: '1771' abstract: - lang: eng text: The exceptionally strong coupling realizable between superconducting qubits and photons stored in an on-chip microwave resonator allows for the detailed study of matter-light interactions in the realm of circuit quantum electrodynamics (QED). Here we investigate the resonant interaction between a single transmon-type multilevel artificial atom and weak thermal and coherent fields. We explore up to three photon dressed states of the coupled system in a linear response heterodyne transmission measurement. The results are in good quantitative agreement with a generalized Jaynes-Cummings model. Our data indicate that the role of thermal fields in resonant cavity QED can be studied in detail using superconducting circuits. acknowledgement: Nobel Foundation author: - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: M full_name: Göppl, M last_name: Göppl - first_name: Peter full_name: Leek, Peter J last_name: Leek - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Fink JM, Baur M, Bianchetti R, et al. Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics. Physica Scripta T. 2009;T137. doi:10.1088/0031-8949/2009/T137/014013 apa: Fink, J. M., Baur, M., Bianchetti, R., Filipp, S., Göppl, M., Leek, P., … Wallraff, A. (2009). Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics. Physica Scripta T. IOP Publishing Ltd. https://doi.org/10.1088/0031-8949/2009/T137/014013 chicago: Fink, Johannes M, Matthias Baur, R Bianchetti, Stefan Filipp, M Göppl, Peter Leek, L. Steffen, Alexandre Blais, and Andreas Wallraff. “Thermal Excitation of Multi-Photon Dressed States in Circuit Quantum Electrodynamics.” Physica Scripta T. IOP Publishing Ltd., 2009. https://doi.org/10.1088/0031-8949/2009/T137/014013. ieee: J. M. Fink et al., “Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics,” Physica Scripta T, vol. T137. IOP Publishing Ltd., 2009. ista: Fink JM, Baur M, Bianchetti R, Filipp S, Göppl M, Leek P, Steffen L, Blais A, Wallraff A. 2009. Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics. Physica Scripta T. T137. mla: Fink, Johannes M., et al. “Thermal Excitation of Multi-Photon Dressed States in Circuit Quantum Electrodynamics.” Physica Scripta T, vol. T137, IOP Publishing Ltd., 2009, doi:10.1088/0031-8949/2009/T137/014013. short: J.M. Fink, M. Baur, R. Bianchetti, S. Filipp, M. Göppl, P. Leek, L. Steffen, A. Blais, A. Wallraff, Physica Scripta T T137 (2009). date_created: 2018-12-11T11:53:55Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T06:53:06Z day: '01' doi: 10.1088/0031-8949/2009/T137/014013 extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/0911.3797 month: '01' oa: 1 publication: Physica Scripta T publication_status: published publisher: IOP Publishing Ltd. publist_id: '5348' quality_controlled: 0 status: public title: Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics type: journal_article volume: T137 year: '2009' ... --- _id: '1799' abstract: - lang: eng text: 'The detection of approaching objects, such as looming predators, is necessary for survival. Which neurons and circuits mediate this function? We combined genetic labeling of cell types, two-photon microscopy, electrophysiology and theoretical modeling to address this question. We identify an approach-sensitive ganglion cell type in the mouse retina, resolve elements of its afferent neural circuit, and describe how these confer approach sensitivity on the ganglion cell. The circuit''s essential building block is a rapid inhibitory pathway: it selectively suppresses responses to non-approaching objects. This rapid inhibitory pathway, which includes AII amacrine cells connected to bipolar cells through electrical synapses, was previously described in the context of night-time vision. In the daytime conditions of our experiments, the same pathway conveys signals in the reverse direction. The dual use of a neural pathway in different physiological conditions illustrates the efficiency with which several functions can be accommodated in a single circuit.' acknowledgement: The study was supported by Friedrich Miescher Institute funds, a US Office of Naval Research Naval International Cooperative Opportunities in Science and Technology program grant, a Marie Curie Excellence Grant, a Human Frontier Science Program Young Investigator grant, a National Centers of Competence in Research in Genetics grant and a European Union HEALTH-F2-223156 grant to B.R., a Marie Curie Postdoctoral Fellowship to T.A.M., the Centre National de la Recherche Scientifique through the Unité Mixte de Recherche 8550 to R.A.d.S. author: - first_name: Thomas full_name: Münch, Thomas A last_name: Münch - first_name: Ravá full_name: Da Silveira, Ravá A last_name: Da Silveira - first_name: Sandra full_name: Sandra Siegert id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 - first_name: Tim full_name: Viney, Tim J last_name: Viney - first_name: Gautam full_name: Awatramani, Gautam B last_name: Awatramani - first_name: Botond full_name: Roska, Botond M last_name: Roska citation: ama: Münch T, Da Silveira R, Siegert S, Viney T, Awatramani G, Roska B. Approach sensitivity in the retina processed by a multifunctional neural circuit. Nature Neuroscience. 2009;12(10):1308-1316. doi:10.1038/nn.2389 apa: Münch, T., Da Silveira, R., Siegert, S., Viney, T., Awatramani, G., & Roska, B. (2009). Approach sensitivity in the retina processed by a multifunctional neural circuit. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2389 chicago: Münch, Thomas, Ravá Da Silveira, Sandra Siegert, Tim Viney, Gautam Awatramani, and Botond Roska. “Approach Sensitivity in the Retina Processed by a Multifunctional Neural Circuit.” Nature Neuroscience. Nature Publishing Group, 2009. https://doi.org/10.1038/nn.2389. ieee: T. Münch, R. Da Silveira, S. Siegert, T. Viney, G. Awatramani, and B. Roska, “Approach sensitivity in the retina processed by a multifunctional neural circuit,” Nature Neuroscience, vol. 12, no. 10. Nature Publishing Group, pp. 1308–1316, 2009. ista: Münch T, Da Silveira R, Siegert S, Viney T, Awatramani G, Roska B. 2009. Approach sensitivity in the retina processed by a multifunctional neural circuit. Nature Neuroscience. 12(10), 1308–1316. mla: Münch, Thomas, et al. “Approach Sensitivity in the Retina Processed by a Multifunctional Neural Circuit.” Nature Neuroscience, vol. 12, no. 10, Nature Publishing Group, 2009, pp. 1308–16, doi:10.1038/nn.2389. short: T. Münch, R. Da Silveira, S. Siegert, T. Viney, G. Awatramani, B. Roska, Nature Neuroscience 12 (2009) 1308–1316. date_created: 2018-12-11T11:54:04Z date_published: 2009-10-01T00:00:00Z date_updated: 2021-01-12T06:53:16Z day: '01' doi: 10.1038/nn.2389 extern: 1 intvolume: ' 12' issue: '10' month: '10' page: 1308 - 1316 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '5311' quality_controlled: 0 status: public title: Approach sensitivity in the retina processed by a multifunctional neural circuit type: journal_article volume: 12 year: '2009' ... --- _id: '1798' abstract: - lang: eng text: The mammalian brain is assembled from thousands of neuronal cell types that are organized in distinct circuits to perform behaviorally relevant computations. Transgenic mouse lines with selectively marked cell types would facilitate our ability to dissect functional components of complex circuits. We carried out a screen for cell type-specific green fluorescent protein expression in the retina using BAC transgenic mice from the GENSAT project. Among others, we identified mouse lines in which the inhibitory cell types of the night vision and directional selective circuit were selectively labeled. We quantified the stratification patterns to predict potential synaptic connectivity between marked cells of different lines and found that some of the lines enabled targeted recordings and imaging of cell types from developing or mature retinal circuits. Our results suggest the potential use of a stratification-based screening approach for characterizing neuronal circuitry in other layered brain structures, such as the neocortex. acknowledgement: This study was supported by Friedrich Miescher Institute funds, a US Office of Naval Research Naval International Cooperative Opportunities in Science and Technology Program grant, a Marie Curie Excellence grant, a National Center for Competence in Research in Genetics grant and a European Union HEALTH-F2-223156 grant to B.R., and by National Institute of Neurological Disorders and Stroke contracts N01NS02331 and HHSN271200723701C to N.H. author: - first_name: Sandra full_name: Sandra Siegert id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 - first_name: Brigitte full_name: Scherf, Brigitte G last_name: Scherf - first_name: Karina full_name: Del Punta, Karina last_name: Del Punta - first_name: Nick full_name: Didkovsky, Nick last_name: Didkovsky - first_name: Nathaniel full_name: Heintz, Nathaniel M last_name: Heintz - first_name: Botond full_name: Roska, Botond M last_name: Roska citation: ama: Siegert S, Scherf B, Del Punta K, Didkovsky N, Heintz N, Roska B. Genetic address book for retinal cell types. Nature Neuroscience. 2009;12(9):1197-1204. doi:10.1038/nn.2370 apa: Siegert, S., Scherf, B., Del Punta, K., Didkovsky, N., Heintz, N., & Roska, B. (2009). Genetic address book for retinal cell types. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2370 chicago: Siegert, Sandra, Brigitte Scherf, Karina Del Punta, Nick Didkovsky, Nathaniel Heintz, and Botond Roska. “Genetic Address Book for Retinal Cell Types.” Nature Neuroscience. Nature Publishing Group, 2009. https://doi.org/10.1038/nn.2370. ieee: S. Siegert, B. Scherf, K. Del Punta, N. Didkovsky, N. Heintz, and B. Roska, “Genetic address book for retinal cell types,” Nature Neuroscience, vol. 12, no. 9. Nature Publishing Group, pp. 1197–1204, 2009. ista: Siegert S, Scherf B, Del Punta K, Didkovsky N, Heintz N, Roska B. 2009. Genetic address book for retinal cell types. Nature Neuroscience. 12(9), 1197–1204. mla: Siegert, Sandra, et al. “Genetic Address Book for Retinal Cell Types.” Nature Neuroscience, vol. 12, no. 9, Nature Publishing Group, 2009, pp. 1197–204, doi:10.1038/nn.2370. short: S. Siegert, B. Scherf, K. Del Punta, N. Didkovsky, N. Heintz, B. Roska, Nature Neuroscience 12 (2009) 1197–1204. date_created: 2018-12-11T11:54:04Z date_published: 2009-09-01T00:00:00Z date_updated: 2021-01-12T06:53:16Z day: '01' doi: 10.1038/nn.2370 extern: 1 intvolume: ' 12' issue: '9' month: '09' page: 1197 - 1204 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '5312' quality_controlled: 0 status: public title: Genetic address book for retinal cell types type: journal_article volume: 12 year: '2009' ... --- _id: '1825' abstract: - lang: eng text: 'Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus. A key mechanism that underlies this response is the slow, activity-dependent removal of responding molecules to a pool which is unavailable to respond immediately to the input. This mechanism is implemented in different ways in various biological systems and has traditionally been studied separately for each. Here we highlight the common aspects of this principle, shared by many biological systems, and suggest a unifying theoretical framework. We study theoretically a class of models which describes the general mechanism and allows us to distinguish its universal from system-specific features. We show that under general conditions, regardless of the details of kinetics, molecule availability encodes an averaging over past activity and feeds back multiplicatively on the system output. The kinetics of recovery from unavailability determines the effective memory kernel inside the feedback branch, giving rise to a variety of system-specific forms of adaptive response—precise or input-dependent, exponential or power-law—as special cases of the same model. ' author: - first_name: Tamar full_name: Tamar Friedlander id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Naama full_name: Brenner, Naama last_name: Brenner citation: ama: Friedlander T, Brenner N. Adaptive response by state-dependent inactivation. PNAS. 2009;106(52):22558-22563. doi:10.1073/pnas.0902146106 apa: Friedlander, T., & Brenner, N. (2009). Adaptive response by state-dependent inactivation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0902146106 chicago: Friedlander, Tamar, and Naama Brenner. “Adaptive Response by State-Dependent Inactivation.” PNAS. National Academy of Sciences, 2009. https://doi.org/10.1073/pnas.0902146106 . ieee: T. Friedlander and N. Brenner, “Adaptive response by state-dependent inactivation,” PNAS, vol. 106, no. 52. National Academy of Sciences, pp. 22558–22563, 2009. ista: Friedlander T, Brenner N. 2009. Adaptive response by state-dependent inactivation. PNAS. 106(52), 22558–22563. mla: Friedlander, Tamar, and Naama Brenner. “Adaptive Response by State-Dependent Inactivation.” PNAS, vol. 106, no. 52, National Academy of Sciences, 2009, pp. 22558–63, doi:10.1073/pnas.0902146106 . short: T. Friedlander, N. Brenner, PNAS 106 (2009) 22558–22563. date_created: 2018-12-11T11:54:13Z date_published: 2009-12-01T00:00:00Z date_updated: 2021-01-12T06:53:26Z day: '01' doi: '10.1073/pnas.0902146106 ' extern: 1 intvolume: ' 106' issue: '52' main_file_link: - open_access: '1' url: http://www.pnas.org/content/106/52/22558.full.pdf month: '12' oa: 1 page: 22558 - 22563 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5281' quality_controlled: 0 status: public title: Adaptive response by state-dependent inactivation type: journal_article volume: 106 year: '2009' ... --- _id: '1971' abstract: - lang: eng text: Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 Å resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several α-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines. acknowledgement: 'This work was supported by the Medical Research Council. ' author: - first_name: John full_name: Berrisford, John M last_name: Berrisford - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Berrisford J, Sazanov LA. Structural basis for the mechanism of respiratory complex I. Journal of Biological Chemistry. 2009;284(43):29773-29783. doi:10.1074/jbc.M109.032144 apa: Berrisford, J., & Sazanov, L. A. (2009). Structural basis for the mechanism of respiratory complex I. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M109.032144 chicago: Berrisford, John, and Leonid A Sazanov. “Structural Basis for the Mechanism of Respiratory Complex I.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2009. https://doi.org/10.1074/jbc.M109.032144. ieee: J. Berrisford and L. A. Sazanov, “Structural basis for the mechanism of respiratory complex I,” Journal of Biological Chemistry, vol. 284, no. 43. American Society for Biochemistry and Molecular Biology, pp. 29773–29783, 2009. ista: Berrisford J, Sazanov LA. 2009. Structural basis for the mechanism of respiratory complex I. Journal of Biological Chemistry. 284(43), 29773–29783. mla: Berrisford, John, and Leonid A. Sazanov. “Structural Basis for the Mechanism of Respiratory Complex I.” Journal of Biological Chemistry, vol. 284, no. 43, American Society for Biochemistry and Molecular Biology, 2009, pp. 29773–83, doi:10.1074/jbc.M109.032144. short: J. Berrisford, L.A. Sazanov, Journal of Biological Chemistry 284 (2009) 29773–29783. date_created: 2018-12-11T11:54:59Z date_published: 2009-10-23T00:00:00Z date_updated: 2021-01-12T06:54:26Z day: '23' doi: 10.1074/jbc.M109.032144 extern: 1 intvolume: ' 284' issue: '43' month: '10' page: 29773 - 29783 publication: Journal of Biological Chemistry publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '5114' quality_controlled: 0 status: public title: Structural basis for the mechanism of respiratory complex I type: journal_article volume: 284 year: '2009' ... --- _id: '1984' abstract: - lang: eng text: In animal and plant cells, mitotic chromatin locally generates microtubules that self-organize into a mitotic spindle, and its dimensions and bipolar symmetry are essential for accurate chromosome segregation. By immobilizing microscopic chromatin-coated beads on slide surfaces using a microprinting technique, we have examined the effect of chromatin on the dimensions and symmetry of spindles in Xenopus laevis cytoplasmic extracts. While circular spots with diameters around 14-18 μm trigger bipolar spindle formation, larger spots generate an incorrect number of poles. We also examined lines of chromatin with various dimensions. Their length determined the number of poles that formed, with a 6 × 18 μm rectangular patch generating normal spindle morphology. Around longer lines, multiple poles formed and the structures were disorganized. While lines thinner than 10 μm generated symmetric structures, thicker lines induced the formation of asymmetric structures where all microtubules are on the same side of the line. Our results show that chromatin defines spindle shape and orientation. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data. acknowledgement: This work was supported by EU contract LSHG-CT-2004-503568 ComBio, the Spanish ministry of education (M.M.C.), and EU-STREP active BioMics (A.D.). Research in the Nedelec lab is funded by the Center for Modeling and Simulation in the Biosciences (http://www.bioms.de), the Volkswagenstiftung, and Human Frontier Science Program grant RGY84. author: - first_name: Ana full_name: Dinarina, Ana last_name: Dinarina - first_name: Céline full_name: Pugieux, Céline last_name: Pugieux - first_name: Maria full_name: Corral, Maria M last_name: Corral - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Joachim full_name: Spatz, Joachim P last_name: Spatz - first_name: Éric full_name: Karsenti, Éric last_name: Karsenti - first_name: François full_name: Nédélec, François J last_name: Nédélec citation: ama: Dinarina A, Pugieux C, Corral M, et al. Chromatin shapes the mitotic spindle. Cell. 2009;138(3):502-513. doi:10.1016/j.cell.2009.05.027 apa: Dinarina, A., Pugieux, C., Corral, M., Loose, M., Spatz, J., Karsenti, É., & Nédélec, F. (2009). Chromatin shapes the mitotic spindle. Cell. Cell Press. https://doi.org/10.1016/j.cell.2009.05.027 chicago: Dinarina, Ana, Céline Pugieux, Maria Corral, Martin Loose, Joachim Spatz, Éric Karsenti, and François Nédélec. “Chromatin Shapes the Mitotic Spindle.” Cell. Cell Press, 2009. https://doi.org/10.1016/j.cell.2009.05.027. ieee: A. Dinarina et al., “Chromatin shapes the mitotic spindle,” Cell, vol. 138, no. 3. Cell Press, pp. 502–513, 2009. ista: Dinarina A, Pugieux C, Corral M, Loose M, Spatz J, Karsenti É, Nédélec F. 2009. Chromatin shapes the mitotic spindle. Cell. 138(3), 502–513. mla: Dinarina, Ana, et al. “Chromatin Shapes the Mitotic Spindle.” Cell, vol. 138, no. 3, Cell Press, 2009, pp. 502–13, doi:10.1016/j.cell.2009.05.027. short: A. Dinarina, C. Pugieux, M. Corral, M. Loose, J. Spatz, É. Karsenti, F. Nédélec, Cell 138 (2009) 502–513. date_created: 2018-12-11T11:55:03Z date_published: 2009-08-07T00:00:00Z date_updated: 2021-01-12T06:54:30Z day: '07' doi: 10.1016/j.cell.2009.05.027 extern: 1 intvolume: ' 138' issue: '3' month: '08' page: 502 - 513 publication: Cell publication_status: published publisher: Cell Press publist_id: '5100' quality_controlled: 0 status: public title: Chromatin shapes the mitotic spindle type: journal_article volume: 138 year: '2009' ... --- _id: '1983' abstract: - lang: eng text: 'During many cellular processes such as cell division, polarization and motility, the plasma membrane does not only represent a passive physical barrier, but also provides a highly dynamic platform for the interplay between lipids, membrane binding proteins and cytoskeletal elements. Even though many regulators of these interactions are known, their mutual interdependence appears to be highly complex and difficult to study in a living cell. Over the past few years, in vitro studies on membrane-cytoskeleton interactions using biomimetic membranes turned out to be extremely helpful to get better mechanistic insight into the dynamics of these processes. In this review, we discuss some of the recent developments using in vitro assays to dissect the role of the players involved: lipids in the membrane, proteins binding to membranes and proteins binding to membrane proteins. We also summarize advantages and disadvantages of supported lipid bilayers as model membrane.' author: - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Petra full_name: 'Schwille, Petra ' last_name: Schwille citation: ama: Loose M, Schwille P. Biomimetic membrane systems to study cellular organization. Journal of Structural Biology. 2009;168(1):143-151. doi:10.1016/j.jsb.2009.03.016 apa: Loose, M., & Schwille, P. (2009). Biomimetic membrane systems to study cellular organization. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2009.03.016 chicago: Loose, Martin, and Petra Schwille. “Biomimetic Membrane Systems to Study Cellular Organization.” Journal of Structural Biology. Academic Press, 2009. https://doi.org/10.1016/j.jsb.2009.03.016. ieee: M. Loose and P. Schwille, “Biomimetic membrane systems to study cellular organization,” Journal of Structural Biology, vol. 168, no. 1. Academic Press, pp. 143–151, 2009. ista: Loose M, Schwille P. 2009. Biomimetic membrane systems to study cellular organization. Journal of Structural Biology. 168(1), 143–151. mla: Loose, Martin, and Petra Schwille. “Biomimetic Membrane Systems to Study Cellular Organization.” Journal of Structural Biology, vol. 168, no. 1, Academic Press, 2009, pp. 143–51, doi:10.1016/j.jsb.2009.03.016. short: M. Loose, P. Schwille, Journal of Structural Biology 168 (2009) 143–151. date_created: 2018-12-11T11:55:03Z date_published: 2009-10-01T00:00:00Z date_updated: 2021-01-12T06:54:30Z day: '01' doi: 10.1016/j.jsb.2009.03.016 extern: 1 intvolume: ' 168' issue: '1' month: '10' page: 143 - 151 publication: Journal of Structural Biology publication_status: published publisher: Academic Press publist_id: '5099' quality_controlled: 0 status: public title: Biomimetic membrane systems to study cellular organization type: journal_article volume: 168 year: '2009' ... --- _id: '2067' acknowledgement: This work was funded by a Portuguese Foundation for Science and Technology scholarship to B.V., and B.C. was supported by the Royal Society author: - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth citation: ama: Vicoso B, Charlesworth B. Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster. Genetics. 2009;181(4):1699-1701. doi:10.1534/genetics.108.098004 apa: Vicoso, B., & Charlesworth, B. (2009). Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.108.098004 chicago: Vicoso, Beatriz, and Brian Charlesworth. “Recombination Rates May Affect the Ratio of X to Autosomal Noncoding Polymorphism in African Populations of Drosophila Melanogaster.” Genetics. Genetics Society of America, 2009. https://doi.org/10.1534/genetics.108.098004. ieee: B. Vicoso and B. Charlesworth, “Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster,” Genetics, vol. 181, no. 4. Genetics Society of America, pp. 1699–1701, 2009. ista: Vicoso B, Charlesworth B. 2009. Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster. Genetics. 181(4), 1699–1701. mla: Vicoso, Beatriz, and Brian Charlesworth. “Recombination Rates May Affect the Ratio of X to Autosomal Noncoding Polymorphism in African Populations of Drosophila Melanogaster.” Genetics, vol. 181, no. 4, Genetics Society of America, 2009, pp. 1699–701, doi:10.1534/genetics.108.098004. short: B. Vicoso, B. Charlesworth, Genetics 181 (2009) 1699–1701. date_created: 2018-12-11T11:55:31Z date_published: 2009-04-01T00:00:00Z date_updated: 2021-01-12T06:55:06Z day: '01' doi: 10.1534/genetics.108.098004 extern: 1 intvolume: ' 181' issue: '4' month: '04' page: 1699 - 1701 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '4971' quality_controlled: 0 status: public title: Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster type: journal_article volume: 181 year: '2009' ... --- _id: '2068' abstract: - lang: eng text: In Drosophila, there is a consistent deficit of male-biased genes on the X chromosome. It has been suggested that male-biased genes may evolve from initially unbiased genes as a result of increased expression levels in males. If transcription rates are limited, a large increase in expression in the testis may be harder to achieve for single-copy X-linked genes than for autosomal genes, because they are already hypertranscribed due to dosage compensation. This hypothesis predicts that the larger the increase in expression required to make a male-biased gene, the lower the chance of this being achievable if it is located on the X chromosome. Consequently, highly expressed male-biased genes should be located on the X chromosome less often than lowly expressed male-biased genes. This pattern is observed in our analysis of publicly available data, where microarray data or EST data are used to detect male-biased genes in D. melanogaster and to measure their expression levels. This is consistent with the idea that limitations in transcription rates may prevent male-biased genes from accumulating on the X chromosome. acknowledgement: This work was funded by a Portuguese Foundation for Science and Technology scholarship to B.V., and B.C. was supported by the Royal Society author: - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth citation: ama: 'Vicoso B, Charlesworth B. The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation? Journal of Molecular Evolution. 2009;68(5):576-583. doi:10.1007/s00239-009-9235-4' apa: 'Vicoso, B., & Charlesworth, B. (2009). The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation? Journal of Molecular Evolution. Springer. https://doi.org/10.1007/s00239-009-9235-4' chicago: 'Vicoso, Beatriz, and Brian Charlesworth. “The Deficit of Male-Biased Genes on the D. Melanogaster X Chromosome Is Expression-Dependent: A Consequence of Dosage Compensation?” Journal of Molecular Evolution. Springer, 2009. https://doi.org/10.1007/s00239-009-9235-4.' ieee: 'B. Vicoso and B. Charlesworth, “The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation?,” Journal of Molecular Evolution, vol. 68, no. 5. Springer, pp. 576–583, 2009.' ista: 'Vicoso B, Charlesworth B. 2009. The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation? Journal of Molecular Evolution. 68(5), 576–583.' mla: 'Vicoso, Beatriz, and Brian Charlesworth. “The Deficit of Male-Biased Genes on the D. Melanogaster X Chromosome Is Expression-Dependent: A Consequence of Dosage Compensation?” Journal of Molecular Evolution, vol. 68, no. 5, Springer, 2009, pp. 576–83, doi:10.1007/s00239-009-9235-4.' short: B. Vicoso, B. Charlesworth, Journal of Molecular Evolution 68 (2009) 576–583. date_created: 2018-12-11T11:55:31Z date_published: 2009-05-01T00:00:00Z date_updated: 2021-01-12T06:55:06Z day: '01' doi: 10.1007/s00239-009-9235-4 extern: 1 intvolume: ' 68' issue: '5' month: '05' page: 576 - 583 publication: Journal of Molecular Evolution publication_status: published publisher: Springer publist_id: '4970' quality_controlled: 0 status: public title: 'The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation?' type: journal_article volume: 68 year: '2009' ... --- _id: '2069' abstract: - lang: eng text: Current models of X-linked and autosomal evolutionary rates often assume that the effective population size of the X chromosome (NeX) is equal to three-quarters of the autosomal population size (NeA). However, polymorphism studies of Drosophila melanogaster and D. simulans suggest that there are often significant deviations from this value. We have computed fixation rates of beneficial and deleterious mutations at X-linked and autosomal sites when this occurs. We find that NeX/NeA is a crucial parameter for the rates of evolution of X-linked sites compared to autosomal sites. Faster-X evolution due to the fixation of beneficial mutations can occur under a much wider range of levels of dominance when NeX/N eA > 3/4. We also examined various parameters that are known to influence the rates of evolution at X-linked and autosomal sites, such as different mutation rates in males and females and mutations that are sexually antagonistic, to determine which cases can lead to faster-X evolution. We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution. acknowledgement: This work was funded by a Portuguese Foundation for Science and Technology scholarship to BV, and BC was supported by the Royal Society author: - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth citation: ama: 'Vicoso B, Charlesworth B. Effective population size and the faster-X effect: An extended model. Evolution. 2009;63(9):2413-2426. doi:10.1111/j.1558-5646.2009.00719.x' apa: 'Vicoso, B., & Charlesworth, B. (2009). Effective population size and the faster-X effect: An extended model. Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2009.00719.x' chicago: 'Vicoso, Beatriz, and Brian Charlesworth. “Effective Population Size and the Faster-X Effect: An Extended Model.” Evolution. Wiley-Blackwell, 2009. https://doi.org/10.1111/j.1558-5646.2009.00719.x.' ieee: 'B. Vicoso and B. Charlesworth, “Effective population size and the faster-X effect: An extended model,” Evolution, vol. 63, no. 9. Wiley-Blackwell, pp. 2413–2426, 2009.' ista: 'Vicoso B, Charlesworth B. 2009. Effective population size and the faster-X effect: An extended model. Evolution. 63(9), 2413–2426.' mla: 'Vicoso, Beatriz, and Brian Charlesworth. “Effective Population Size and the Faster-X Effect: An Extended Model.” Evolution, vol. 63, no. 9, Wiley-Blackwell, 2009, pp. 2413–26, doi:10.1111/j.1558-5646.2009.00719.x.' short: B. Vicoso, B. Charlesworth, Evolution 63 (2009) 2413–2426. date_created: 2018-12-11T11:55:32Z date_published: 2009-09-01T00:00:00Z date_updated: 2021-01-12T06:55:06Z day: '01' doi: 10.1111/j.1558-5646.2009.00719.x extern: 1 intvolume: ' 63' issue: '9' month: '09' page: 2413 - 2426 publication: Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '4968' quality_controlled: 0 status: public title: 'Effective population size and the faster-X effect: An extended model' type: journal_article volume: 63 year: '2009' ... --- _id: '2070' abstract: - lang: eng text: In many eukaryotic organisms, gender is determined by a pair of heteromorphic sex chromosomes. Degeneration of the non-recombining Y chromosome is a general facet of sex chromosome evolution. Selective pressure to restore expression levels of X-linked genes relative to autosomes accompanies Y-chromosome degeneration, thus driving the evolution of dosage compensation mechanisms. This review focuses on evolutionary aspects of dosage compensation, in light of recent advances in comparative and functional genomics that have substantially increased our understanding of the molecular mechanisms of dosage compensation and how it evolved. We review processes involved in sex chromosome evolution, and discuss the dynamic interaction between Y degeneration and the acquisition of dosage compensation. We compare mechanisms of dosage compensation and the origin of dosage compensation genes between different taxa and comment on sex chromosomes that apparently lack compensation mechanisms. Finally, we discuss how dosage compensation systems can also influence the evolution of well-established sex chromosomes. acknowledgement: This research is funded by NIH Grant GM076007 and a Sloan Research Fellowship and a David and Lucile Packard Fellowship to D.B. author: - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Doris full_name: Bachtrog, Doris last_name: Bachtrog citation: ama: Vicoso B, Bachtrog D. Progress and prospects toward our understanding of the evolution of dosage compensation. Chromosome Research. 2009;17(5):585-602. doi:10.1007/s10577-009-9053-y apa: Vicoso, B., & Bachtrog, D. (2009). Progress and prospects toward our understanding of the evolution of dosage compensation. Chromosome Research. Springer. https://doi.org/10.1007/s10577-009-9053-y chicago: Vicoso, Beatriz, and Doris Bachtrog. “Progress and Prospects toward Our Understanding of the Evolution of Dosage Compensation.” Chromosome Research. Springer, 2009. https://doi.org/10.1007/s10577-009-9053-y. ieee: B. Vicoso and D. Bachtrog, “Progress and prospects toward our understanding of the evolution of dosage compensation,” Chromosome Research, vol. 17, no. 5. Springer, pp. 585–602, 2009. ista: Vicoso B, Bachtrog D. 2009. Progress and prospects toward our understanding of the evolution of dosage compensation. Chromosome Research. 17(5), 585–602. mla: Vicoso, Beatriz, and Doris Bachtrog. “Progress and Prospects toward Our Understanding of the Evolution of Dosage Compensation.” Chromosome Research, vol. 17, no. 5, Springer, 2009, pp. 585–602, doi:10.1007/s10577-009-9053-y. short: B. Vicoso, D. Bachtrog, Chromosome Research 17 (2009) 585–602. date_created: 2018-12-11T11:55:32Z date_published: 2009-07-01T00:00:00Z date_updated: 2021-01-12T06:55:07Z day: '01' doi: 10.1007/s10577-009-9053-y extern: 1 intvolume: ' 17' issue: '5' month: '07' page: 585 - 602 publication: Chromosome Research publication_status: published publisher: Springer publist_id: '4969' quality_controlled: 0 status: public title: Progress and prospects toward our understanding of the evolution of dosage compensation type: journal_article volume: 17 year: '2009' ... --- _id: '2094' abstract: - lang: eng text: 'This paper introduces a data-driven representation and modeling technique for simulating non-linear heterogeneous soft tissue. It simplifies the construction of convincing deformable models by avoiding complex selection and tuning of physical material parameters, yet retaining the richness of non-linear heterogeneous behavior. We acquire a set of example deformations of a real object, and represent each of them as a spatially varying stress-strain relationship in a finite-element model. We then model the material by non-linear interpolation of these stress-strain relationships in strain-space. Our method relies on a simple-to-build capture system and an efficient run-time simulation algorithm based on incremental loading, making it suitable for interactive computer graphics applications. We present the results of our approach for several non-linear materials and biological soft tissue, with accurate agreement of our model to the measured data. ' acknowledgement: 'This research was supported by the NCCR Co-Me grant of the Swiss National Science Foundation. Moritz Bacher was partially supported by the Initiative in Innovative Computing (IIC) and the School of Engineering and Applied Sciences (SEAS) at Harvard. ' author: - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Moritz full_name: Bac̈her, Moritz last_name: Bac̈Her - first_name: Miguel full_name: Otaduy, Miguel A last_name: Otaduy - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: 'Bickel B, Bac̈Her M, Otaduy M, Matusik W, Pfister H, Groß M. Capture and modeling of non-linear heterogeneous soft tissue. In: Vol 28. ACM; 2009. doi:10.1145/1576246.1531395 ' apa: Bickel, B., Bac̈Her, M., Otaduy, M., Matusik, W., Pfister, H., & Groß, M. (2009). Capture and modeling of non-linear heterogeneous soft tissue (Vol. 28). Presented at the ACM SIGGRAPH, ACM. https://doi.org/10.1145/1576246.1531395 chicago: Bickel, Bernd, Moritz Bac̈Her, Miguel Otaduy, Wojciech Matusik, Hanspeter Pfister, and Markus Groß. “Capture and Modeling of Non-Linear Heterogeneous Soft Tissue,” Vol. 28. ACM, 2009. https://doi.org/10.1145/1576246.1531395 . ieee: B. Bickel, M. Bac̈Her, M. Otaduy, W. Matusik, H. Pfister, and M. Groß, “Capture and modeling of non-linear heterogeneous soft tissue,” presented at the ACM SIGGRAPH, 2009, vol. 28, no. 3. ista: Bickel B, Bac̈Her M, Otaduy M, Matusik W, Pfister H, Groß M. 2009. Capture and modeling of non-linear heterogeneous soft tissue. ACM SIGGRAPH vol. 28. mla: Bickel, Bernd, et al. Capture and Modeling of Non-Linear Heterogeneous Soft Tissue. Vol. 28, no. 3, ACM, 2009, doi:10.1145/1576246.1531395 . short: B. Bickel, M. Bac̈Her, M. Otaduy, W. Matusik, H. Pfister, M. Groß, in:, ACM, 2009. conference: name: ACM SIGGRAPH date_created: 2018-12-11T11:55:40Z date_published: 2009-07-27T00:00:00Z date_updated: 2019-04-26T07:22:08Z day: '27' doi: '10.1145/1576246.1531395 ' extern: 1 intvolume: ' 28' issue: '3' month: '07' publication_status: published publisher: ACM publist_id: '4940' quality_controlled: 0 status: public title: Capture and modeling of non-linear heterogeneous soft tissue type: conference volume: 28 year: '2009' ... --- _id: '2119' abstract: - lang: eng text: 'Let (E, H, μ) be an abstract Wiener space and let DV : = V D, where D denotes the Malliavin derivative and V is a closed and densely defined operator from H into another Hilbert space under(H, {combining low line}). Given a bounded operator B on under(H, {combining low line}), coercive on the range over(R (V), -), we consider the operators A : = V* B V in H and under(A, {combining low line}) : = V V* B in under(H, {combining low line}), as well as the realisations of the operators L : = DV* B DV and under(L, {combining low line}) : = DV DV* B in Lp (E, μ) and Lp (E, μ ; under(H, {combining low line})) respectively, where 1 < p < ∞. Our main result asserts that the following four assertions are equivalent: (1)D (sqrt(L)) = D (DV) with {norm of matrix} sqrt(L) f {norm of matrix}p {minus tilde} {norm of matrix} DV f {norm of matrix}p for f ∈ D (sqrt(L));(2)under(L, {combining low line}) admits a bounded H∞-functional calculus on over(R (DV), -);(3)D (sqrt(A)) = D (V) with {norm of matrix} sqrt(A) h {norm of matrix} {minus tilde} {norm of matrix} V h {norm of matrix} for h ∈ D (sqrt(A));(4)under(A, {combining low line}) admits a bounded H∞-functional calculus on over(R (V), -). Moreover, if these conditions are satisfied, then D (L) = D (DV2) ∩ D (DA). The equivalence (1)-(4) is a non-symmetric generalisation of the classical Meyer inequalities of Malliavin calculus (where under(H, {combining low line}) = H, V = I, B = frac(1, 2) I). A one-sided version of (1)-(4), giving Lp-boundedness of the Riesz transform DV / sqrt(L) in terms of a square function estimate, is also obtained. As an application let -A generate an analytic C0-contraction semigroup on a Hilbert space H and let -L be the Lp-realisation of the generator of its second quantisation. Our results imply that two-sided bounds for the Riesz transform of L are equivalent with the Kato square root property for A. The boundedness of the Riesz transform is used to obtain an Lp-domain characterisation for the operator L.' author: - first_name: Jan full_name: Jan Maas id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Jan full_name: van Neerven, Jan M last_name: Van Neerven citation: ama: Maas J, Van Neerven J. Boundedness of Riesz transforms for elliptic operators on abstract Wiener spaces. Journal of Functional Analysis. 2009;257(8):2410-2475. doi:10.1016/j.jfa.2009.07.001 apa: Maas, J., & Van Neerven, J. (2009). Boundedness of Riesz transforms for elliptic operators on abstract Wiener spaces. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2009.07.001 chicago: Maas, Jan, and Jan Van Neerven. “Boundedness of Riesz Transforms for Elliptic Operators on Abstract Wiener Spaces.” Journal of Functional Analysis. Academic Press, 2009. https://doi.org/10.1016/j.jfa.2009.07.001. ieee: J. Maas and J. Van Neerven, “Boundedness of Riesz transforms for elliptic operators on abstract Wiener spaces,” Journal of Functional Analysis, vol. 257, no. 8. Academic Press, pp. 2410–2475, 2009. ista: Maas J, Van Neerven J. 2009. Boundedness of Riesz transforms for elliptic operators on abstract Wiener spaces. Journal of Functional Analysis. 257(8), 2410–2475. mla: Maas, Jan, and Jan Van Neerven. “Boundedness of Riesz Transforms for Elliptic Operators on Abstract Wiener Spaces.” Journal of Functional Analysis, vol. 257, no. 8, Academic Press, 2009, pp. 2410–75, doi:10.1016/j.jfa.2009.07.001. short: J. Maas, J. Van Neerven, Journal of Functional Analysis 257 (2009) 2410–2475. date_created: 2018-12-11T11:55:49Z date_published: 2009-10-15T00:00:00Z date_updated: 2021-01-12T06:55:25Z day: '15' doi: 10.1016/j.jfa.2009.07.001 extern: 1 intvolume: ' 257' issue: '8' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0804.1432 month: '10' oa: 1 page: 2410 - 2475 publication: Journal of Functional Analysis publication_status: published publisher: Academic Press publist_id: '4913' quality_controlled: 0 status: public title: Boundedness of Riesz transforms for elliptic operators on abstract Wiener spaces type: journal_article volume: 257 year: '2009' ... --- _id: '2136' abstract: - lang: eng text: The local atomic structure of PbTiO3, BaTiO3, and KNbO3 perovskite-type crystals and K x Na1 − x NbO3 solid solutions in different phases is investigated using the angular dependence of the pre-edge structure of the Ti and Nb K X-ray absorption spectra and the EXAFS data. In noncubic phases, a considerable deviation of the local structure from the structure determined from diffraction data is observed only for the tetragonal phase of the BaTiO3 crystal. It is revealed that, in the cubic phase of niobates, the niobium atoms are characterized by significant displacements from the centrosymmetric positions along the threefold axes, so that they are close in the magnitude and the direction to the displacements in the low-temperatures rhombohedral phases. acknowledgement: This study was supported by the Russian Founda*tion for Basic Research (project no. 07*02*00796a). author: - first_name: Rostislav full_name: Vedrinskiǐ, Rostislav V last_name: Vedrinskiǐ - first_name: V. full_name: Kraǐzman, V. L last_name: Kraǐzman - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Elena full_name: Nazarenko, Elena S last_name: Nazarenko - first_name: Alexander full_name: Novakovich, Alexander A last_name: Novakovich - first_name: Larisa full_name: Reznichenko, Larisa A last_name: Reznichenko - first_name: Vladimir full_name: Fokin, Vladimir N last_name: Fokin - first_name: Victoria full_name: Shuvaeva, Victoria A last_name: Shuvaeva citation: ama: 'Vedrinskiǐ R, Kraǐzman V, Lemeshko M, et al. Local atomic structure of niobates and titanates from X-ray absorption spectroscopic data. In: Vol 51. Springer; 2009:1394-1398. doi:10.1134/S106378340907018X' apa: 'Vedrinskiǐ, R., Kraǐzman, V., Lemeshko, M., Nazarenko, E., Novakovich, A., Reznichenko, L., … Shuvaeva, V. (2009). Local atomic structure of niobates and titanates from X-ray absorption spectroscopic data (Vol. 51, pp. 1394–1398). Presented at the CoPoF: 18th All-Russia Conference on Physics of Ferroelectrics (VKS-XVIII), Springer. https://doi.org/10.1134/S106378340907018X' chicago: Vedrinskiǐ, Rostislav, V. Kraǐzman, Mikhail Lemeshko, Elena Nazarenko, Alexander Novakovich, Larisa Reznichenko, Vladimir Fokin, and Victoria Shuvaeva. “Local Atomic Structure of Niobates and Titanates from X-Ray Absorption Spectroscopic Data,” 51:1394–98. Springer, 2009. https://doi.org/10.1134/S106378340907018X. ieee: 'R. Vedrinskiǐ et al., “Local atomic structure of niobates and titanates from X-ray absorption spectroscopic data,” presented at the CoPoF: 18th All-Russia Conference on Physics of Ferroelectrics (VKS-XVIII), 2009, vol. 51, no. 7, pp. 1394–1398.' ista: 'Vedrinskiǐ R, Kraǐzman V, Lemeshko M, Nazarenko E, Novakovich A, Reznichenko L, Fokin V, Shuvaeva V. 2009. Local atomic structure of niobates and titanates from X-ray absorption spectroscopic data. CoPoF: 18th All-Russia Conference on Physics of Ferroelectrics (VKS-XVIII) vol. 51, 1394–1398.' mla: Vedrinskiǐ, Rostislav, et al. Local Atomic Structure of Niobates and Titanates from X-Ray Absorption Spectroscopic Data. Vol. 51, no. 7, Springer, 2009, pp. 1394–98, doi:10.1134/S106378340907018X. short: R. Vedrinskiǐ, V. Kraǐzman, M. Lemeshko, E. Nazarenko, A. Novakovich, L. Reznichenko, V. Fokin, V. Shuvaeva, in:, Springer, 2009, pp. 1394–1398. conference: name: 'CoPoF: 18th All-Russia Conference on Physics of Ferroelectrics (VKS-XVIII)' date_created: 2018-12-11T11:55:55Z date_published: 2009-07-12T00:00:00Z date_updated: 2021-01-12T06:55:31Z day: '12' doi: 10.1134/S106378340907018X extern: 1 intvolume: ' 51' issue: '7' month: '07' page: 1394 - 1398 publication_status: published publisher: Springer publist_id: '4898' quality_controlled: 0 status: public title: Local atomic structure of niobates and titanates from X-ray absorption spectroscopic data type: conference volume: 51 year: '2009' ... --- _id: '2137' abstract: - lang: eng text: Relying on the quantization rule of Raab and Friedrich [Phys. Rev. A (2009) in press], we derive simple and accurate formulae for the number of rotational states supported by a weakly bound vibrational level of a diatomic molecular ion. We also provide analytic estimates of the rotational constants of any such levels up to threshold for dissociation and obtain a criterion for determining whether a given weakly bound vibrational level is rotationless. The results depend solely on the long-range part of the molecular potential. author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Bretislav full_name: Frierich, Bretislav last_name: Frierich citation: ama: Lemeshko M, Frierich B. Rotational structure of weakly bound molecular ions. Journal of Atomic and Molecular Sciences. 2009;1(1):41-47. doi:10.4208/jams.101009.110209a apa: Lemeshko, M., & Frierich, B. (2009). Rotational structure of weakly bound molecular ions. Journal of Atomic and Molecular Sciences. Global Science Press. https://doi.org/10.4208/jams.101009.110209a chicago: Lemeshko, Mikhail, and Bretislav Frierich. “Rotational Structure of Weakly Bound Molecular Ions.” Journal of Atomic and Molecular Sciences. Global Science Press, 2009. https://doi.org/10.4208/jams.101009.110209a. ieee: M. Lemeshko and B. Frierich, “Rotational structure of weakly bound molecular ions,” Journal of Atomic and Molecular Sciences, vol. 1, no. 1. Global Science Press, pp. 41–47, 2009. ista: Lemeshko M, Frierich B. 2009. Rotational structure of weakly bound molecular ions. Journal of Atomic and Molecular Sciences. 1(1), 41–47. mla: Lemeshko, Mikhail, and Bretislav Frierich. “Rotational Structure of Weakly Bound Molecular Ions.” Journal of Atomic and Molecular Sciences, vol. 1, no. 1, Global Science Press, 2009, pp. 41–47, doi:10.4208/jams.101009.110209a. short: M. Lemeshko, B. Frierich, Journal of Atomic and Molecular Sciences 1 (2009) 41–47. date_created: 2018-12-11T11:55:55Z date_published: 2009-10-10T00:00:00Z date_updated: 2021-01-12T06:55:32Z day: '10' doi: 10.4208/jams.101009.110209a extern: 1 intvolume: ' 1' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0910.5743 month: '10' oa: 1 page: 41 - 47 publication: Journal of Atomic and Molecular Sciences publication_status: published publisher: Global Science Press publist_id: '4887' quality_controlled: 0 status: public title: Rotational structure of weakly bound molecular ions type: journal_article volume: 1 year: '2009' ... --- _id: '2149' abstract: - lang: eng text: We investigate the effects of a magnetic field on the dynamics of rotationally inelastic collisions of open-shell molecules (Σ2, Σ3, and Π2) with closed-shell atoms. Our treatment makes use of the Fraunhofer model of matter wave scattering and its recent extension to collisions in electric [M. Lemeshko and B. Friedrich, J. Chem. Phys. 129, 024301 (2008)] and radiative fields [M. Lemeshko and B. Friedrich, Int. J. Mass. Spec. 280, 19 (2009)]. A magnetic field aligns the molecule in the space-fixed frame and thereby alters the effective shape of the diffraction target. This significantly affects the differential and integral scattering cross sections. We exemplify our treatment by evaluating the magnetic-field-dependent scattering characteristics of the He-CaH (XΣ+2), He-O2 (XΣ–3), and He-OH (XΠΩ2) systems at thermal collision energies. Since the cross sections can be obtained for different orientations of the magnetic field with respect to the relative velocity vector, the model also offers predictions about the frontal-versus-lateral steric asymmetry of the collisions. The steric asymmetry is found to be almost negligible for the He-OH system, weak for the He-CaH collisions, and strong for the He-O2. While odd ΔM transitions dominate the He-OH [J=3/2,f→J′,e/f] integral cross sections in a magnetic field parallel to the relative velocity vector, even ΔM transitions prevail in the case of the He-CaH (X2Σ+) and He-O2 (XΣ−3) collision systems. For the latter system, the magnetic field opens inelastic channels that are closed in the absence of the field. These involve the transitions N=1,J=0→N′, J′ with J′=N′. author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Břetislav full_name: Friedrich, Břetislav last_name: Friedrich citation: ama: 'Lemeshko M, Friedrich B. Collisions of paramagnetic molecules in magnetic fields: An analytic model based on Fraunhofer diffraction of matter waves. Physical Review A - Atomic, Molecular, and Optical Physics. 2009;79(1). doi:10.1103/PhysRevA.79.012718' apa: 'Lemeshko, M., & Friedrich, B. (2009). Collisions of paramagnetic molecules in magnetic fields: An analytic model based on Fraunhofer diffraction of matter waves. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.79.012718' chicago: 'Lemeshko, Mikhail, and Břetislav Friedrich. “Collisions of Paramagnetic Molecules in Magnetic Fields: An Analytic Model Based on Fraunhofer Diffraction of Matter Waves.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2009. https://doi.org/10.1103/PhysRevA.79.012718.' ieee: 'M. Lemeshko and B. Friedrich, “Collisions of paramagnetic molecules in magnetic fields: An analytic model based on Fraunhofer diffraction of matter waves,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 79, no. 1. American Physical Society, 2009.' ista: 'Lemeshko M, Friedrich B. 2009. Collisions of paramagnetic molecules in magnetic fields: An analytic model based on Fraunhofer diffraction of matter waves. Physical Review A - Atomic, Molecular, and Optical Physics. 79(1).' mla: 'Lemeshko, Mikhail, and Břetislav Friedrich. “Collisions of Paramagnetic Molecules in Magnetic Fields: An Analytic Model Based on Fraunhofer Diffraction of Matter Waves.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 79, no. 1, American Physical Society, 2009, doi:10.1103/PhysRevA.79.012718.' short: M. Lemeshko, B. Friedrich, Physical Review A - Atomic, Molecular, and Optical Physics 79 (2009). date_created: 2018-12-11T11:55:59Z date_published: 2009-01-30T00:00:00Z date_updated: 2021-01-12T06:55:36Z day: '30' doi: 10.1103/PhysRevA.79.012718 extern: 1 intvolume: ' 79' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0809.3331 month: '01' oa: 1 publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '4875' quality_controlled: 0 status: public title: 'Collisions of paramagnetic molecules in magnetic fields: An analytic model based on Fraunhofer diffraction of matter waves' type: journal_article volume: 79 year: '2009' ... --- _id: '2150' abstract: - lang: eng text: We examine the effects of a linearly polarized nonresonant radiative field on the dynamics of rotationally inelastic Na+ + N2 collisions at eV collision energies. Our treatment is based on the Fraunhofer model of matter wave scattering and its recent extension to collisions in electric fields [M. Lemeshko, B. Friedrich, J. Chem. Phys. 129 (2008) 024301]. The nonresonant radiative field changes the effective shape of the target molecule by aligning it in the space-fixed frame. This markedly alters the differential and integral scattering cross-sections. As the cross-sections can be evaluated for a polarization of the radiative field collinear or perpendicular to the relative velocity vector, the model also offers predictions about steric asymmetry of the collisions. author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Břetislav full_name: Friedrich, Břetislav last_name: Friedrich citation: ama: Lemeshko M, Friedrich B. The effect of a nonresonant radiative field on low-energy rotationally inelastic Na+ + N2 collisions. International Journal of Mass Spectrometry. 2009;280(1-3):19-25. doi:10.1016/j.ijms.2008.06.010 apa: Lemeshko, M., & Friedrich, B. (2009). The effect of a nonresonant radiative field on low-energy rotationally inelastic Na+ + N2 collisions. International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2008.06.010 chicago: Lemeshko, Mikhail, and Břetislav Friedrich. “The Effect of a Nonresonant Radiative Field on Low-Energy Rotationally Inelastic Na+ + N2 Collisions.” International Journal of Mass Spectrometry. Elsevier, 2009. https://doi.org/10.1016/j.ijms.2008.06.010 . ieee: M. Lemeshko and B. Friedrich, “The effect of a nonresonant radiative field on low-energy rotationally inelastic Na+ + N2 collisions,” International Journal of Mass Spectrometry, vol. 280, no. 1–3. Elsevier, pp. 19–25, 2009. ista: Lemeshko M, Friedrich B. 2009. The effect of a nonresonant radiative field on low-energy rotationally inelastic Na+ + N2 collisions. International Journal of Mass Spectrometry. 280(1–3), 19–25. mla: Lemeshko, Mikhail, and Břetislav Friedrich. “The Effect of a Nonresonant Radiative Field on Low-Energy Rotationally Inelastic Na+ + N2 Collisions.” International Journal of Mass Spectrometry, vol. 280, no. 1–3, Elsevier, 2009, pp. 19–25, doi:10.1016/j.ijms.2008.06.010 . short: M. Lemeshko, B. Friedrich, International Journal of Mass Spectrometry 280 (2009) 19–25. date_created: 2018-12-11T11:56:00Z date_published: 2009-02-01T00:00:00Z date_updated: 2021-01-12T06:55:37Z day: '01' doi: '10.1016/j.ijms.2008.06.010 ' extern: 1 intvolume: ' 280' issue: 1-3 main_file_link: - open_access: '1' url: http://arxiv.org/abs/0804.4845 month: '02' oa: 1 page: 19 - 25 publication: International Journal of Mass Spectrometry publication_status: published publisher: Elsevier publist_id: '4874' quality_controlled: 0 status: public title: The effect of a nonresonant radiative field on low-energy rotationally inelastic Na+ + N2 collisions type: journal_article volume: 280 year: '2009' ... --- _id: '2192' abstract: - lang: eng text: We develop an analytic model of thermal state-to-state rotationally inelastic collisions of asymmetric-top molecules with closed-shell atoms in electric fields and apply it to the Ar-H2O collision system. The predicted cross sections as well as the steric asymmetry of the collisions show at fields up to 150 kV/cm characteristic field-dependent features which can be experimentally tested. Particularly suitable candidates for such tests are the 000 → 220 and 101→ 221 channels, arising from the relaxation of the field-free selection rules due to the hybridization of J states by the field. Averaging over the M' product channels is found to largely obliterate the orientation effects brought about by the field. author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Břetislav full_name: Friedrich, Břetislav last_name: Friedrich citation: ama: Lemeshko M, Friedrich B. Model analysis of rotationally inelastic Ar + H2O scattering in an electric field. Journal of Physical Chemistry A. 2009;113(52):15055-15063. doi:10.1021/jp9051598 apa: Lemeshko, M., & Friedrich, B. (2009). Model analysis of rotationally inelastic Ar + H2O scattering in an electric field. Journal of Physical Chemistry A. American Chemical Society. https://doi.org/10.1021/jp9051598 chicago: Lemeshko, Mikhail, and Břetislav Friedrich. “Model Analysis of Rotationally Inelastic Ar + H2O Scattering in an Electric Field.” Journal of Physical Chemistry A. American Chemical Society, 2009. https://doi.org/10.1021/jp9051598. ieee: M. Lemeshko and B. Friedrich, “Model analysis of rotationally inelastic Ar + H2O scattering in an electric field,” Journal of Physical Chemistry A, vol. 113, no. 52. American Chemical Society, pp. 15055–15063, 2009. ista: Lemeshko M, Friedrich B. 2009. Model analysis of rotationally inelastic Ar + H2O scattering in an electric field. Journal of Physical Chemistry A. 113(52), 15055–15063. mla: Lemeshko, Mikhail, and Břetislav Friedrich. “Model Analysis of Rotationally Inelastic Ar + H2O Scattering in an Electric Field.” Journal of Physical Chemistry A, vol. 113, no. 52, American Chemical Society, 2009, pp. 15055–63, doi:10.1021/jp9051598. short: M. Lemeshko, B. Friedrich, Journal of Physical Chemistry A 113 (2009) 15055–15063. date_created: 2018-12-11T11:56:14Z date_published: 2009-12-31T00:00:00Z date_updated: 2021-01-12T06:55:53Z day: '31' doi: 10.1021/jp9051598 extern: 1 intvolume: ' 113' issue: '52' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0906.0443 month: '12' oa: 1 page: 15055 - 15063 publication: Journal of Physical Chemistry A publication_status: published publisher: American Chemical Society publist_id: '4781' quality_controlled: 0 status: public title: Model analysis of rotationally inelastic Ar + H2O scattering in an electric field type: journal_article volume: 113 year: '2009' ... --- _id: '2191' abstract: - lang: eng text: 'By making use of the quantization rule of Raab and Friedrich [Phys. Rev. A 78, 022707 (2008)], we derive simple and accurate formulae for the number of rotational states supported by a weakly bound vibrational level of a diatomic molecule and the rotational constants of any such levels up to the threshold, and provide a criterion for determining whether a given weakly bound vibrational level is rotationless. The results depend solely on the long-range part of the molecular potential and are applicable to halo molecules. ' author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Břetislav full_name: Friedrich, Břetislav last_name: Friedrich citation: ama: Lemeshko M, Friedrich B. Rotational and rotationless states of weakly bound molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 2009;79(5). doi:10.1103/PhysRevA.79.050501 apa: Lemeshko, M., & Friedrich, B. (2009). Rotational and rotationless states of weakly bound molecules. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.79.050501 chicago: Lemeshko, Mikhail, and Břetislav Friedrich. “Rotational and Rotationless States of Weakly Bound Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2009. https://doi.org/10.1103/PhysRevA.79.050501. ieee: M. Lemeshko and B. Friedrich, “Rotational and rotationless states of weakly bound molecules,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 79, no. 5. American Physical Society, 2009. ista: Lemeshko M, Friedrich B. 2009. Rotational and rotationless states of weakly bound molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 79(5). mla: Lemeshko, Mikhail, and Břetislav Friedrich. “Rotational and Rotationless States of Weakly Bound Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 79, no. 5, American Physical Society, 2009, doi:10.1103/PhysRevA.79.050501. short: M. Lemeshko, B. Friedrich, Physical Review A - Atomic, Molecular, and Optical Physics 79 (2009). date_created: 2018-12-11T11:56:14Z date_published: 2009-05-26T00:00:00Z date_updated: 2021-01-12T06:55:53Z day: '26' doi: 10.1103/PhysRevA.79.050501 extern: 1 intvolume: ' 79' issue: '5' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0904.0567 month: '05' oa: 1 publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '4783' quality_controlled: 0 status: public title: Rotational and rotationless states of weakly bound molecules type: journal_article volume: 79 year: '2009' ... --- _id: '2193' abstract: - lang: eng text: We show that weakly bound molecules can be probed by "shaking" in a pulsed nonresonant laser field. The field introduces a centrifugal term which expels the highest vibrational level from the potential that binds it. Our numerical simulations applied to the Rb2 and KRb Feshbach molecules indicate that shaking by feasible laser pulses can be used to accurately recover the square of the vibrational wave function and, by inversion, also the long-range part of the molecular potential. author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Břetislav full_name: Friedrich, Břetislav last_name: Friedrich citation: ama: Lemeshko M, Friedrich B. Probing weakly bound molecules with nonresonant light. Physical Review Letters. 2009;103(5). doi:10.1103/PhysRevLett.103.053003 apa: Lemeshko, M., & Friedrich, B. (2009). Probing weakly bound molecules with nonresonant light. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.103.053003 chicago: Lemeshko, Mikhail, and Břetislav Friedrich. “Probing Weakly Bound Molecules with Nonresonant Light.” Physical Review Letters. American Physical Society, 2009. https://doi.org/10.1103/PhysRevLett.103.053003. ieee: M. Lemeshko and B. Friedrich, “Probing weakly bound molecules with nonresonant light,” Physical Review Letters, vol. 103, no. 5. American Physical Society, 2009. ista: Lemeshko M, Friedrich B. 2009. Probing weakly bound molecules with nonresonant light. Physical Review Letters. 103(5). mla: Lemeshko, Mikhail, and Břetislav Friedrich. “Probing Weakly Bound Molecules with Nonresonant Light.” Physical Review Letters, vol. 103, no. 5, American Physical Society, 2009, doi:10.1103/PhysRevLett.103.053003. short: M. Lemeshko, B. Friedrich, Physical Review Letters 103 (2009). date_created: 2018-12-11T11:56:15Z date_published: 2009-07-31T00:00:00Z date_updated: 2021-01-12T06:55:54Z day: '31' doi: 10.1103/PhysRevLett.103.053003 extern: 1 intvolume: ' 103' issue: '5' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0903.0811 month: '07' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '4782' quality_controlled: 0 status: public title: Probing weakly bound molecules with nonresonant light type: journal_article volume: 103 year: '2009' ... --- _id: '226' abstract: - lang: eng text: The Manin conjecture is established for a split singular del Pezzo surface of degree four, with singularity type A4. author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Ulrich full_name: Derenthal, Ulrich last_name: Derenthal citation: ama: Browning TD, Derenthal U. Manin’s conjecture for a quartic del Pezzo surface with A4 singularity. Annales de l’Institut Fourier. 2009;59(3):1231-1265. doi:10.5802/aif.2462 apa: Browning, T. D., & Derenthal, U. (2009). Manin’s conjecture for a quartic del Pezzo surface with A4 singularity. Annales de l’Institut Fourier. Association des Annales de l’Institut Fourier. https://doi.org/10.5802/aif.2462 chicago: Browning, Timothy D, and Ulrich Derenthal. “Manin’s Conjecture for a Quartic Del Pezzo Surface with A4 Singularity.” Annales de l’Institut Fourier. Association des Annales de l’Institut Fourier, 2009. https://doi.org/10.5802/aif.2462. ieee: T. D. Browning and U. Derenthal, “Manin’s conjecture for a quartic del Pezzo surface with A4 singularity,” Annales de l’Institut Fourier, vol. 59, no. 3. Association des Annales de l’Institut Fourier, pp. 1231–1265, 2009. ista: Browning TD, Derenthal U. 2009. Manin’s conjecture for a quartic del Pezzo surface with A4 singularity. Annales de l’Institut Fourier. 59(3), 1231–1265. mla: Browning, Timothy D., and Ulrich Derenthal. “Manin’s Conjecture for a Quartic Del Pezzo Surface with A4 Singularity.” Annales de l’Institut Fourier, vol. 59, no. 3, Association des Annales de l’Institut Fourier, 2009, pp. 1231–65, doi:10.5802/aif.2462. short: T.D. Browning, U. Derenthal, Annales de l’Institut Fourier 59 (2009) 1231–1265. date_created: 2018-12-11T11:45:18Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T06:56:21Z day: '01' doi: 10.5802/aif.2462 extern: 1 intvolume: ' 59' issue: '3' month: '01' page: 1231 - 1265 publication: Annales de l'Institut Fourier publication_status: published publisher: Association des Annales de l'Institut Fourier publist_id: '7686' quality_controlled: 0 status: public title: Manin's conjecture for a quartic del Pezzo surface with A4 singularity type: journal_article volume: 59 year: '2009' ... --- _id: '227' abstract: - lang: eng text: Winner of the Ferran Sunyer i Balaguer Prize 2009. First attempt to systematically survey the range of available tools from analytic number theory that can be applied to study the density of rational points on projective varieties. Designed to rapidly guide the reader to the many areas of ongoing research in the domain. Provides an extensive bibliography. alternative_title: - Progress in Mathematics article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: Browning TD. Quantitative Arithmetic of Projective Varieties. Vol 277. Birkhäuser Basel; 2009. doi:10.1007/978-3-0346-0129-0 apa: Browning, T. D. (2009). Quantitative Arithmetic of Projective Varieties (Vol. 277). Birkhäuser Basel. https://doi.org/10.1007/978-3-0346-0129-0 chicago: Browning, Timothy D. Quantitative Arithmetic of Projective Varieties. Vol. 277. Birkhäuser Basel, 2009. https://doi.org/10.1007/978-3-0346-0129-0. ieee: T. D. Browning, Quantitative Arithmetic of Projective Varieties, vol. 277. Birkhäuser Basel, 2009. ista: Browning TD. 2009. Quantitative Arithmetic of Projective Varieties, Birkhäuser Basel, XIII, 160p. mla: Browning, Timothy D. Quantitative Arithmetic of Projective Varieties. Vol. 277, Birkhäuser Basel, 2009, doi:10.1007/978-3-0346-0129-0. short: T.D. Browning, Quantitative Arithmetic of Projective Varieties, Birkhäuser Basel, 2009. date_created: 2018-12-11T11:45:19Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-12-21T10:56:12Z day: '01' doi: 10.1007/978-3-0346-0129-0 extern: '1' intvolume: ' 277' language: - iso: eng month: '01' oa_version: None page: XIII, 160 publication_identifier: eisbn: - 9-783-0346-0129-0 eissn: - 2296-505X isbn: - 9-783-0346-0128-3 issn: - 0743-1643 publication_status: published publisher: Birkhäuser Basel publist_id: '7682' quality_controlled: '1' scopus_import: '1' status: public title: Quantitative Arithmetic of Projective Varieties type: book user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 277 year: '2009' ... --- _id: '228' abstract: - lang: eng text: Let X be a projective non-singular quartic hypersurface of dimension 39 or more, which is defined over . We show that X() is non-empty provided that X() is non-empty and X has p-adic points for every prime p. acknowledgement: "EP/F060661/1\tEngineering and Physical Sciences Research Council" author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Roger full_name: Heath-Brown, Roger last_name: Heath Brown citation: ama: Browning TD, Heath Brown R. Rational points on quartic hypersurfaces. Journal fur die Reine und Angewandte Mathematik. 2009;(629):37-88. doi:10.1515/CRELLE.2009.026 apa: Browning, T. D., & Heath Brown, R. (2009). Rational points on quartic hypersurfaces. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/CRELLE.2009.026 chicago: Browning, Timothy D, and Roger Heath Brown. “Rational Points on Quartic Hypersurfaces.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, 2009. https://doi.org/10.1515/CRELLE.2009.026. ieee: T. D. Browning and R. Heath Brown, “Rational points on quartic hypersurfaces,” Journal fur die Reine und Angewandte Mathematik, no. 629. Walter de Gruyter, pp. 37–88, 2009. ista: Browning TD, Heath Brown R. 2009. Rational points on quartic hypersurfaces. Journal fur die Reine und Angewandte Mathematik. (629), 37–88. mla: Browning, Timothy D., and Roger Heath Brown. “Rational Points on Quartic Hypersurfaces.” Journal Fur Die Reine Und Angewandte Mathematik, no. 629, Walter de Gruyter, 2009, pp. 37–88, doi:10.1515/CRELLE.2009.026. short: T.D. Browning, R. Heath Brown, Journal Fur Die Reine Und Angewandte Mathematik (2009) 37–88. date_created: 2018-12-11T11:45:19Z date_published: 2009-04-01T00:00:00Z date_updated: 2021-01-12T06:56:29Z day: '01' doi: 10.1515/CRELLE.2009.026 extern: 1 issue: '629' main_file_link: - open_access: '1' url: https://arxiv.org/abs/math/0701348 month: '04' oa: 1 page: 37 - 88 publication: Journal fur die Reine und Angewandte Mathematik publication_status: published publisher: Walter de Gruyter publist_id: '7676' quality_controlled: 0 status: public title: Rational points on quartic hypersurfaces type: journal_article year: '2009' ... --- _id: '229' abstract: - lang: eng text: An upper bound of the expected order of magnitude is established for the number of ℚ-rational points of bounded height on Châtelet surfaces defined over ℚ. acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: Browning TD. Linear growth for Châtelet surfaces. Mathematische Annalen. 2009;346(1):41-50. doi:10.1007/s00208-009-0383-z apa: Browning, T. D. (2009). Linear growth for Châtelet surfaces. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-009-0383-z chicago: Browning, Timothy D. “Linear Growth for Châtelet Surfaces.” Mathematische Annalen. Springer Nature, 2009. https://doi.org/10.1007/s00208-009-0383-z. ieee: T. D. Browning, “Linear growth for Châtelet surfaces,” Mathematische Annalen, vol. 346, no. 1. Springer Nature, pp. 41–50, 2009. ista: Browning TD. 2009. Linear growth for Châtelet surfaces. Mathematische Annalen. 346(1), 41–50. mla: Browning, Timothy D. “Linear Growth for Châtelet Surfaces.” Mathematische Annalen, vol. 346, no. 1, Springer Nature, 2009, pp. 41–50, doi:10.1007/s00208-009-0383-z. short: T.D. Browning, Mathematische Annalen 346 (2009) 41–50. date_created: 2018-12-11T11:45:19Z date_published: 2009-06-18T00:00:00Z date_updated: 2021-01-12T06:56:33Z day: '18' doi: 10.1007/s00208-009-0383-z extern: 1 intvolume: ' 346' issue: '1' main_file_link: - open_access: '1' url: https://arxiv.org/abs/0901.1963 month: '06' oa: 1 page: 41 - 50 publication: Mathematische Annalen publication_status: published publisher: Springer Nature publist_id: '7675' quality_controlled: 0 status: public title: Linear growth for Châtelet surfaces type: journal_article volume: 346 year: '2009' ... --- _id: '230' abstract: - lang: eng text: The Manin conjecture is established for a split singular cubic surface in ℙ 3, with singularity type D 5. acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Ulrich full_name: Derenthal, Ulrich last_name: Derenthal citation: ama: Browning TD, Derenthal U. Manin’s conjecture for a cubic surface with  D 5 singularity. International Mathematics Research Notices. 2009;2009(14):2620-2647. doi:10.1093/imrn/rnp029 apa: Browning, T. D., & Derenthal, U. (2009). Manin’s conjecture for a cubic surface with  D 5 singularity. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnp029 chicago: Browning, Timothy D, and Ulrich Derenthal. “Manin’s Conjecture for a Cubic Surface with  D 5 Singularity.” International Mathematics Research Notices. Oxford University Press, 2009. https://doi.org/10.1093/imrn/rnp029. ieee: T. D. Browning and U. Derenthal, “Manin’s conjecture for a cubic surface with  D 5 singularity,” International Mathematics Research Notices, vol. 2009, no. 14. Oxford University Press, pp. 2620–2647, 2009. ista: Browning TD, Derenthal U. 2009. Manin’s conjecture for a cubic surface with  D 5 singularity. International Mathematics Research Notices. 2009(14), 2620–2647. mla: Browning, Timothy D., and Ulrich Derenthal. “Manin’s Conjecture for a Cubic Surface with  D 5 Singularity.” International Mathematics Research Notices, vol. 2009, no. 14, Oxford University Press, 2009, pp. 2620–47, doi:10.1093/imrn/rnp029. short: T.D. Browning, U. Derenthal, International Mathematics Research Notices 2009 (2009) 2620–2647. date_created: 2018-12-11T11:45:20Z date_published: 2009-03-09T00:00:00Z date_updated: 2021-01-12T06:56:38Z day: '09' doi: 10.1093/imrn/rnp029 extern: 1 intvolume: ' 2009' issue: '14' month: '03' page: 2620 - 2647 publication: International Mathematics Research Notices publication_status: published publisher: Oxford University Press publist_id: '7674' quality_controlled: 0 status: public title: Manin's conjecture for a cubic surface with D 5 singularity type: journal_article volume: 2009 year: '2009' ... --- _id: '2326' abstract: - lang: eng text: Research into the stability of matter has been one of the most successful chapters in mathematical physics, and is a prime example of how modern mathematics can be applied to problems in physics. A unique account of the subject, this book provides a complete, self-contained description of research on the stability of matter problem. It introduces the necessary quantum mechanics to mathematicians, and aspects of functional analysis to physicists. The topics covered include electrodynamics of classical and quantized fields, Lieb-Thirring and other inequalities in spectral theory, inequalities in electrostatics, stability of large Coulomb systems, gravitational stability of stars, basics of equilibrium statistical mechanics, and the existence of the thermodynamic limit. The book is an up-to-date account for researchers, and its pedagogical style makes it suitable for advanced undergraduate and graduate courses in mathematical physics. article_processing_charge: No author: - first_name: Élliott full_name: Lieb, Élliott last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Lieb É, Seiringer R. The Stability of Matter in Quantum Mechanics. Cambridge University Press; 2009. apa: Lieb, É., & Seiringer, R. (2009). The Stability of Matter in Quantum Mechanics. Cambridge University Press. chicago: Lieb, Élliott, and Robert Seiringer. The Stability of Matter in Quantum Mechanics. Cambridge University Press, 2009. ieee: É. Lieb and R. Seiringer, The Stability of Matter in Quantum Mechanics. Cambridge University Press, 2009. ista: Lieb É, Seiringer R. 2009. The Stability of Matter in Quantum Mechanics, Cambridge University Press, 310p. mla: Lieb, Élliott, and Robert Seiringer. The Stability of Matter in Quantum Mechanics. Cambridge University Press, 2009. short: É. Lieb, R. Seiringer, The Stability of Matter in Quantum Mechanics, Cambridge University Press, 2009. date_created: 2018-12-11T11:57:00Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-12-21T15:45:31Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: http://www.cambridge.org/9780521191180 month: '01' oa_version: None page: '310' publication_identifier: isbn: - '978-0-521-19118-0 ' publication_status: published publisher: Cambridge University Press publist_id: '4601' quality_controlled: '1' status: public title: The Stability of Matter in Quantum Mechanics type: book user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2009' ... --- _id: '2330' alternative_title: - Contemporary Mathematics author: - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Hainzl C, Seiringer R. A linear criterion for solutions of non-linear equations, with application to the BCS gap equation. In: Vol 500. American Mathematical Society; 2009:101-104. doi:10.1090/conm/500/09823' apa: Hainzl, C., & Seiringer, R. (2009). A linear criterion for solutions of non-linear equations, with application to the BCS gap equation (Vol. 500, pp. 101–104). Presented at the Spectral and Scattering Theory for Quantum Magnetic Systems, American Mathematical Society. https://doi.org/10.1090/conm/500/09823 chicago: Hainzl, Christian, and Robert Seiringer. “A Linear Criterion for Solutions of Non-Linear Equations, with Application to the BCS Gap Equation,” 500:101–4. American Mathematical Society, 2009. https://doi.org/10.1090/conm/500/09823. ieee: C. Hainzl and R. Seiringer, “A linear criterion for solutions of non-linear equations, with application to the BCS gap equation,” presented at the Spectral and Scattering Theory for Quantum Magnetic Systems, 2009, vol. 500, pp. 101–104. ista: Hainzl C, Seiringer R. 2009. A linear criterion for solutions of non-linear equations, with application to the BCS gap equation. Spectral and Scattering Theory for Quantum Magnetic Systems, Contemporary Mathematics, vol. 500, 101–104. mla: Hainzl, Christian, and Robert Seiringer. A Linear Criterion for Solutions of Non-Linear Equations, with Application to the BCS Gap Equation. Vol. 500, American Mathematical Society, 2009, pp. 101–04, doi:10.1090/conm/500/09823. short: C. Hainzl, R. Seiringer, in:, American Mathematical Society, 2009, pp. 101–104. conference: name: Spectral and Scattering Theory for Quantum Magnetic Systems date_created: 2018-12-11T11:57:02Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T06:56:50Z day: '01' doi: 10.1090/conm/500/09823 extern: 1 intvolume: ' 500' month: '01' page: 101 - 104 publication_status: published publisher: American Mathematical Society publist_id: '4596' quality_controlled: 0 status: public title: A linear criterion for solutions of non-linear equations, with application to the BCS gap equation type: conference volume: 500 year: '2009' ... --- _id: '2384' abstract: - lang: eng text: We prove the Lee-Huang-Yang formula for the ground state energy of the 3D Bose gas with repulsive interactions described by the exponential function, in a simultaneous limit of weak coupling and high density. In particular, we show that the Bogoliubov approximation is exact in an appropriate parameter regime, as far as the ground state energy is concerned. author: - first_name: Alessandro full_name: Giuliani, Alessandro last_name: Giuliani - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Giuliani A, Seiringer R. The ground state energy of the weakly interacting Bose gas at high density. Journal of Statistical Physics. 2009;135(5-6):915-934. doi:10.1007/s10955-009-9718-0 apa: Giuliani, A., & Seiringer, R. (2009). The ground state energy of the weakly interacting Bose gas at high density. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-009-9718-0 chicago: Giuliani, Alessandro, and Robert Seiringer. “The Ground State Energy of the Weakly Interacting Bose Gas at High Density.” Journal of Statistical Physics. Springer, 2009. https://doi.org/10.1007/s10955-009-9718-0. ieee: A. Giuliani and R. Seiringer, “The ground state energy of the weakly interacting Bose gas at high density,” Journal of Statistical Physics, vol. 135, no. 5–6. Springer, pp. 915–934, 2009. ista: Giuliani A, Seiringer R. 2009. The ground state energy of the weakly interacting Bose gas at high density. Journal of Statistical Physics. 135(5–6), 915–934. mla: Giuliani, Alessandro, and Robert Seiringer. “The Ground State Energy of the Weakly Interacting Bose Gas at High Density.” Journal of Statistical Physics, vol. 135, no. 5–6, Springer, 2009, pp. 915–34, doi:10.1007/s10955-009-9718-0. short: A. Giuliani, R. Seiringer, Journal of Statistical Physics 135 (2009) 915–934. date_created: 2018-12-11T11:57:21Z date_published: 2009-06-01T00:00:00Z date_updated: 2021-01-12T06:57:09Z day: '01' doi: 10.1007/s10955-009-9718-0 extern: 1 intvolume: ' 135' issue: 5-6 main_file_link: - open_access: '1' url: http://arxiv.org/abs/0811.1166 month: '06' oa: 1 page: 915 - 934 publication: Journal of Statistical Physics publication_status: published publisher: Springer publist_id: '4542' quality_controlled: 0 status: public title: The ground state energy of the weakly interacting Bose gas at high density type: journal_article volume: 135 year: '2009' ... --- _id: '2385' abstract: - lang: eng text: We consider an ultracold rotating Bose gas in a harmonic trap close to the critical angular velocity, so that the system can be considered to be confined to the lowest Landau level. With this assumption we prove that the Gross-Pitaevskii energy functional accurately describes the ground-state energy of the corresponding N -body Hamiltonian with contact interaction provided the total angular momentum L is much less than N2. While the Gross-Pitaevskii energy is always an obvious variational upper bound to the ground-state energy, a more refined analysis is needed to establish it as an exact lower bound. We also discuss the question of Bose-Einstein condensation in the parameter range considered. Coherent states together with inequalities in spaces of analytic functions are the main technical tools. author: - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason citation: ama: 'Lieb É, Seiringer R, Yngvason J. Yrast line of a rapidly rotating Bose gas: Gross-Pitaevskii regime. Physical Review A - Atomic, Molecular, and Optical Physics. 2009;79(6). doi:10.1103/PhysRevA.79.063626' apa: 'Lieb, É., Seiringer, R., & Yngvason, J. (2009). Yrast line of a rapidly rotating Bose gas: Gross-Pitaevskii regime. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.79.063626' chicago: 'Lieb, Élliott, Robert Seiringer, and Jakob Yngvason. “Yrast Line of a Rapidly Rotating Bose Gas: Gross-Pitaevskii Regime.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2009. https://doi.org/10.1103/PhysRevA.79.063626.' ieee: 'É. Lieb, R. Seiringer, and J. Yngvason, “Yrast line of a rapidly rotating Bose gas: Gross-Pitaevskii regime,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 79, no. 6. American Physical Society, 2009.' ista: 'Lieb É, Seiringer R, Yngvason J. 2009. Yrast line of a rapidly rotating Bose gas: Gross-Pitaevskii regime. Physical Review A - Atomic, Molecular, and Optical Physics. 79(6).' mla: 'Lieb, Élliott, et al. “Yrast Line of a Rapidly Rotating Bose Gas: Gross-Pitaevskii Regime.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 79, no. 6, American Physical Society, 2009, doi:10.1103/PhysRevA.79.063626.' short: É. Lieb, R. Seiringer, J. Yngvason, Physical Review A - Atomic, Molecular, and Optical Physics 79 (2009). date_created: 2018-12-11T11:57:22Z date_published: 2009-06-24T00:00:00Z date_updated: 2021-01-12T06:57:09Z day: '24' doi: 10.1103/PhysRevA.79.063626 extern: 1 intvolume: ' 79' issue: '6' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0904.1750 month: '06' oa: 1 publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '4541' quality_controlled: 0 status: public title: 'Yrast line of a rapidly rotating Bose gas: Gross-Pitaevskii regime' type: journal_article volume: 79 year: '2009' ... --- _id: '2386' abstract: - lang: eng text: We prove exponential decay of the off-diagonal correlation function in the two-dimensional homogeneous Bose gas when a2 ρ is small and the temperature T satisfies T> 4πρ ln | ln (a2 ρ) |. Here, a is the scattering length of the repulsive interaction potential and ρ is the density. To the leading order in a2 ρ, this bound agrees with the expected critical temperature for superfluidity. In the three-dimensional Bose gas, exponential decay is proved when T- Tc (0) Tc (0) >5 a ρ1/3, where Tc (0) is the critical temperature of the ideal gas. While this condition is not expected to be sharp, it gives a rigorous upper bound on the critical temperature for Bose-Einstein condensation. author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Daniel full_name: Ueltschi, Daniel last_name: Ueltschi citation: ama: Seiringer R, Ueltschi D. Rigorous upper bound on the critical temperature of dilute Bose gases. Physical Review B - Condensed Matter and Materials Physics. 2009;80(1). doi:10.1103/PhysRevB.80.014502 apa: Seiringer, R., & Ueltschi, D. (2009). Rigorous upper bound on the critical temperature of dilute Bose gases. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.80.014502 chicago: Seiringer, Robert, and Daniel Ueltschi. “Rigorous Upper Bound on the Critical Temperature of Dilute Bose Gases.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2009. https://doi.org/10.1103/PhysRevB.80.014502. ieee: R. Seiringer and D. Ueltschi, “Rigorous upper bound on the critical temperature of dilute Bose gases,” Physical Review B - Condensed Matter and Materials Physics, vol. 80, no. 1. American Physical Society, 2009. ista: Seiringer R, Ueltschi D. 2009. Rigorous upper bound on the critical temperature of dilute Bose gases. Physical Review B - Condensed Matter and Materials Physics. 80(1). mla: Seiringer, Robert, and Daniel Ueltschi. “Rigorous Upper Bound on the Critical Temperature of Dilute Bose Gases.” Physical Review B - Condensed Matter and Materials Physics, vol. 80, no. 1, American Physical Society, 2009, doi:10.1103/PhysRevB.80.014502. short: R. Seiringer, D. Ueltschi, Physical Review B - Condensed Matter and Materials Physics 80 (2009). date_created: 2018-12-11T11:57:22Z date_published: 2009-06-02T00:00:00Z date_updated: 2021-01-12T06:57:10Z day: '02' doi: 10.1103/PhysRevB.80.014502 extern: 1 intvolume: ' 80' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0904.0050 month: '06' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '4540' quality_controlled: 0 status: public title: Rigorous upper bound on the critical temperature of dilute Bose gases type: journal_article volume: 80 year: '2009' ... --- _id: '2387' abstract: - lang: eng text: We consider a system of trapped spinless bosons interacting with a repulsive potential and subject to rotation. In the limit of rapid rotation and small scattering length, we rigorously show that the ground state energy converges to that of a simplified model Hamiltonian with contact interaction projected onto the Lowest Landau Level. This effective Hamiltonian models the bosonic analogue of the Fractional Quantum Hall Effect (FQHE). For a fixed number of particles, we also prove convergence of states; in particular, in a certain regime we show convergence towards the bosonic Laughlin wavefunction. This is the first rigorous justification of the effective FQHE Hamiltonian for rapidly rotating Bose gases. We review previous results on this effective Hamiltonian and outline open problems. author: - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Lewin M, Seiringer R. Strongly correlated phases in rapidly rotating Bose gases. Journal of Statistical Physics. 2009;137(5):1040-1062. doi:10.1007/s10955-009-9833-y apa: Lewin, M., & Seiringer, R. (2009). Strongly correlated phases in rapidly rotating Bose gases. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-009-9833-y chicago: Lewin, Mathieu, and Robert Seiringer. “Strongly Correlated Phases in Rapidly Rotating Bose Gases.” Journal of Statistical Physics. Springer, 2009. https://doi.org/10.1007/s10955-009-9833-y. ieee: M. Lewin and R. Seiringer, “Strongly correlated phases in rapidly rotating Bose gases,” Journal of Statistical Physics, vol. 137, no. 5. Springer, pp. 1040–1062, 2009. ista: Lewin M, Seiringer R. 2009. Strongly correlated phases in rapidly rotating Bose gases. Journal of Statistical Physics. 137(5), 1040–1062. mla: Lewin, Mathieu, and Robert Seiringer. “Strongly Correlated Phases in Rapidly Rotating Bose Gases.” Journal of Statistical Physics, vol. 137, no. 5, Springer, 2009, pp. 1040–62, doi:10.1007/s10955-009-9833-y. short: M. Lewin, R. Seiringer, Journal of Statistical Physics 137 (2009) 1040–1062. date_created: 2018-12-11T11:57:22Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T06:57:10Z day: '01' doi: 10.1007/s10955-009-9833-y extern: 1 intvolume: ' 137' issue: '5' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0906.0741 month: '01' oa: 1 page: 1040 - 1062 publication: Journal of Statistical Physics publication_status: published publisher: Springer publist_id: '4538' quality_controlled: 0 status: public title: Strongly correlated phases in rapidly rotating Bose gases type: journal_article volume: 137 year: '2009' ... --- _id: '2388' abstract: - lang: eng text: This paper provides self-contained proof of a theorem relating probabilistic coherence of forecasts to their non-domination by rival forecasts with respect to any proper scoring rule. The theorem recapitulates insights achieved by other investigators, and clarifies the connection of coherence and proper scoring rules to Bregman divergence. author: - first_name: Joel full_name: Predd, Joel B last_name: Predd - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Daniel full_name: Osherson, Daniel N last_name: Osherson - first_name: Harold full_name: Poor, Harold V last_name: Poor - first_name: Sanjeev full_name: Kulkarni, Sanjeev R last_name: Kulkarni citation: ama: Predd J, Seiringer R, Lieb É, Osherson D, Poor H, Kulkarni S. Probabilistic coherence and proper scoring rules. IEEE Transactions on Information Theory. 2009;55(10):4786-4792. doi:10.1109/TIT.2009.2027573 apa: Predd, J., Seiringer, R., Lieb, É., Osherson, D., Poor, H., & Kulkarni, S. (2009). Probabilistic coherence and proper scoring rules. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2009.2027573 chicago: Predd, Joel, Robert Seiringer, Élliott Lieb, Daniel Osherson, Harold Poor, and Sanjeev Kulkarni. “Probabilistic Coherence and Proper Scoring Rules.” IEEE Transactions on Information Theory. IEEE, 2009. https://doi.org/10.1109/TIT.2009.2027573. ieee: J. Predd, R. Seiringer, É. Lieb, D. Osherson, H. Poor, and S. Kulkarni, “Probabilistic coherence and proper scoring rules,” IEEE Transactions on Information Theory, vol. 55, no. 10. IEEE, pp. 4786–4792, 2009. ista: Predd J, Seiringer R, Lieb É, Osherson D, Poor H, Kulkarni S. 2009. Probabilistic coherence and proper scoring rules. IEEE Transactions on Information Theory. 55(10), 4786–4792. mla: Predd, Joel, et al. “Probabilistic Coherence and Proper Scoring Rules.” IEEE Transactions on Information Theory, vol. 55, no. 10, IEEE, 2009, pp. 4786–92, doi:10.1109/TIT.2009.2027573. short: J. Predd, R. Seiringer, É. Lieb, D. Osherson, H. Poor, S. Kulkarni, IEEE Transactions on Information Theory 55 (2009) 4786–4792. date_created: 2018-12-11T11:57:23Z date_published: 2009-10-01T00:00:00Z date_updated: 2021-01-12T06:57:11Z day: '01' doi: 10.1109/TIT.2009.2027573 extern: 1 intvolume: ' 55' issue: '10' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0710.3183 month: '10' oa: 1 page: 4786 - 4792 publication: IEEE Transactions on Information Theory publication_status: published publisher: IEEE publist_id: '4539' quality_controlled: 0 status: public title: Probabilistic coherence and proper scoring rules type: journal_article volume: 55 year: '2009' ... --- _id: '2434' abstract: - lang: eng text: For a planar point set we consider the graph whose vertices are the crossing-free straight-line spanning trees of the point set, and two such spanning trees are adjacent if their union is crossing-free. An upper bound on the diameter of this graph implies an upper bound on the diameter of the flip graph of pseudo-triangulations of the underlying point set. We prove a lower bound of Ω(logn/loglogn) for the diameter of the transformation graph of spanning trees on a set of n points in the plane. This nearly matches the known upper bound of O(logn). If we measure the diameter in terms of the number of convex layers k of the point set, our lower bound construction is tight, i.e., the diameter is in Ω(logk) which matches the known upper bound of O(logk). So far only constant lower bounds were known. author: - first_name: Kevin full_name: Buchin, Kevin last_name: Buchin - first_name: Andreas full_name: Razen, Andreas last_name: Razen - first_name: Takeaki full_name: Uno, Takeaki last_name: Uno - first_name: Uli full_name: Uli Wagner id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Buchin K, Razen A, Uno T, Wagner U. Transforming spanning trees: A lower bound. Computational Geometry: Theory and Applications. 2009;42(8):724-730. doi:10.1016/j.comgeo.2008.03.005' apa: 'Buchin, K., Razen, A., Uno, T., & Wagner, U. (2009). Transforming spanning trees: A lower bound. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2008.03.005' chicago: 'Buchin, Kevin, Andreas Razen, Takeaki Uno, and Uli Wagner. “Transforming Spanning Trees: A Lower Bound.” Computational Geometry: Theory and Applications. Elsevier, 2009. https://doi.org/10.1016/j.comgeo.2008.03.005.' ieee: 'K. Buchin, A. Razen, T. Uno, and U. Wagner, “Transforming spanning trees: A lower bound,” Computational Geometry: Theory and Applications, vol. 42, no. 8. Elsevier, pp. 724–730, 2009.' ista: 'Buchin K, Razen A, Uno T, Wagner U. 2009. Transforming spanning trees: A lower bound. Computational Geometry: Theory and Applications. 42(8), 724–730.' mla: 'Buchin, Kevin, et al. “Transforming Spanning Trees: A Lower Bound.” Computational Geometry: Theory and Applications, vol. 42, no. 8, Elsevier, 2009, pp. 724–30, doi:10.1016/j.comgeo.2008.03.005.' short: 'K. Buchin, A. Razen, T. Uno, U. Wagner, Computational Geometry: Theory and Applications 42 (2009) 724–730.' date_created: 2018-12-11T11:57:38Z date_published: 2009-10-01T00:00:00Z date_updated: 2021-01-12T06:57:28Z day: '01' doi: 10.1016/j.comgeo.2008.03.005 extern: 1 intvolume: ' 42' issue: '8' month: '10' page: 724 - 730 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '4475' quality_controlled: 0 status: public title: 'Transforming spanning trees: A lower bound' type: journal_article volume: 42 year: '2009' ... --- _id: '2433' abstract: - lang: eng text: 'Let EMBEDk→d be the following algorithmic problem: Given a finite simplicial complex K of dimension at most k, does there exist a (piecewise linear) embedding of K into ℝd? Known results easily imply polynomiality of EMBEDk→2 (k = 1, 2; the case k = 1, d = 2 is graph planarity) and of EMBEDk→2k for all k ≥ 3 (even if k is not considered fixed). We show that the celebrated result of Novikov on the algorithmic unsolvability of recognizing the 5-sphere implies that EMBED d→d and EMBED(d-1)→d are undecidable for each d ≥ 5. Our main result is NP-hardness of EMBED2→4 and, more generally, of EMBEDk→d for all k, d with d ≥ 4 and d ≥ k ≥ (2d - 2)/3.' author: - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Martin full_name: Martin Tancer id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Uli Wagner id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Matoušek J, Tancer M, Wagner U. Hardness of embedding simplicial complexes in ℝd. In: SIAM; 2009:855-864.' apa: 'Matoušek, J., Tancer, M., & Wagner, U. (2009). Hardness of embedding simplicial complexes in ℝd (pp. 855–864). Presented at the SODA: Symposium on Discrete Algorithms, SIAM.' chicago: Matoušek, Jiří, Martin Tancer, and Uli Wagner. “Hardness of Embedding Simplicial Complexes in ℝd,” 855–64. SIAM, 2009. ieee: 'J. Matoušek, M. Tancer, and U. Wagner, “Hardness of embedding simplicial complexes in ℝd,” presented at the SODA: Symposium on Discrete Algorithms, 2009, pp. 855–864.' ista: 'Matoušek J, Tancer M, Wagner U. 2009. Hardness of embedding simplicial complexes in ℝd. SODA: Symposium on Discrete Algorithms, 855–864.' mla: Matoušek, Jiří, et al. Hardness of Embedding Simplicial Complexes in ℝd. SIAM, 2009, pp. 855–64. short: J. Matoušek, M. Tancer, U. Wagner, in:, SIAM, 2009, pp. 855–864. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T11:57:38Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T06:57:27Z day: '01' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/0807.0336 month: '01' oa: 1 page: 855 - 864 publication_status: published publisher: SIAM publist_id: '4476' quality_controlled: 0 status: public title: Hardness of embedding simplicial complexes in ℝd type: conference year: '2009' ... --- _id: '2498' abstract: - lang: eng text: Activation of G protein-gated inwardly-rectifying K+ (GIRK or Kir3) channels by metabotropic gamma-aminobutyric acid (B) (GABAB) receptors is an essential signalling pathway controlling neuronal excitability and synaptic transmission in the brain. To investigate the relationship between GIRK channel subunits and GABAB receptors in cerebellar Purkinje cells at post- and pre-synaptic sites, we used biochemical, functional and immunohistochemical techniques. Co-immunoprecipitation analysis demonstrated that GIRK subunits are co-assembled with GABAB receptors in the cerebellum. Immunoelectron microscopy showed that the subunit composition of GIRK channels in Purkinje cell spines is compartment-dependent. Thus, at extrasynaptic sites GIRK channels are formed by GIRK1/GIRK2/GIRK3, post-synaptic densities contain GIRK2/GIRK3 and dendritic shafts contain GIRK1/GIRK3. The post-synaptic association of GIRK subunits with GABAB receptors in Purkinje cells is supported by the subcellular regulation of the ion channel and the receptor in mutant mice. At pre-synaptic sites, GIRK channels localized to parallel fibre terminals are formed by GIRK1/GIRK2/GIRK3 and co-localize with GABAB receptors. Consistent with this morphological evidence we demonstrate their functional interaction at axon terminals in the cerebellum by showing that GIRK channels play a role in the inhibition of glutamate release by GABAB receptors. The association of GIRK channels and GABA B receptors with excitatory synapses at both post- and pre-synaptic sites indicates their intimate involvement in the modulation of glutamatergic neurotransmission in the cerebellum. author: - first_name: Laura full_name: Fernández-Alacid, Laura last_name: Fernández Alacid - first_name: Carolina full_name: Aguado, Carolina last_name: Aguado - first_name: Francisco full_name: Ciruela, Francisco last_name: Ciruela - first_name: Ricardo full_name: Martín, Ricardo J last_name: Martín - first_name: José full_name: Colón, José last_name: Colón - first_name: María full_name: Cabañero, María José last_name: Cabañero - first_name: Martin full_name: Gassmann, Martin last_name: Gassmann - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Kevin full_name: Wickman, Kevin D last_name: Wickman - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler - first_name: José full_name: Sánchez-Prieto, José last_name: Sánchez Prieto - first_name: Rafael full_name: Luján, Rafael last_name: Luján citation: ama: Fernández Alacid L, Aguado C, Ciruela F, et al. Subcellular compartment-specific molecular diversity of pre- and post-synaptic GABAB-activated GIRK channels in Purkinje cells. Journal of Neurochemistry. 2009;110(4):1363-1376. doi:10.1111/j.1471-4159.2009.06229.x apa: Fernández Alacid, L., Aguado, C., Ciruela, F., Martín, R., Colón, J., Cabañero, M., … Luján, R. (2009). Subcellular compartment-specific molecular diversity of pre- and post-synaptic GABAB-activated GIRK channels in Purkinje cells. Journal of Neurochemistry. Wiley-Blackwell. https://doi.org/10.1111/j.1471-4159.2009.06229.x chicago: Fernández Alacid, Laura, Carolina Aguado, Francisco Ciruela, Ricardo Martín, José Colón, María Cabañero, Martin Gassmann, et al. “ Subcellular Compartment-Specific Molecular Diversity of Pre- and Post-Synaptic GABAB-Activated GIRK Channels in Purkinje Cells.” Journal of Neurochemistry. Wiley-Blackwell, 2009. https://doi.org/10.1111/j.1471-4159.2009.06229.x. ieee: L. Fernández Alacid et al., “ Subcellular compartment-specific molecular diversity of pre- and post-synaptic GABAB-activated GIRK channels in Purkinje cells,” Journal of Neurochemistry, vol. 110, no. 4. Wiley-Blackwell, pp. 1363–1376, 2009. ista: Fernández Alacid L, Aguado C, Ciruela F, Martín R, Colón J, Cabañero M, Gassmann M, Watanabe M, Shigemoto R, Wickman K, Bettler B, Sánchez Prieto J, Luján R. 2009. Subcellular compartment-specific molecular diversity of pre- and post-synaptic GABAB-activated GIRK channels in Purkinje cells. Journal of Neurochemistry. 110(4), 1363–1376. mla: Fernández Alacid, Laura, et al. “ Subcellular Compartment-Specific Molecular Diversity of Pre- and Post-Synaptic GABAB-Activated GIRK Channels in Purkinje Cells.” Journal of Neurochemistry, vol. 110, no. 4, Wiley-Blackwell, 2009, pp. 1363–76, doi:10.1111/j.1471-4159.2009.06229.x. short: L. Fernández Alacid, C. Aguado, F. Ciruela, R. Martín, J. Colón, M. Cabañero, M. Gassmann, M. Watanabe, R. Shigemoto, K. Wickman, B. Bettler, J. Sánchez Prieto, R. Luján, Journal of Neurochemistry 110 (2009) 1363–1376. date_created: 2018-12-11T11:58:01Z date_published: 2009-08-01T00:00:00Z date_updated: 2021-01-12T06:57:50Z day: '01' doi: 10.1111/j.1471-4159.2009.06229.x extern: 1 intvolume: ' 110' issue: '4' month: '08' page: 1363 - 1376 publication: Journal of Neurochemistry publication_status: published publisher: Wiley-Blackwell publist_id: '4403' quality_controlled: 0 status: public title: ' Subcellular compartment-specific molecular diversity of pre- and post-synaptic GABAB-activated GIRK channels in Purkinje cells' type: journal_article volume: 110 year: '2009' ... --- _id: '2500' abstract: - lang: eng text: 'To examine the intrasynaptic arrangement of postsynaptic receptors in relation to the functional role of the synapse,we quantitatively analyzed the two-dimensional distribution of AMPA and NMDA receptors (AMPARs and NMDARs, respectively) using SDS-digested freeze-fracture replica labeling (SDS-FRL) and assessed the implication of distribution differences on the postsynaptic responses by simulation. In the dorsal lateral geniculate nucleus, corticogeniculate (CG) synapses were twice as large as retinogeniculate (RG) synapses but expressed similar numbers of AMPARs. Two-dimensional views of replicas revealed that AMPARs form microclusters in both synapses to a similar extent, resulting in larger AMPAR-lacking areas in the CG synapses. Despite the broad difference in the AMPAR distribution within a synapse, our simulations based on the actual receptor distributions suggested that the AMPAR quantal response at individual RG synapses is only slightly larger in amplitude, less variable, and faster in kinetics than that at CG synapses having a similar number of the receptors. NMDARs at the CG synapses were expressed twice as many as those in the RG synapses. Electrophysiological recordings confirmed a larger contribution of NMDAR relative to AMPAR-mediated responses in CG synapses. We conclude that synapse size and the density and distribution of receptors have minor influences on quantal responses and that the number of receptors acts as a predominant postsynaptic determinant of the synaptic strength mediated by both the AMPARs and NMDARs. ' author: - first_name: Etsuko full_name: Tarusawa, Etsuko last_name: Tarusawa - first_name: Ko full_name: Matsui, Ko last_name: Matsui - first_name: Timotheus full_name: Budisantoso, Timotheus last_name: Budisantoso - first_name: Elek full_name: Molnár, Elek last_name: Molnár - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Minoru full_name: Matsui, Minoru last_name: Matsui - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Tarusawa E, Matsui K, Budisantoso T, et al. Input-specific intrasynaptic arrangements of ionotropic glutamate receptors and their impact on postsynaptic responses. Journal of Neuroscience. 2009;29(41):12896-12908. doi:10.1523/JNEUROSCI.6160-08.2009 apa: Tarusawa, E., Matsui, K., Budisantoso, T., Molnár, E., Watanabe, M., Matsui, M., … Shigemoto, R. (2009). Input-specific intrasynaptic arrangements of ionotropic glutamate receptors and their impact on postsynaptic responses. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.6160-08.2009 chicago: Tarusawa, Etsuko, Ko Matsui, Timotheus Budisantoso, Elek Molnár, Masahiko Watanabe, Minoru Matsui, Yugo Fukazawa, and Ryuichi Shigemoto. “Input-Specific Intrasynaptic Arrangements of Ionotropic Glutamate Receptors and Their Impact on Postsynaptic Responses.” Journal of Neuroscience. Society for Neuroscience, 2009. https://doi.org/10.1523/JNEUROSCI.6160-08.2009. ieee: E. Tarusawa et al., “Input-specific intrasynaptic arrangements of ionotropic glutamate receptors and their impact on postsynaptic responses,” Journal of Neuroscience, vol. 29, no. 41. Society for Neuroscience, pp. 12896–12908, 2009. ista: Tarusawa E, Matsui K, Budisantoso T, Molnár E, Watanabe M, Matsui M, Fukazawa Y, Shigemoto R. 2009. Input-specific intrasynaptic arrangements of ionotropic glutamate receptors and their impact on postsynaptic responses. Journal of Neuroscience. 29(41), 12896–12908. mla: Tarusawa, Etsuko, et al. “Input-Specific Intrasynaptic Arrangements of Ionotropic Glutamate Receptors and Their Impact on Postsynaptic Responses.” Journal of Neuroscience, vol. 29, no. 41, Society for Neuroscience, 2009, pp. 12896–908, doi:10.1523/JNEUROSCI.6160-08.2009. short: E. Tarusawa, K. Matsui, T. Budisantoso, E. Molnár, M. Watanabe, M. Matsui, Y. Fukazawa, R. Shigemoto, Journal of Neuroscience 29 (2009) 12896–12908. date_created: 2018-12-11T11:58:02Z date_published: 2009-10-14T00:00:00Z date_updated: 2021-01-12T06:57:52Z day: '14' doi: 10.1523/JNEUROSCI.6160-08.2009 extern: 1 intvolume: ' 29' issue: '41' month: '10' page: 12896 - 12908 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4401' quality_controlled: 0 status: public title: Input-specific intrasynaptic arrangements of ionotropic glutamate receptors and their impact on postsynaptic responses type: journal_article volume: 29 year: '2009' ... --- _id: '2499' abstract: - lang: eng text: G protein-coupled receptors (GPCRs) have critical functions in intercellular communication. Although a wide range of different receptors have been identified in the same cells, the mechanism by which signals are integrated remains elusive. The ability of GPCRs to form dimers or larger hetero-oligomers is thought to generate such signal integration. We examined the molecular mechanisms responsible for the GABAB receptor-mediated potentiation of the mGlu receptor signalling reported in Purkinje neurons. We showed that this effect does not require a physical interaction between both receptors. Instead, it is the result of a more general mechanism in which the βγ subunits produced by the Gi-coupled GABAB receptor enhance the mGlu-mediated Gq response. Most importantly, this mechanism could be generally applied to other pairs of Gi- and Gq-coupled receptors and the signal integration varied depending on the time delay between activation of each receptor. Such a mechanism helps explain specific properties of cells expressing two different Gi- and Gq-coupled receptors activated by a single transmitter, or properties of GPCRs naturally coupled to both types of the G protein. author: - first_name: Marie full_name: Rives, Marie L last_name: Rives - first_name: Claire full_name: Vol, Claire last_name: Vol - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Norbert full_name: Tinel, Norbert last_name: Tinel - first_name: Eric full_name: Trinquet, Eric last_name: Trinquet - first_name: Mohammed full_name: Ayoub, Mohammed A last_name: Ayoub - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Jean full_name: Pin, Jean-Philippe last_name: Pin - first_name: Laurent full_name: Prezèau, Laurent last_name: Prezèau citation: ama: Rives M, Vol C, Fukazawa Y, et al. Crosstalk between GABAB and mGlu1a receptors reveals new insight into GPCR signal integration. EMBO Journal. 2009;28(15):2195-2208. doi:10.1038/emboj.2009.177 apa: Rives, M., Vol, C., Fukazawa, Y., Tinel, N., Trinquet, E., Ayoub, M., … Prezèau, L. (2009). Crosstalk between GABAB and mGlu1a receptors reveals new insight into GPCR signal integration. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2009.177 chicago: Rives, Marie, Claire Vol, Yugo Fukazawa, Norbert Tinel, Eric Trinquet, Mohammed Ayoub, Ryuichi Shigemoto, Jean Pin, and Laurent Prezèau. “Crosstalk between GABAB and MGlu1a Receptors Reveals New Insight into GPCR Signal Integration.” EMBO Journal. Wiley-Blackwell, 2009. https://doi.org/10.1038/emboj.2009.177. ieee: M. Rives et al., “Crosstalk between GABAB and mGlu1a receptors reveals new insight into GPCR signal integration,” EMBO Journal, vol. 28, no. 15. Wiley-Blackwell, pp. 2195–2208, 2009. ista: Rives M, Vol C, Fukazawa Y, Tinel N, Trinquet E, Ayoub M, Shigemoto R, Pin J, Prezèau L. 2009. Crosstalk between GABAB and mGlu1a receptors reveals new insight into GPCR signal integration. EMBO Journal. 28(15), 2195–2208. mla: Rives, Marie, et al. “Crosstalk between GABAB and MGlu1a Receptors Reveals New Insight into GPCR Signal Integration.” EMBO Journal, vol. 28, no. 15, Wiley-Blackwell, 2009, pp. 2195–208, doi:10.1038/emboj.2009.177. short: M. Rives, C. Vol, Y. Fukazawa, N. Tinel, E. Trinquet, M. Ayoub, R. Shigemoto, J. Pin, L. Prezèau, EMBO Journal 28 (2009) 2195–2208. date_created: 2018-12-11T11:58:01Z date_published: 2009-08-15T00:00:00Z date_updated: 2021-01-12T06:57:51Z day: '15' doi: 10.1038/emboj.2009.177 extern: 1 intvolume: ' 28' issue: '15' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726695/ month: '08' oa: 1 page: 2195 - 2208 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '4402' quality_controlled: 0 status: public title: Crosstalk between GABAB and mGlu1a receptors reveals new insight into GPCR signal integration type: journal_article volume: 28 year: '2009' ... --- _id: '2502' abstract: - lang: eng text: In order to acquire phase-contrast images with adequate contrast, conventional TEM requires large amount of defocus. Increasing the defocus improves the low-frequency components but attenuates the high-frequency ones. On the other hand, Zernike phase-contrast TEM (ZPC-TEM) can recover low-frequency components without losing the high-frequency ones under in-focus conditions. ZPC-TEM however, has another problem, especially in imaging of complex biological specimens such as cells and tissues; strong halos appear around specimen structures, and these halos hinder the interpretation of images. Due to this problem, the application of ZPC-TEM has been restricted to imaging of smaller particles. In order to improve the halo appearance, we fabricated a new quarter-wave thin film phase-plate with a smaller central hole and tested it on vitreous biological specimens. ZPC-TEM with the new plate could successfully visualize, in in-focus images, the intracellular fine features of cultured cells and brain tissues. This result indicates that reduction of the central hole diameter makes ZPC-TEM applicable on size scales ranging from protein particles to tissue sections. The application of ZPC-TEM to vitreous biological specimens will be a powerful method to advance the new field of imaging science for ultrastructures in close-to-physiological state. author: - first_name: Yoshiyuki full_name: Fukuda, Yoshiyuki last_name: Fukuda - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Radostin full_name: Danev, Radostin S last_name: Danev - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Kuniaki full_name: Nagayama, Kuniaki last_name: Nagayama citation: ama: Fukuda Y, Fukazawa Y, Danev R, Shigemoto R, Nagayama K. Tuning of the Zernike phase-plate for visualization of detailed ultrastructure in complex biological specimens. Journal of Structural Biology. 2009;168(3):476-484. doi:10.1016/j.jsb.2009.08.011 apa: Fukuda, Y., Fukazawa, Y., Danev, R., Shigemoto, R., & Nagayama, K. (2009). Tuning of the Zernike phase-plate for visualization of detailed ultrastructure in complex biological specimens. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2009.08.011 chicago: Fukuda, Yoshiyuki, Yugo Fukazawa, Radostin Danev, Ryuichi Shigemoto, and Kuniaki Nagayama. “Tuning of the Zernike Phase-Plate for Visualization of Detailed Ultrastructure in Complex Biological Specimens.” Journal of Structural Biology. Academic Press, 2009. https://doi.org/10.1016/j.jsb.2009.08.011. ieee: Y. Fukuda, Y. Fukazawa, R. Danev, R. Shigemoto, and K. Nagayama, “Tuning of the Zernike phase-plate for visualization of detailed ultrastructure in complex biological specimens,” Journal of Structural Biology, vol. 168, no. 3. Academic Press, pp. 476–484, 2009. ista: Fukuda Y, Fukazawa Y, Danev R, Shigemoto R, Nagayama K. 2009. Tuning of the Zernike phase-plate for visualization of detailed ultrastructure in complex biological specimens. Journal of Structural Biology. 168(3), 476–484. mla: Fukuda, Yoshiyuki, et al. “Tuning of the Zernike Phase-Plate for Visualization of Detailed Ultrastructure in Complex Biological Specimens.” Journal of Structural Biology, vol. 168, no. 3, Academic Press, 2009, pp. 476–84, doi:10.1016/j.jsb.2009.08.011. short: Y. Fukuda, Y. Fukazawa, R. Danev, R. Shigemoto, K. Nagayama, Journal of Structural Biology 168 (2009) 476–484. date_created: 2018-12-11T11:58:03Z date_published: 2009-12-01T00:00:00Z date_updated: 2021-01-12T06:57:52Z day: '01' doi: 10.1016/j.jsb.2009.08.011 extern: 1 intvolume: ' 168' issue: '3' month: '12' page: 476 - 484 publication: Journal of Structural Biology publication_status: published publisher: Academic Press publist_id: '4399' quality_controlled: 0 status: public title: Tuning of the Zernike phase-plate for visualization of detailed ultrastructure in complex biological specimens type: journal_article volume: 168 year: '2009' ... --- _id: '2501' abstract: - lang: eng text: The brain-specific immediate early gene Arc/Arg3.1 is induced in response to a variety of stimuli, including sensory and behavior-linked neural activity. Here we report the generation of transgenic mice, termed TgArc/Arg3.1-d4EGFP, expressing a 4-h half-life form of enhanced green fluorescent protein (d4EGFP) under the control of the Arc/Arg3.1 promoter. We show that d4EGFP-mediated fluorescence faithfully reports Arc/Arg3.1 induction in response to physiological, pathological and pharmacological stimuli, and that this fluorescence permits electrical recording from activated neurons in the live mouse. Moreover, the fluorescent Arc/Arg3.1 indicator revealed activity changes in circumscribed brain areas in distinct modes of stress and in a mouse model of Alzheimer's disease. These findings identify the TgArc/Arg3.1-d4EGFP mouse as a versatile tool to monitor Arc/Arg3.1 induction in neural circuits, both in vitro and in vivo. author: - first_name: Valery full_name: Grinevich, Valery V last_name: Grinevich - first_name: Alexander full_name: Kolleker, Alexander last_name: Kolleker - first_name: Marina full_name: Eliava, Marina I last_name: Eliava - first_name: Naoki full_name: Takada, Naoki last_name: Takada - first_name: Hiroshi full_name: Takuma, Hiroshi last_name: Takuma - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Dietmar full_name: Kuhl, Dietmar last_name: Kuhl - first_name: Jack full_name: Waters, Jack last_name: Waters - first_name: Peter full_name: Seeburg, Peter H last_name: Seeburg - first_name: Pavel full_name: Osten, Pavel last_name: Osten citation: ama: 'Grinevich V, Kolleker A, Eliava M, et al. Fluorescent Arc/Arg3.1 indicator mice: A versatile tool to study brain activity changes in vitro and in vivo. Journal of Neuroscience Methods. 2009;184(1):25-36. doi:10.1016/j.jneumeth.2009.07.015' apa: 'Grinevich, V., Kolleker, A., Eliava, M., Takada, N., Takuma, H., Fukazawa, Y., … Osten, P. (2009). Fluorescent Arc/Arg3.1 indicator mice: A versatile tool to study brain activity changes in vitro and in vivo. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2009.07.015' chicago: 'Grinevich, Valery, Alexander Kolleker, Marina Eliava, Naoki Takada, Hiroshi Takuma, Yugo Fukazawa, Ryuichi Shigemoto, et al. “Fluorescent Arc/Arg3.1 Indicator Mice: A Versatile Tool to Study Brain Activity Changes in Vitro and in Vivo.” Journal of Neuroscience Methods. Elsevier, 2009. https://doi.org/10.1016/j.jneumeth.2009.07.015.' ieee: 'V. Grinevich et al., “Fluorescent Arc/Arg3.1 indicator mice: A versatile tool to study brain activity changes in vitro and in vivo,” Journal of Neuroscience Methods, vol. 184, no. 1. Elsevier, pp. 25–36, 2009.' ista: 'Grinevich V, Kolleker A, Eliava M, Takada N, Takuma H, Fukazawa Y, Shigemoto R, Kuhl D, Waters J, Seeburg P, Osten P. 2009. Fluorescent Arc/Arg3.1 indicator mice: A versatile tool to study brain activity changes in vitro and in vivo. Journal of Neuroscience Methods. 184(1), 25–36.' mla: 'Grinevich, Valery, et al. “Fluorescent Arc/Arg3.1 Indicator Mice: A Versatile Tool to Study Brain Activity Changes in Vitro and in Vivo.” Journal of Neuroscience Methods, vol. 184, no. 1, Elsevier, 2009, pp. 25–36, doi:10.1016/j.jneumeth.2009.07.015.' short: V. Grinevich, A. Kolleker, M. Eliava, N. Takada, H. Takuma, Y. Fukazawa, R. Shigemoto, D. Kuhl, J. Waters, P. Seeburg, P. Osten, Journal of Neuroscience Methods 184 (2009) 25–36. date_created: 2018-12-11T11:58:02Z date_published: 2009-10-30T00:00:00Z date_updated: 2021-01-12T06:57:52Z day: '30' doi: 10.1016/j.jneumeth.2009.07.015 extern: 1 intvolume: ' 184' issue: '1' month: '10' page: 25 - 36 publication: Journal of Neuroscience Methods publication_status: published publisher: Elsevier publist_id: '4400' quality_controlled: 0 status: public title: 'Fluorescent Arc/Arg3.1 indicator mice: A versatile tool to study brain activity changes in vitro and in vivo' type: journal_article volume: 184 year: '2009' ... --- _id: '2684' abstract: - lang: eng text: Calcium-activated potassium channels have been shown to be critically involved in neuronal function, but an elucidation of their detailed roles awaits identification of the microdomains where they are located. This study was undertaken to unravel the precise subcellular distribution of the large-conductance calcium-activated potassium channels (called BK, KCa1.1, or Slo1) in the somatodendritic compartment of cerebellar Purkinje cells by means of postembedding immunogold cytochemistry and SDS-digested freeze-fracture replica labeling (SDS-FRL). We found BK channels to be unevenly distributed over the Purkinje cell plasma membrane. At distal dendritic compartments, BK channels were scattered over the plasma membrane of dendritic shafts and spines but absent from postsynaptic densities. At the soma and proximal dendrites, BK channels formed two distinct pools. One pool was scattered over the plasma membrane, whereas the other pool was clustered in plasma membrane domains overlying subsurface cisterns. The labeling density ratio of clustered to scattered channels was about 60:1, established in SDS-FRL. Subsurface cisterns, also called hypolemmal cisterns, are subcompartments of the endoplasmic reticulum likely representing calciosomes that unload and refill Ca2+ independently. Purkinje cell subsurface cisterns are enriched in inositol 1,4,5-triphosphate receptors that mediate the effects of several neurotransmitters, hormones, and growth factors by releasing Ca2+ into the cytosol, generating local Ca2+ sparks. Such increases in cytosolic [Ca2+] may be sufficient for BK channel activation. Clustered BK channels in the plasma membrane may thus participate in building a functional unit (plasmerosome) with the underlying calciosome that contributes significantly to local signaling in Purkinje cells. author: - first_name: Walter full_name: Walter Kaufmann id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Francesco full_name: Ferraguti, Francesco last_name: Ferraguti - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Yu full_name: Kasugai, Yu last_name: Kasugai - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Petter full_name: Laake, Petter last_name: Laake - first_name: Joseph full_name: Sexton, Joseph A last_name: Sexton - first_name: Peter full_name: Ruth, Peter last_name: Ruth - first_name: Georg full_name: Wietzorrek, Georg last_name: Wietzorrek - first_name: Hans full_name: Knaus, Hans G last_name: Knaus - first_name: Johan full_name: Storm, Johan F last_name: Storm - first_name: Ole full_name: Ottersen, Ole P last_name: Ottersen citation: ama: Kaufmann W, Ferraguti F, Fukazawa Y, et al. Large-conductance calcium-activated potassium channels in Purkinje cell plasma membranes are clustered at sites of hypolemmal microdomains. Journal of Comparative Neurology. 2009;515(2):215-230. doi:10.1002/cne.22066 apa: Kaufmann, W., Ferraguti, F., Fukazawa, Y., Kasugai, Y., Shigemoto, R., Laake, P., … Ottersen, O. (2009). Large-conductance calcium-activated potassium channels in Purkinje cell plasma membranes are clustered at sites of hypolemmal microdomains. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.22066 chicago: Kaufmann, Walter, Francesco Ferraguti, Yugo Fukazawa, Yu Kasugai, Ryuichi Shigemoto, Petter Laake, Joseph Sexton, et al. “Large-Conductance Calcium-Activated Potassium Channels in Purkinje Cell Plasma Membranes Are Clustered at Sites of Hypolemmal Microdomains.” Journal of Comparative Neurology. Wiley-Blackwell, 2009. https://doi.org/10.1002/cne.22066. ieee: W. Kaufmann et al., “Large-conductance calcium-activated potassium channels in Purkinje cell plasma membranes are clustered at sites of hypolemmal microdomains,” Journal of Comparative Neurology, vol. 515, no. 2. Wiley-Blackwell, pp. 215–230, 2009. ista: Kaufmann W, Ferraguti F, Fukazawa Y, Kasugai Y, Shigemoto R, Laake P, Sexton J, Ruth P, Wietzorrek G, Knaus H, Storm J, Ottersen O. 2009. Large-conductance calcium-activated potassium channels in Purkinje cell plasma membranes are clustered at sites of hypolemmal microdomains. Journal of Comparative Neurology. 515(2), 215–230. mla: Kaufmann, Walter, et al. “Large-Conductance Calcium-Activated Potassium Channels in Purkinje Cell Plasma Membranes Are Clustered at Sites of Hypolemmal Microdomains.” Journal of Comparative Neurology, vol. 515, no. 2, Wiley-Blackwell, 2009, pp. 215–30, doi:10.1002/cne.22066. short: W. Kaufmann, F. Ferraguti, Y. Fukazawa, Y. Kasugai, R. Shigemoto, P. Laake, J. Sexton, P. Ruth, G. Wietzorrek, H. Knaus, J. Storm, O. Ottersen, Journal of Comparative Neurology 515 (2009) 215–230. date_created: 2018-12-11T11:59:03Z date_published: 2009-07-10T00:00:00Z date_updated: 2023-02-23T10:53:41Z day: '10' doi: 10.1002/cne.22066 extern: 1 intvolume: ' 515' issue: '2' month: '07' page: 215 - 230 publication: Journal of Comparative Neurology publication_status: published publisher: Wiley-Blackwell publist_id: '4212' quality_controlled: 0 status: public title: Large-conductance calcium-activated potassium channels in Purkinje cell plasma membranes are clustered at sites of hypolemmal microdomains type: journal_article volume: 515 year: '2009' ... --- _id: '2680' abstract: - lang: eng text: 'GABA B receptor subtypes are based on the subunit isoforms GABA B1a and GABA B1b, which associate with GABA B2 subunits to form pharmacologically indistinguishable GABA B(1a,2) and GABA B(1b,2) receptors. Studies with mice selectively expressing GABA B1a or GABA B1b subunits revealed that GABA B(1a,2) receptors are more abundant than GABA B(1b,2) receptors at glutamatergic terminals. Accordingly, it was found that GABA B(1a,2) receptors are more efficient than GABA B(1b,2) receptors in inhibiting glutamate release when maximally activated by exogenous application of the agonist baclofen. Here, we used a combination of genetic, ultrastructural and electrophysiological approaches to analyze to what extent GABA B(1a,2) and GABA B(1b,2) receptors inhibit glutamate release in response to physiological activation. We first show that at hippocampal mossy fiber (MF)-CA3 pyramidal neuron synapses more GABA B1a than GABA B1b protein is present at presynaptic sites, consistent with the findings at other glutamatergic synapses. In the presence of baclofen at concentrations ≥1 μM, both GABA B(1a,2) and GABA B(1b,2) receptors contribute to presynaptic inhibition of glutamate release. However, at lower concentrations of baclofen, selectively GABA B(1a,2) receptors contribute to presynaptic inhibition. Remarkably, exclusively GABA B(1a,2) receptors inhibit glutamate release in response to synaptically released GABA. Specifically, we demonstrate that selectively GABA B(1a,2) receptors mediate heterosynaptic depression of MF transmission, a physiological phenomenon involving transsynaptic inhibition of glutamate release via presynaptic GABA B receptors. Our data demonstrate that the difference in GABA B1a and GABA B1b protein levels at MF terminals is sufficient to produce a strictly GABA B1a-specific effect under physiological conditions. This consolidates that the differential subcellular localization of the GABA B1a and GABA B1b proteins is of regulatory relevance. ' author: - first_name: Nicole full_name: Guetg, Nicole last_name: Guetg - first_name: Riad full_name: Seddik, Riad last_name: Seddik - first_name: Réjan full_name: Vigot, Réjan last_name: Vigot - first_name: Rostislav full_name: Tureček, Rostislav last_name: Tureček - first_name: Martin full_name: Gassmann, Martin last_name: Gassmann - first_name: Kaspar full_name: Vogt, Kaspar E last_name: Vogt - first_name: Hans full_name: Bräuner-Osborne, Hans last_name: Bräuner Osborne - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Oliver full_name: Kretz, Oliver last_name: Kretz - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Ákos full_name: Kulik, Ákos last_name: Kulik - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler citation: ama: Guetg N, Seddik R, Vigot R, et al. The GABA B1a isoform mediates heterosynaptic depression at hippocampal mossy fiber synapses. Journal of Neuroscience. 2009;29(5):1414-1423. doi:10.1523/JNEUROSCI.3697-08.2009 apa: Guetg, N., Seddik, R., Vigot, R., Tureček, R., Gassmann, M., Vogt, K., … Bettler, B. (2009). The GABA B1a isoform mediates heterosynaptic depression at hippocampal mossy fiber synapses. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.3697-08.2009 chicago: Guetg, Nicole, Riad Seddik, Réjan Vigot, Rostislav Tureček, Martin Gassmann, Kaspar Vogt, Hans Bräuner Osborne, et al. “The GABA B1a Isoform Mediates Heterosynaptic Depression at Hippocampal Mossy Fiber Synapses.” Journal of Neuroscience. Society for Neuroscience, 2009. https://doi.org/10.1523/JNEUROSCI.3697-08.2009. ieee: N. Guetg et al., “The GABA B1a isoform mediates heterosynaptic depression at hippocampal mossy fiber synapses,” Journal of Neuroscience, vol. 29, no. 5. Society for Neuroscience, pp. 1414–1423, 2009. ista: Guetg N, Seddik R, Vigot R, Tureček R, Gassmann M, Vogt K, Bräuner Osborne H, Shigemoto R, Kretz O, Frotscher M, Kulik Á, Bettler B. 2009. The GABA B1a isoform mediates heterosynaptic depression at hippocampal mossy fiber synapses. Journal of Neuroscience. 29(5), 1414–1423. mla: Guetg, Nicole, et al. “The GABA B1a Isoform Mediates Heterosynaptic Depression at Hippocampal Mossy Fiber Synapses.” Journal of Neuroscience, vol. 29, no. 5, Society for Neuroscience, 2009, pp. 1414–23, doi:10.1523/JNEUROSCI.3697-08.2009. short: N. Guetg, R. Seddik, R. Vigot, R. Tureček, M. Gassmann, K. Vogt, H. Bräuner Osborne, R. Shigemoto, O. Kretz, M. Frotscher, Á. Kulik, B. Bettler, Journal of Neuroscience 29 (2009) 1414–1423. date_created: 2018-12-11T11:59:02Z date_published: 2009-02-04T00:00:00Z date_updated: 2021-01-12T06:59:01Z day: '04' doi: 10.1523/JNEUROSCI.3697-08.2009 extern: 1 intvolume: ' 29' issue: '5' month: '02' page: 1414 - 1423 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4216' quality_controlled: 0 status: public title: The GABA B1a isoform mediates heterosynaptic depression at hippocampal mossy fiber synapses type: journal_article volume: 29 year: '2009' ... --- _id: '2683' abstract: - lang: eng text: GABAb receptor (GABAbR)-mediated suppression of glutamate release is critical for limiting glutamatergic transmission across the central nervous system (CNS). Here we show that, upon tetanic stimulation of afferents to lateral amygdala, presynaptic GABAbR-mediated inhibition only occurs in glutamatergic inputs to principle neurons (PNs), not to interneurons (INs), despite the presence of GABAbR in terminals to both types of neurons. The selectivity is caused by differential local GABA accumulation; it requires GABA reuptake and parallels distinct spatial distributions of presynaptic GABAbR in terminals to PNs and INs. Moreover, GABAbR-mediated suppression of theta-burst-induced long-term potentiation (LTP) occurs only in the inputs to PNs, not to INs. Thus, target-cell-specific control of glutamate release by presynaptic GABAbR orchestrates the inhibitory dominance inside amygdala and might contribute to prevention of nonadaptive defensive behaviors. author: - first_name: Bingxing full_name: Pan, Bingxing last_name: Pan - first_name: Yu full_name: Dong, Yu-Lin last_name: Dong - first_name: Wataru full_name: Ito, Wataru last_name: Ito - first_name: Yuchio full_name: Yanagawa, Yuchio last_name: Yanagawa - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Alexei full_name: Morozov, Alexei A last_name: Morozov citation: ama: Pan B, Dong Y, Ito W, Yanagawa Y, Shigemoto R, Morozov A. Selective gating of glutamatergic inputs to excitatory neurons of amygdala by presynaptic GABAb receptor. Neuron. 2009;61(6):917-929. doi:10.1016/j.neuron.2009.01.029 apa: Pan, B., Dong, Y., Ito, W., Yanagawa, Y., Shigemoto, R., & Morozov, A. (2009). Selective gating of glutamatergic inputs to excitatory neurons of amygdala by presynaptic GABAb receptor. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2009.01.029 chicago: Pan, Bingxing, Yu Dong, Wataru Ito, Yuchio Yanagawa, Ryuichi Shigemoto, and Alexei Morozov. “Selective Gating of Glutamatergic Inputs to Excitatory Neurons of Amygdala by Presynaptic GABAb Receptor.” Neuron. Elsevier, 2009. https://doi.org/10.1016/j.neuron.2009.01.029. ieee: B. Pan, Y. Dong, W. Ito, Y. Yanagawa, R. Shigemoto, and A. Morozov, “Selective gating of glutamatergic inputs to excitatory neurons of amygdala by presynaptic GABAb receptor,” Neuron, vol. 61, no. 6. Elsevier, pp. 917–929, 2009. ista: Pan B, Dong Y, Ito W, Yanagawa Y, Shigemoto R, Morozov A. 2009. Selective gating of glutamatergic inputs to excitatory neurons of amygdala by presynaptic GABAb receptor. Neuron. 61(6), 917–929. mla: Pan, Bingxing, et al. “Selective Gating of Glutamatergic Inputs to Excitatory Neurons of Amygdala by Presynaptic GABAb Receptor.” Neuron, vol. 61, no. 6, Elsevier, 2009, pp. 917–29, doi:10.1016/j.neuron.2009.01.029. short: B. Pan, Y. Dong, W. Ito, Y. Yanagawa, R. Shigemoto, A. Morozov, Neuron 61 (2009) 917–929. date_created: 2018-12-11T11:59:03Z date_published: 2009-03-26T00:00:00Z date_updated: 2021-01-12T06:59:02Z day: '26' doi: 10.1016/j.neuron.2009.01.029 extern: 1 intvolume: ' 61' issue: '6' month: '03' page: 917 - 929 publication: Neuron publication_status: published publisher: Elsevier publist_id: '4215' quality_controlled: 0 status: public title: Selective gating of glutamatergic inputs to excitatory neurons of amygdala by presynaptic GABAb receptor type: journal_article volume: 61 year: '2009' ... --- _id: '2682' abstract: - lang: eng text: The living cell imaging using a two-photon microscope using gold nanoplates and nanoparticle aggregates was demonstrated. The dimensions of the nanoplates were determined through scanning electron microscopy (SEM) and atomic force microscopy. The height of a 100 nm base-length nanotriangle was around 10 nm, while the height of 300 nm base-length nanotriangle was around 12 nm. A spectrophotometer was also used to determine the extinction spectra of gold nanoparticle colloids. Two-photon-induced photoluminescence (TPIPL) under far-field excitation was tested for gold nanoplates on a glass substrate using two-photon laser scanning microscopy (TPLSM). It was observed that living-cell microscopic imaging can be carried out with TPIPL from gold nanoplates and aggregated nanosphere. This method provided a platform for developing tools for biological and biomedical studies. author: - first_name: Yuqiang full_name: Jiang, Yuqiang last_name: Jiang - first_name: Noriko full_name: Horimoto, Noriko N last_name: Horimoto - first_name: Kohei full_name: Imura, Kohei last_name: Imura - first_name: Ko full_name: Matsui, Ko last_name: Matsui - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Jiang Y, Horimoto N, Imura K, Matsui K, Shigemoto R. Bioimaging with two-photon-induced luminescence from triangular nanoplates and nanoparticle aggregates of gold. Advanced Materials. 2009;21(22):2309-2313. doi:10.1002/adma.200802312 apa: Jiang, Y., Horimoto, N., Imura, K., Matsui, K., & Shigemoto, R. (2009). Bioimaging with two-photon-induced luminescence from triangular nanoplates and nanoparticle aggregates of gold. Advanced Materials. Wiley-Blackwell. https://doi.org/10.1002/adma.200802312 chicago: Jiang, Yuqiang, Noriko Horimoto, Kohei Imura, Ko Matsui, and Ryuichi Shigemoto. “Bioimaging with Two-Photon-Induced Luminescence from Triangular Nanoplates and Nanoparticle Aggregates of Gold.” Advanced Materials. Wiley-Blackwell, 2009. https://doi.org/10.1002/adma.200802312. ieee: Y. Jiang, N. Horimoto, K. Imura, K. Matsui, and R. Shigemoto, “Bioimaging with two-photon-induced luminescence from triangular nanoplates and nanoparticle aggregates of gold,” Advanced Materials, vol. 21, no. 22. Wiley-Blackwell, pp. 2309–2313, 2009. ista: Jiang Y, Horimoto N, Imura K, Matsui K, Shigemoto R. 2009. Bioimaging with two-photon-induced luminescence from triangular nanoplates and nanoparticle aggregates of gold. Advanced Materials. 21(22), 2309–2313. mla: Jiang, Yuqiang, et al. “Bioimaging with Two-Photon-Induced Luminescence from Triangular Nanoplates and Nanoparticle Aggregates of Gold.” Advanced Materials, vol. 21, no. 22, Wiley-Blackwell, 2009, pp. 2309–13, doi:10.1002/adma.200802312. short: Y. Jiang, N. Horimoto, K. Imura, K. Matsui, R. Shigemoto, Advanced Materials 21 (2009) 2309–2313. date_created: 2018-12-11T11:59:02Z date_published: 2009-06-12T00:00:00Z date_updated: 2021-01-12T06:59:01Z day: '12' doi: 10.1002/adma.200802312 extern: 1 intvolume: ' 21' issue: '22' month: '06' page: 2309 - 2313 publication: Advanced Materials publication_status: published publisher: Wiley-Blackwell publist_id: '4214' quality_controlled: 0 status: public title: Bioimaging with two-photon-induced luminescence from triangular nanoplates and nanoparticle aggregates of gold type: journal_article volume: 21 year: '2009' ... --- _id: '2685' abstract: - lang: eng text: Conduction velocity (CV) of myelinated axons has been shown to be regulated by oligodendrocytes even after myelination has been completed. However, how myelinating oligodendrocytes regulate CV, and what the significance of this regulation is for normal brain function remain unknown. To address these questions, we analyzed a transgenic mouse line harboring extra copies of the myelin proteolipid protein 1 (plp1) gene (plp1tg/- mice) at 2 months of age. At this stage, the plp1tg/- mice have an unaffected myelin structure with a normally appearing ion channel distribution, but the CV in all axonal tracts tested in the CNS is greatly reduced. We also found decreased axonal diameters and slightly abnormal paranodal structures, both of which can be a cause for the reduced CV. Interestingly the plp1tg/- mice showed altered anxiety-like behaviors, reduced prepulse inhibitions, spatial learning deficits and working memory deficit, all of which are schizophrenia-related behaviors. Our results implicate that abnormalities in the neuron-glia interactions at the paranodal junctions can result in reduced CV in the CNS, which then induces behavioral abnormalities related to schizophrenia. author: - first_name: Hisataka full_name: Tanaka, Hisataka last_name: Tanaka - first_name: Jianmei full_name: Ma, Jianmei last_name: Ma - first_name: Kenji full_name: Tanaka, Kenji F last_name: Tanaka - first_name: Keizo full_name: Takao, Keizo last_name: Takao - first_name: Munekazu full_name: Komada, Munekazu last_name: Komada - first_name: Koichi full_name: Tanda, Koichi last_name: Tanda - first_name: Ayaka full_name: Suzuki, Ayaka last_name: Suzuki - first_name: Tomoko full_name: Ishibashi, Tomoko last_name: Ishibashi - first_name: Hiroko full_name: Baba, Hiroko last_name: Baba - first_name: Tadashi full_name: Isa, Tadashi last_name: Isa - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Katsuhiko full_name: Ono, Katsuhiko last_name: Ono - first_name: Tsuyoshi full_name: Miyakawa, Tsuyoshi last_name: Miyakawa - first_name: Kazuhiro full_name: Ikenaka, Kazuhiro last_name: Ikenaka citation: ama: Tanaka H, Ma J, Tanaka K, et al. Mice with altered myelin proteolipid protein gene expression display cognitive deficits accompanied by abnormal neuron-glia interactions and decreased conduction velocities. Journal of Neuroscience. 2009;29(26):8363-8371. doi:10.1523/JNEUROSCI.3216-08.2009 apa: Tanaka, H., Ma, J., Tanaka, K., Takao, K., Komada, M., Tanda, K., … Ikenaka, K. (2009). Mice with altered myelin proteolipid protein gene expression display cognitive deficits accompanied by abnormal neuron-glia interactions and decreased conduction velocities. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.3216-08.2009 chicago: Tanaka, Hisataka, Jianmei Ma, Kenji Tanaka, Keizo Takao, Munekazu Komada, Koichi Tanda, Ayaka Suzuki, et al. “Mice with Altered Myelin Proteolipid Protein Gene Expression Display Cognitive Deficits Accompanied by Abnormal Neuron-Glia Interactions and Decreased Conduction Velocities.” Journal of Neuroscience. Society for Neuroscience, 2009. https://doi.org/10.1523/JNEUROSCI.3216-08.2009. ieee: H. Tanaka et al., “Mice with altered myelin proteolipid protein gene expression display cognitive deficits accompanied by abnormal neuron-glia interactions and decreased conduction velocities,” Journal of Neuroscience, vol. 29, no. 26. Society for Neuroscience, pp. 8363–8371, 2009. ista: Tanaka H, Ma J, Tanaka K, Takao K, Komada M, Tanda K, Suzuki A, Ishibashi T, Baba H, Isa T, Shigemoto R, Ono K, Miyakawa T, Ikenaka K. 2009. Mice with altered myelin proteolipid protein gene expression display cognitive deficits accompanied by abnormal neuron-glia interactions and decreased conduction velocities. Journal of Neuroscience. 29(26), 8363–8371. mla: Tanaka, Hisataka, et al. “Mice with Altered Myelin Proteolipid Protein Gene Expression Display Cognitive Deficits Accompanied by Abnormal Neuron-Glia Interactions and Decreased Conduction Velocities.” Journal of Neuroscience, vol. 29, no. 26, Society for Neuroscience, 2009, pp. 8363–71, doi:10.1523/JNEUROSCI.3216-08.2009. short: H. Tanaka, J. Ma, K. Tanaka, K. Takao, M. Komada, K. Tanda, A. Suzuki, T. Ishibashi, H. Baba, T. Isa, R. Shigemoto, K. Ono, T. Miyakawa, K. Ikenaka, Journal of Neuroscience 29 (2009) 8363–8371. date_created: 2018-12-11T11:59:03Z date_published: 2009-07-01T00:00:00Z date_updated: 2021-01-12T06:59:02Z day: '01' doi: 10.1523/JNEUROSCI.3216-08.2009 extern: 1 intvolume: ' 29' issue: '26' month: '07' page: 8363 - 8371 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4213' quality_controlled: 0 status: public title: Mice with altered myelin proteolipid protein gene expression display cognitive deficits accompanied by abnormal neuron-glia interactions and decreased conduction velocities type: journal_article volume: 29 year: '2009' ... --- _id: '2686' abstract: - lang: eng text: Channelrhodopsin-2 (ChR2), one of the archea-type rhodopsins from green algae, is a potentially useful optogenetic tool for restoring vision in patients with photoreceptor degeneration, such as retinitis pigmentosa. If the ChR2 gene is transferred to retinal ganglion cells (RGCs), which send visual information to the brain, the RGCs may be repurposed to act as photoreceptors. In this study, by using a transgenic rat expressing ChR2 specifically in the RGCs under the regulation of a Thy-1.2 promoter, we tested the possibility that direct photoactivation of RGCs could restore effective vision. Although the contrast sensitivities of the optomotor responses of transgenic rats were similar to those observed in the wild-type rats, they were enhanced for visual stimuli of low-spatial frequency after the degeneration of native photoreceptors. This result suggests that the visual signals derived from the ChR2-expressing RGCs were reinterpreted by the brain to form behavior-related vision. author: - first_name: Hiroshi full_name: Tomita, Hiroshi last_name: Tomita - first_name: Eriko full_name: Sugano, Eriko last_name: Sugano - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Hitomi full_name: Isago, Hitomi last_name: Isago - first_name: Yuka full_name: Sugiyama, Yuka last_name: Sugiyama - first_name: Teru full_name: Hiroi, Teru last_name: Hiroi - first_name: Toru full_name: Ishizuka, Toru last_name: Ishizuka - first_name: Hajime full_name: Mushiake, Hajime last_name: Mushiake - first_name: Megumi full_name: Kato, Megumi last_name: Kato - first_name: Masumi full_name: Hirabayashi, Masumi last_name: Hirabayashi - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Hiromu full_name: Yawo, Hiromu last_name: Yawo - first_name: Makoto full_name: Tamai, Makoto last_name: Tamai citation: ama: Tomita H, Sugano E, Fukazawa Y, et al. Visual properties of transgenic rats harboring the channelrhodopsin-2 gene regulated by the thy-1.2 promoter. PLoS One. 2009;4(11). doi:10.1371/journal.pone.0007679 apa: Tomita, H., Sugano, E., Fukazawa, Y., Isago, H., Sugiyama, Y., Hiroi, T., … Tamai, M. (2009). Visual properties of transgenic rats harboring the channelrhodopsin-2 gene regulated by the thy-1.2 promoter. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0007679 chicago: Tomita, Hiroshi, Eriko Sugano, Yugo Fukazawa, Hitomi Isago, Yuka Sugiyama, Teru Hiroi, Toru Ishizuka, et al. “Visual Properties of Transgenic Rats Harboring the Channelrhodopsin-2 Gene Regulated by the Thy-1.2 Promoter.” PLoS One. Public Library of Science, 2009. https://doi.org/10.1371/journal.pone.0007679. ieee: H. Tomita et al., “Visual properties of transgenic rats harboring the channelrhodopsin-2 gene regulated by the thy-1.2 promoter,” PLoS One, vol. 4, no. 11. Public Library of Science, 2009. ista: Tomita H, Sugano E, Fukazawa Y, Isago H, Sugiyama Y, Hiroi T, Ishizuka T, Mushiake H, Kato M, Hirabayashi M, Shigemoto R, Yawo H, Tamai M. 2009. Visual properties of transgenic rats harboring the channelrhodopsin-2 gene regulated by the thy-1.2 promoter. PLoS One. 4(11). mla: Tomita, Hiroshi, et al. “Visual Properties of Transgenic Rats Harboring the Channelrhodopsin-2 Gene Regulated by the Thy-1.2 Promoter.” PLoS One, vol. 4, no. 11, Public Library of Science, 2009, doi:10.1371/journal.pone.0007679. short: H. Tomita, E. Sugano, Y. Fukazawa, H. Isago, Y. Sugiyama, T. Hiroi, T. Ishizuka, H. Mushiake, M. Kato, M. Hirabayashi, R. Shigemoto, H. Yawo, M. Tamai, PLoS One 4 (2009). date_created: 2018-12-11T11:59:04Z date_published: 2009-11-05T00:00:00Z date_updated: 2021-01-12T06:59:03Z day: '05' doi: 10.1371/journal.pone.0007679 extern: 1 intvolume: ' 4' issue: '11' month: '11' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4211' quality_controlled: 0 status: public title: Visual properties of transgenic rats harboring the channelrhodopsin-2 gene regulated by the thy-1.2 promoter tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 4 year: '2009' ... --- _id: '2703' abstract: - lang: eng text: 'We consider N×N Hermitian random matrices with i.i.d. entries. The matrix is normalized so that the average spacing between consecutive eigenvalues is of order 1/N. We study the connection between eigenvalue statistics on microscopic energy scales η≪1 and (de)localization properties of the eigenvectors. Under suitable assumptions on the distribution of the single matrix elements, we first give an upper bound on the density of states on short energy scales of order η∼log N/N. We then prove that the density of states concentrates around the Wigner semicircle law on energy scales η≫N−2/3. We show that most eigenvectors are fully delocalized in the sense that their ℓp-norms are comparable with N1/p−1/2 for p≥2, and we obtain the weaker bound N2/3(1/p−1/2) for all eigenvectors whose eigenvalues are separated away from the spectral edges. We also prove that, with a probability very close to one, no eigenvector can be localized. Finally, we give an optimal bound on the second moment of the Green function. ' author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: Erdös L, Schlein B, Yau H. Semicircle law on short scales and delocalization of eigenvectors for Wigner random matrices. Annals of Probability. 2009;37(3):815-852. doi:10.1214/08-AOP421 apa: Erdös, L., Schlein, B., & Yau, H. (2009). Semicircle law on short scales and delocalization of eigenvectors for Wigner random matrices. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/08-AOP421 chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Semicircle Law on Short Scales and Delocalization of Eigenvectors for Wigner Random Matrices.” Annals of Probability. Institute of Mathematical Statistics, 2009. https://doi.org/10.1214/08-AOP421. ieee: L. Erdös, B. Schlein, and H. Yau, “Semicircle law on short scales and delocalization of eigenvectors for Wigner random matrices,” Annals of Probability, vol. 37, no. 3. Institute of Mathematical Statistics, pp. 815–852, 2009. ista: Erdös L, Schlein B, Yau H. 2009. Semicircle law on short scales and delocalization of eigenvectors for Wigner random matrices. Annals of Probability. 37(3), 815–852. mla: Erdös, László, et al. “Semicircle Law on Short Scales and Delocalization of Eigenvectors for Wigner Random Matrices.” Annals of Probability, vol. 37, no. 3, Institute of Mathematical Statistics, 2009, pp. 815–52, doi:10.1214/08-AOP421. short: L. Erdös, B. Schlein, H. Yau, Annals of Probability 37 (2009) 815–852. date_created: 2018-12-11T11:59:09Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T06:59:09Z day: '01' doi: 10.1214/08-AOP421 extern: 1 intvolume: ' 37' issue: '3' main_file_link: - open_access: '0' url: http://xxx.lanl.gov/abs/0711.1730 month: '01' page: 815 - 852 publication: Annals of Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '4193' quality_controlled: 0 status: public title: Semicircle law on short scales and delocalization of eigenvectors for Wigner random matrices type: journal_article volume: 37 year: '2009' ... --- _id: '2759' abstract: - lang: eng text: We consider the evolution of N bosons interacting with a repulsive short range pair potential in three dimensions. The potential is scaled according to the Gross-Pitaevskii scaling, i.e. it is given by N 2 V(N(x i - x j )). We monitor the behaviour of the solution to the N-particle Schrödinger equation in a spatial window where two particles are close to each other. We prove that within this window a short-scale interparticle structure emerges dynamically. The local correlation between the particles is given by the two-body zero energy scattering mode. This is the characteristic structure that was expected to form within a very short initial time layer and to persist for all later times, on the basis of the validity of the Gross-Pitaevskii equation for the evolution of the Bose-Einstein condensate. The zero energy scattering mode emerges after an initial time layer where all higher energy modes disperse out of the spatial window. We can prove the persistence of this structure up to sufficiently small times before three-particle correlations could develop. author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Alessandro full_name: Michelangeli, Alessandro last_name: Michelangeli - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein citation: ama: Erdös L, Michelangeli A, Schlein B. Dynamical formation of correlations in a Bose-Einstein condensate. Communications in Mathematical Physics. 2009;289(3):1171-1210. doi:10.1007/s00220-009-0828-y apa: Erdös, L., Michelangeli, A., & Schlein, B. (2009). Dynamical formation of correlations in a Bose-Einstein condensate. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-009-0828-y chicago: Erdös, László, Alessandro Michelangeli, and Benjamin Schlein. “Dynamical Formation of Correlations in a Bose-Einstein Condensate.” Communications in Mathematical Physics. Springer, 2009. https://doi.org/10.1007/s00220-009-0828-y. ieee: L. Erdös, A. Michelangeli, and B. Schlein, “Dynamical formation of correlations in a Bose-Einstein condensate,” Communications in Mathematical Physics, vol. 289, no. 3. Springer, pp. 1171–1210, 2009. ista: Erdös L, Michelangeli A, Schlein B. 2009. Dynamical formation of correlations in a Bose-Einstein condensate. Communications in Mathematical Physics. 289(3), 1171–1210. mla: Erdös, László, et al. “Dynamical Formation of Correlations in a Bose-Einstein Condensate.” Communications in Mathematical Physics, vol. 289, no. 3, Springer, 2009, pp. 1171–210, doi:10.1007/s00220-009-0828-y. short: L. Erdös, A. Michelangeli, B. Schlein, Communications in Mathematical Physics 289 (2009) 1171–1210. date_created: 2018-12-11T11:59:27Z date_published: 2009-08-01T00:00:00Z date_updated: 2021-01-12T06:59:30Z day: '01' doi: 10.1007/s00220-009-0828-y extern: 1 intvolume: ' 289' issue: '3' month: '08' page: 1171 - 1210 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4133' quality_controlled: 0 status: public title: Dynamical formation of correlations in a Bose-Einstein condensate type: journal_article volume: 289 year: '2009' ... --- _id: '2758' abstract: - lang: eng text: We consider N × N Hermitian random matrices with independent identical distributed entries. The matrix is normalized so that the average spacing between consecutive eigenvalues is of order 1/N. Under suitable assumptions on the distribution of the single matrix element, we prove that, away from the spectral edges, the density of eigenvalues concentrates around the Wigner semicircle law on energy scales n ≫ N -1 (log N) 8 . Up to the logarithmic factor, this is the smallest energy scale for which the semicircle law may be valid. We also prove that for all eigenvalues away from the spectral edges, the -tempℓ∞-norm of the corresponding eigenvectors is of order O(N -1/2), modulo logarithmic corrections. The upper bound O(N -1/2) implies that every eigenvector is completely delocalized, i.e., the maximum size of the components of the eigenvector is of the same order as their average size. In the Appendix, we include a lemma by J. Bourgain which removes one of our assumptions on the distribution of the matrix elements. author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: Erdös L, Schlein B, Yau H. Local semicircle law and complete delocalization for Wigner random matrices. Communications in Mathematical Physics. 2009;287(2):641-655. doi:10.1007/s00220-008-0636-9 apa: Erdös, L., Schlein, B., & Yau, H. (2009). Local semicircle law and complete delocalization for Wigner random matrices. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-008-0636-9 chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Local Semicircle Law and Complete Delocalization for Wigner Random Matrices.” Communications in Mathematical Physics. Springer, 2009. https://doi.org/10.1007/s00220-008-0636-9. ieee: L. Erdös, B. Schlein, and H. Yau, “Local semicircle law and complete delocalization for Wigner random matrices,” Communications in Mathematical Physics, vol. 287, no. 2. Springer, pp. 641–655, 2009. ista: Erdös L, Schlein B, Yau H. 2009. Local semicircle law and complete delocalization for Wigner random matrices. Communications in Mathematical Physics. 287(2), 641–655. mla: Erdös, László, et al. “Local Semicircle Law and Complete Delocalization for Wigner Random Matrices.” Communications in Mathematical Physics, vol. 287, no. 2, Springer, 2009, pp. 641–55, doi:10.1007/s00220-008-0636-9. short: L. Erdös, B. Schlein, H. Yau, Communications in Mathematical Physics 287 (2009) 641–655. date_created: 2018-12-11T11:59:27Z date_published: 2009-04-01T00:00:00Z date_updated: 2021-01-12T06:59:30Z day: '01' doi: 10.1007/s00220-008-0636-9 extern: 1 intvolume: ' 287' issue: '2' month: '04' page: 641 - 655 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4134' quality_controlled: 0 status: public title: Local semicircle law and complete delocalization for Wigner random matrices type: journal_article volume: 287 year: '2009' ... --- _id: '2757' abstract: - lang: eng text: We propose a new approach for the study of the time evolution of a factorized N-particle bosonic wave function with respect to a mean-field dynamics with a bounded interaction potential. The new technique, which is based on the control of the growth of the correlations among the particles, leads to quantitative bounds on the difference between the many-particle Schrödinger dynamics and the one-particle nonlinear Hartree dynamics. In particular the one-particle density matrix associated with the solution to the N-particle Schrödinger equation is shown to converge to the projection onto the one-dimensional sub-space spanned by the solution to the Hartree equation with a speed of convergence of order 1/N for all fixed times. author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein citation: ama: 'Erdös L, Schlein B. Quantum dynamics with mean field interactions: A new approach. Journal of Statistical Physics. 2009;134(5-6):859-870. doi:10.1007/s10955-008-9570-7' apa: 'Erdös, L., & Schlein, B. (2009). Quantum dynamics with mean field interactions: A new approach. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-008-9570-7' chicago: 'Erdös, László, and Benjamin Schlein. “Quantum Dynamics with Mean Field Interactions: A New Approach.” Journal of Statistical Physics. Springer, 2009. https://doi.org/10.1007/s10955-008-9570-7.' ieee: 'L. Erdös and B. Schlein, “Quantum dynamics with mean field interactions: A new approach,” Journal of Statistical Physics, vol. 134, no. 5–6. Springer, pp. 859–870, 2009.' ista: 'Erdös L, Schlein B. 2009. Quantum dynamics with mean field interactions: A new approach. Journal of Statistical Physics. 134(5–6), 859–870.' mla: 'Erdös, László, and Benjamin Schlein. “Quantum Dynamics with Mean Field Interactions: A New Approach.” Journal of Statistical Physics, vol. 134, no. 5–6, Springer, 2009, pp. 859–70, doi:10.1007/s10955-008-9570-7.' short: L. Erdös, B. Schlein, Journal of Statistical Physics 134 (2009) 859–870. date_created: 2018-12-11T11:59:26Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T06:59:30Z day: '01' doi: 10.1007/s10955-008-9570-7 extern: 1 intvolume: ' 134' issue: 5-6 month: '01' page: 859 - 870 publication: Journal of Statistical Physics publication_status: published publisher: Springer publist_id: '4135' quality_controlled: 0 status: public title: 'Quantum dynamics with mean field interactions: A new approach' type: journal_article volume: 134 year: '2009' ... --- _id: '2760' author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: Erdös L, Schlein B, Yau H. Rigorous derivation of the gross-pitaevskii equation with a large interaction potential. Journal of the American Mathematical Society. 2009;22(4):1099-1156. doi:10.1090/S0894-0347-09-00635-3 apa: Erdös, L., Schlein, B., & Yau, H. (2009). Rigorous derivation of the gross-pitaevskii equation with a large interaction potential. Journal of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0894-0347-09-00635-3 chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Rigorous Derivation of the Gross-Pitaevskii Equation with a Large Interaction Potential.” Journal of the American Mathematical Society. American Mathematical Society, 2009. https://doi.org/10.1090/S0894-0347-09-00635-3. ieee: L. Erdös, B. Schlein, and H. Yau, “Rigorous derivation of the gross-pitaevskii equation with a large interaction potential,” Journal of the American Mathematical Society, vol. 22, no. 4. American Mathematical Society, pp. 1099–1156, 2009. ista: Erdös L, Schlein B, Yau H. 2009. Rigorous derivation of the gross-pitaevskii equation with a large interaction potential. Journal of the American Mathematical Society. 22(4), 1099–1156. mla: Erdös, László, et al. “Rigorous Derivation of the Gross-Pitaevskii Equation with a Large Interaction Potential.” Journal of the American Mathematical Society, vol. 22, no. 4, American Mathematical Society, 2009, pp. 1099–156, doi:10.1090/S0894-0347-09-00635-3. short: L. Erdös, B. Schlein, H. Yau, Journal of the American Mathematical Society 22 (2009) 1099–1156. date_created: 2018-12-11T11:59:27Z date_published: 2009-10-01T00:00:00Z date_updated: 2021-01-12T06:59:31Z day: '01' doi: 10.1090/S0894-0347-09-00635-3 extern: 1 intvolume: ' 22' issue: '4' month: '10' page: 1099 - 1156 publication: Journal of the American Mathematical Society publication_status: published publisher: American Mathematical Society publist_id: '4132' quality_controlled: 0 status: public title: Rigorous derivation of the gross-pitaevskii equation with a large interaction potential type: journal_article volume: 22 year: '2009' ... --- _id: '2797' abstract: - lang: eng text: In pipe flow at low Reynolds number, decay of localized disturbances is observed. As the Reynolds number is increased, the question emerges whether the life time of these disturbances diverges at a finite Reynolds number or remains transient. In the current investigation we determine their life time quantitatively from pressure measurements, while in previous investigations the distance over which a structure survives has been determined. The obtained results confirm that the life time of localized disturbances does not diverge in the range of Reynolds numbers covered in the current experiment. alternative_title: - Springer Proceedings in Physics author: - first_name: Dirk full_name: Kuik, Dirk J last_name: Kuik - first_name: Christian full_name: Poelma, Christian last_name: Poelma - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Jerry full_name: Westerweel, Jerry last_name: Westerweel citation: ama: 'Kuik D, Poelma C, Hof B, Westerweel J. Quantitative measurement of the life time of turbulence in pipe flow. In: Vol 132. Springer; 2009:145-148. doi:10.1007/978-3-642-03085-7_36' apa: 'Kuik, D., Poelma, C., Hof, B., & Westerweel, J. (2009). Quantitative measurement of the life time of turbulence in pipe flow (Vol. 132, pp. 145–148). Presented at the EETC11: European Turbulence Conference, Springer. https://doi.org/10.1007/978-3-642-03085-7_36' chicago: Kuik, Dirk, Christian Poelma, Björn Hof, and Jerry Westerweel. “Quantitative Measurement of the Life Time of Turbulence in Pipe Flow,” 132:145–48. Springer, 2009. https://doi.org/10.1007/978-3-642-03085-7_36. ieee: 'D. Kuik, C. Poelma, B. Hof, and J. Westerweel, “Quantitative measurement of the life time of turbulence in pipe flow,” presented at the EETC11: European Turbulence Conference, 2009, vol. 132, pp. 145–148.' ista: 'Kuik D, Poelma C, Hof B, Westerweel J. 2009. Quantitative measurement of the life time of turbulence in pipe flow. EETC11: European Turbulence Conference, Springer Proceedings in Physics, vol. 132, 145–148.' mla: Kuik, Dirk, et al. Quantitative Measurement of the Life Time of Turbulence in Pipe Flow. Vol. 132, Springer, 2009, pp. 145–48, doi:10.1007/978-3-642-03085-7_36. short: D. Kuik, C. Poelma, B. Hof, J. Westerweel, in:, Springer, 2009, pp. 145–148. conference: name: 'EETC11: European Turbulence Conference' date_created: 2018-12-11T11:59:39Z date_published: 2009-09-01T00:00:00Z date_updated: 2021-01-12T06:59:46Z day: '01' doi: 10.1007/978-3-642-03085-7_36 extern: 1 intvolume: ' 132' month: '09' page: 145 - 148 publication_status: published publisher: Springer publist_id: '4092' quality_controlled: 0 status: public title: Quantitative measurement of the life time of turbulence in pipe flow type: conference volume: 132 year: '2009' ... --- _id: '2796' abstract: - lang: eng text: As reported in a number of recent studies, turbulence in pipe flow is transient for Re<2000 and the flow eventually always returns to the laminar state. Generally, the lifetime of turbulence has been observed to increase rapidly with Reynolds number but there is currently no accord on the exact scaling behaviour. In particular, it is not clear whether a critical point exists where turbulence becomes sustained or if it remains transient. We here aim to clarify if these conflicting results may have been caused by the different experimental and numerical protocols used to trigger turbulence in these studies. author: - first_name: Alberto full_name: de Lózar, Alberto last_name: De Lózar - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: De Lózar A, Hof B. An experimental study of the decay of turbulent puffs in pipe flow. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. 2009;367(1888):589-599. doi:10.1098/rsta.2008.0199 apa: De Lózar, A., & Hof, B. (2009). An experimental study of the decay of turbulent puffs in pipe flow. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rsta.2008.0199 chicago: De Lózar, Alberto, and Björn Hof. “An Experimental Study of the Decay of Turbulent Puffs in Pipe Flow.” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. Royal Society of London, 2009. https://doi.org/10.1098/rsta.2008.0199. ieee: A. De Lózar and B. Hof, “An experimental study of the decay of turbulent puffs in pipe flow,” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, vol. 367, no. 1888. Royal Society of London, pp. 589–599, 2009. ista: De Lózar A, Hof B. 2009. An experimental study of the decay of turbulent puffs in pipe flow. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. 367(1888), 589–599. mla: De Lózar, Alberto, and Björn Hof. “An Experimental Study of the Decay of Turbulent Puffs in Pipe Flow.” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, vol. 367, no. 1888, Royal Society of London, 2009, pp. 589–99, doi:10.1098/rsta.2008.0199. short: A. De Lózar, B. Hof, Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences 367 (2009) 589–599. date_created: 2018-12-11T11:59:38Z date_published: 2009-02-13T00:00:00Z date_updated: 2021-01-12T06:59:46Z day: '13' doi: 10.1098/rsta.2008.0199 extern: 1 intvolume: ' 367' issue: '1888' month: '02' page: 589 - 599 publication: Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences publication_status: published publisher: Royal Society of London publist_id: '4093' quality_controlled: 0 status: public title: An experimental study of the decay of turbulent puffs in pipe flow type: journal_article volume: 367 year: '2009' ... --- _id: '2868' abstract: - lang: eng text: | Plants exhibit an amazing developmental flexibility. Plant embryogenesis results in the establishment of a simple apical-basal axis represented by apical shoot and basal root meristems. Later, during postembryonic growth, shaping of the plant body continues by the formation and activation of numerous adjacent meristems that give rise to lateral shoot branches, leaves, flowers, or lateral roots. This developmental plasticity reflects an important feature of the plant's life strategy based on the rapid reaction to different environmental stimuli, such as temperature fluctuations, availability of nutrients, light or water and response resulting in modulation of developmental programs. Plant hormones are important endogenous factors for the integration of these environmental inputs and regulation of plant development. After a period of studies focused primarily on single hormonal pathways that enabled us to understand the hormone perception and signal transduction mechanisms, it became obvious that the developmental output mediated by a single hormonal pathway is largely modified through a whole network of interactions with other hormonal pathways. In this review, we will summarize recent knowledge on hormonal networks that regulate the development and growth of root with focus on the hormonal interactions that shape the root apical meristem. author: - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko citation: ama: Benková E, Hejátko J. Hormone interactions at the root apical meristem. Plant Molecular Biology. 2009;69(4):383-396. doi:10.1007/s11103-008-9393-6 apa: Benková, E., & Hejátko, J. (2009). Hormone interactions at the root apical meristem. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-008-9393-6 chicago: Benková, Eva, and Jan Hejátko. “Hormone Interactions at the Root Apical Meristem.” Plant Molecular Biology. Springer, 2009. https://doi.org/10.1007/s11103-008-9393-6. ieee: E. Benková and J. Hejátko, “Hormone interactions at the root apical meristem,” Plant Molecular Biology, vol. 69, no. 4. Springer, pp. 383–396, 2009. ista: Benková E, Hejátko J. 2009. Hormone interactions at the root apical meristem. Plant Molecular Biology. 69(4), 383–396. mla: Benková, Eva, and Jan Hejátko. “Hormone Interactions at the Root Apical Meristem.” Plant Molecular Biology, vol. 69, no. 4, Springer, 2009, pp. 383–96, doi:10.1007/s11103-008-9393-6. short: E. Benková, J. Hejátko, Plant Molecular Biology 69 (2009) 383–396. date_created: 2018-12-11T12:00:01Z date_published: 2009-03-01T00:00:00Z date_updated: 2021-01-12T07:00:22Z day: '01' doi: 10.1007/s11103-008-9393-6 extern: 1 intvolume: ' 69' issue: '4' month: '03' page: 383 - 396 publication: Plant Molecular Biology publication_status: published publisher: Springer publist_id: '3903' quality_controlled: 0 status: public title: Hormone interactions at the root apical meristem type: journal_article volume: 69 year: '2009' ... --- _id: '2869' abstract: - lang: eng text: Lateral root formation is a major determinant of root systems architecture. The degree of root branching impacts the efficiency of water uptake, acquisition of nutrients and anchorage by plants. Understanding the regulation of lateral root development is therefore of vital agronomic importance. The molecular and cellular basis of lateral root formation has been most extensively studied in the plant model Arabidopsis thaliana (Arabidopsis). Significant progress has recently been made in identifying many new Arabidopsis genes that regulate lateral root initiation, patterning and emergence processes. We review how these studies have revealed that the plant hormone auxin represents a common signal that integrates these distinct yet interconnected developmental processes. author: - first_name: Benjamin full_name: Péret, Benjamin last_name: Péret - first_name: Bert full_name: De Rybel, Bert last_name: De Rybel - first_name: Ilda full_name: Casimiro, Ilda last_name: Casimiro - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Laurent full_name: Laplaze, Laurent last_name: Laplaze - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Malcolm full_name: Bennett, Malcolm J last_name: Bennett citation: ama: 'Péret B, De Rybel B, Casimiro I, et al. Arabidopsis lateral root development: an emerging story. Trends in Plant Science. 2009;14(7):399-408. doi:10.1016/j.tplants.2009.05.002' apa: 'Péret, B., De Rybel, B., Casimiro, I., Benková, E., Swarup, R., Laplaze, L., … Bennett, M. (2009). Arabidopsis lateral root development: an emerging story. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2009.05.002' chicago: 'Péret, Benjamin, Bert De Rybel, Ilda Casimiro, Eva Benková, Ranjan Swarup, Laurent Laplaze, Tom Beeckman, and Malcolm Bennett. “Arabidopsis Lateral Root Development: An Emerging Story.” Trends in Plant Science. Cell Press, 2009. https://doi.org/10.1016/j.tplants.2009.05.002.' ieee: 'B. Péret et al., “Arabidopsis lateral root development: an emerging story,” Trends in Plant Science, vol. 14, no. 7. Cell Press, pp. 399–408, 2009.' ista: 'Péret B, De Rybel B, Casimiro I, Benková E, Swarup R, Laplaze L, Beeckman T, Bennett M. 2009. Arabidopsis lateral root development: an emerging story. Trends in Plant Science. 14(7), 399–408.' mla: 'Péret, Benjamin, et al. “Arabidopsis Lateral Root Development: An Emerging Story.” Trends in Plant Science, vol. 14, no. 7, Cell Press, 2009, pp. 399–408, doi:10.1016/j.tplants.2009.05.002.' short: B. Péret, B. De Rybel, I. Casimiro, E. Benková, R. Swarup, L. Laplaze, T. Beeckman, M. Bennett, Trends in Plant Science 14 (2009) 399–408. date_created: 2018-12-11T12:00:02Z date_published: 2009-07-01T00:00:00Z date_updated: 2021-01-12T07:00:22Z day: '01' doi: 10.1016/j.tplants.2009.05.002 extern: 1 intvolume: ' 14' issue: '7' month: '07' page: 399 - 408 publication: Trends in Plant Science publication_status: published publisher: Cell Press publist_id: '3899' quality_controlled: 0 status: public title: 'Arabidopsis lateral root development: an emerging story' type: journal_article volume: 14 year: '2009' ... --- _id: '2932' abstract: - lang: eng text: |+ We describe a new implementation of the Edmonds’s algorithm for computing a perfect matching of minimum cost, to which we refer as Blossom V. A key feature of our implementation is a combination of two ideas that were shown to be effective for this problem: the “variable dual updates” approach of Cook and Rohe (INFORMS J Comput 11(2):138–148, 1999) and the use of priority queues. We achieve this by maintaining an auxiliary graph whose nodes correspond to alternating trees in the Edmonds’s algorithm. While our use of priority queues does not improve the worst-case complexity, it appears to lead to an efficient technique. In the majority of our tests Blossom V outperformed previous implementations of Cook and Rohe (INFORMS J Comput 11(2):138–148, 1999) and Mehlhorn and Schäfer (J Algorithmics Exp (JEA) 7:4, 2002), sometimes by an order of magnitude. We also show that for large VLSI instances it is beneficial to update duals by solving a linear program, contrary to a conjecture by Cook and Rohe. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Kolmogorov V. Blossom V: A new implementation of a minimum cost perfect matching algorithm. Mathematical Programming Computation. 2009;1(1):43-67. doi:10.1007/s12532-009-0002-8' apa: 'Kolmogorov, V. (2009). Blossom V: A new implementation of a minimum cost perfect matching algorithm. Mathematical Programming Computation. Springer. https://doi.org/10.1007/s12532-009-0002-8' chicago: 'Kolmogorov, Vladimir. “Blossom V: A New Implementation of a Minimum Cost Perfect Matching Algorithm.” Mathematical Programming Computation. Springer, 2009. https://doi.org/10.1007/s12532-009-0002-8.' ieee: 'V. Kolmogorov, “Blossom V: A new implementation of a minimum cost perfect matching algorithm,” Mathematical Programming Computation, vol. 1, no. 1. Springer, pp. 43–67, 2009.' ista: 'Kolmogorov V. 2009. Blossom V: A new implementation of a minimum cost perfect matching algorithm. Mathematical Programming Computation. 1(1), 43–67.' mla: 'Kolmogorov, Vladimir. “Blossom V: A New Implementation of a Minimum Cost Perfect Matching Algorithm.” Mathematical Programming Computation, vol. 1, no. 1, Springer, 2009, pp. 43–67, doi:10.1007/s12532-009-0002-8.' short: V. Kolmogorov, Mathematical Programming Computation 1 (2009) 43–67. date_created: 2018-12-11T12:00:25Z date_published: 2009-07-01T00:00:00Z date_updated: 2021-01-12T07:00:47Z day: '01' doi: 10.1007/s12532-009-0002-8 extern: 1 intvolume: ' 1' issue: '1' month: '07' page: 43 - 67 publication: Mathematical Programming Computation publication_status: published publisher: Springer publist_id: '3804' quality_controlled: 0 status: public title: 'Blossom V: A new implementation of a minimum cost perfect matching algorithm' type: journal_article volume: 1 year: '2009' ... ... --- _id: '3046' abstract: - lang: eng text: Plant-parasitic nematodes are destructive plant pathogens that cause significant yield losses. They induce highly specialized feeding sites (NFS) in infected plant roots from which they withdraw nutrients. In order to establish these NFS, it is thought that the nematodes manipulate the molecular and physiological pathways of their hosts. Evidence is accumulating that the plant signalling molecule auxin is involved in the initiation and development of the feeding sites of sedentary plant-parasitic nematodes. Intercellular transport of auxin is essential for various aspects of plant growth and development. Here, we analysed the spatial and temporal expression of PIN auxin transporters during the early events of NFS establishment using promoter-GUS/GFP fusion lines. Additionally, single and double pin mutants were used in infection studies to analyse the role of the different PIN proteins during cyst nematode infection. Based on our results, we postulate a model in which PIN1-mediated auxin transport is needed to deliver auxin to the initial syncytial cell, whereas PIN3 and PIN4 distribute the accumulated auxin laterally and are involved in the radial expansion of the NFS. Our data demonstrate that cyst nematodes are able to hijack the auxin distribution network in order to facilitate the infection process. © 2009 Grunewald et al author: - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Bernard full_name: Cannoot, Bernard last_name: Cannoot - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Godelieve full_name: Gheysen, Godelieve last_name: Gheysen citation: ama: Grunewald W, Cannoot B, Friml J, Gheysen G. Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection. PLoS Pathogens. 2009;5(1). doi: 10.1371/journal.ppat.1000266 apa: Grunewald, W., Cannoot, B., Friml, J., & Gheysen, G. (2009). Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection. PLoS Pathogens. Public Library of Science. https://doi.org/ 10.1371/journal.ppat.1000266 chicago: Grunewald, Wim, Bernard Cannoot, Jiří Friml, and Godelieve Gheysen. “Parasitic Nematodes Modulate PIN Mediated Auxin Transport to Facilitate Infection.” PLoS Pathogens. Public Library of Science, 2009. https://doi.org/ 10.1371/journal.ppat.1000266. ieee: W. Grunewald, B. Cannoot, J. Friml, and G. Gheysen, “Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection,” PLoS Pathogens, vol. 5, no. 1. Public Library of Science, 2009. ista: Grunewald W, Cannoot B, Friml J, Gheysen G. 2009. Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection. PLoS Pathogens. 5(1). mla: Grunewald, Wim, et al. “Parasitic Nematodes Modulate PIN Mediated Auxin Transport to Facilitate Infection.” PLoS Pathogens, vol. 5, no. 1, Public Library of Science, 2009, doi: 10.1371/journal.ppat.1000266. short: W. Grunewald, B. Cannoot, J. Friml, G. Gheysen, PLoS Pathogens 5 (2009). date_created: 2018-12-11T12:01:03Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T07:40:40Z day: '01' doi: ' 10.1371/journal.ppat.1000266' extern: 1 intvolume: ' 5' issue: '1' month: '01' publication: PLoS Pathogens publication_status: published publisher: Public Library of Science publist_id: '3656' quality_controlled: 0 status: public title: Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection type: journal_article volume: 5 year: '2009' ... --- _id: '3061' abstract: - lang: eng text: The PIN-FORMED (PIN) proteins are secondary transporters acting in the efflux of the plant signal molecule auxin from cells. They are asymmetrically localized within cells and their polarity determines the directionality of intercellular auxin flow. PIN genes are found exclusively in the genomes of multicellular plants and play an important role in regulating asymmetric auxin distribution in multiple developmental processes, including embryogenesis, organogenesis, tissue differentiation and tropic responses. All PIN proteins have a similar structure with amino- and carboxy-terminal hydrophobic, membrane-spanning domains separated by a central hydrophilic domain. The structure of the hydrophobic domains is well conserved. The hydrophilic domain is more divergent and it determines eight groups within the protein family. The activity of PIN proteins is regulated at multiple levels, including transcription, protein stability, subcellular localization and transport activity. Different endogenous and environmental signals can modulate PIN activity and thus modulate auxin-distribution-dependent development. A large group of PIN proteins, including the most ancient members known from mosses, localize to the endoplasmic reticulum and they regulate the subcellular compartmentalization of auxin and thus auxin metabolism. Further work is needed to establish the physiological importance of this unexpected mode of auxin homeostasis regulation. Furthermore, the evolution of PIN-based transport, PIN protein structure and more detailed biochemical characterization of the transport function are important topics for further studies. author: - first_name: Pavel full_name: Křeček, Pavel last_name: Křeček - first_name: Petr full_name: Skůpa, Petr last_name: Skůpa - first_name: Jiří full_name: Libus, Jiří last_name: Libus - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová citation: ama: Křeček P, Skůpa P, Libus J, et al. The PIN-FORMED (PIN) protein family of auxin transporters. Genome Biology. 2009;10(12). doi:10.1186/gb-2009-10-12-249 apa: Křeček, P., Skůpa, P., Libus, J., Naramoto, S., Tejos, R., Friml, J., & Zažímalová, E. (2009). The PIN-FORMED (PIN) protein family of auxin transporters. Genome Biology. BioMed Central. https://doi.org/10.1186/gb-2009-10-12-249 chicago: Křeček, Pavel, Petr Skůpa, Jiří Libus, Satoshi Naramoto, Ricardo Tejos, Jiří Friml, and Eva Zažímalová. “The PIN-FORMED (PIN) Protein Family of Auxin Transporters.” Genome Biology. BioMed Central, 2009. https://doi.org/10.1186/gb-2009-10-12-249. ieee: P. Křeček et al., “The PIN-FORMED (PIN) protein family of auxin transporters,” Genome Biology, vol. 10, no. 12. BioMed Central, 2009. ista: Křeček P, Skůpa P, Libus J, Naramoto S, Tejos R, Friml J, Zažímalová E. 2009. The PIN-FORMED (PIN) protein family of auxin transporters. Genome Biology. 10(12). mla: Křeček, Pavel, et al. “The PIN-FORMED (PIN) Protein Family of Auxin Transporters.” Genome Biology, vol. 10, no. 12, BioMed Central, 2009, doi:10.1186/gb-2009-10-12-249. short: P. Křeček, P. Skůpa, J. Libus, S. Naramoto, R. Tejos, J. Friml, E. Zažímalová, Genome Biology 10 (2009). date_created: 2018-12-11T12:01:08Z date_published: 2009-12-29T00:00:00Z date_updated: 2021-01-12T07:40:46Z day: '29' doi: 10.1186/gb-2009-10-12-249 extern: '1' external_id: pmid: - '20053306' intvolume: ' 10' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812941/ month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_status: published publisher: BioMed Central publist_id: '3640' quality_controlled: '1' status: public title: The PIN-FORMED (PIN) protein family of auxin transporters type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2009' ... --- _id: '3058' abstract: - lang: eng text: The plant signalling molecule auxin provides positional informa-tion in a variety of developmental processes by means of its differential distribution (gradients) within plant tissues. Thus, cellular auxin levels often determine the developmental output of auxin signalling. Conceptually, transmembrane transport and metabolic processes regulate the steady-state levels of auxin in any given cell2,3. In particular, PIN auxin-efflux-carrier-mediated, directional transport between cells is crucial for generating auxin gradients2,4,5. Here we show that Arabidopsis thaliana PIN5, an atypical member of the PIN gene family, encodes a functional auxin transporter that is required for auxin-mediated develop-ment. PIN5 does not have a direct role in cell-to-cell transport but regulates intracellular auxin homeostasis and metabolism. PIN5 localizes, unlike other characterized plasma membrane PIN proteins, to endoplasmic reticulum (ER), presumably medi-ating auxin flow from the cytosol to the lumen of the ER. The ER localization of other PIN5-like transporters (including the moss PIN) indicates that the diversification of PIN protein functions in mediating auxin homeostasis at the ER, and cell-to-cell auxin transport at the plasma membrane, represent an ancient event during the evolution of land plants. author: - first_name: Jozef full_name: Mravec, Jozef last_name: Mravec - first_name: Petr full_name: Skůpa, Petr last_name: Skůpa - first_name: Aurélien full_name: Bailly, Aurélien last_name: Bailly - first_name: Klára full_name: Hoyerová, Klára last_name: Hoyerová - first_name: Pavel full_name: Křeček, Pavel last_name: Křeček - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Jing full_name: Zhang, Jing last_name: Zhang - first_name: Vassilena full_name: Gaykova, Vassilena last_name: Gaykova - first_name: York full_name: Stierhof, York-Dieter last_name: Stierhof - first_name: Petre full_name: Dobrev, Petre I last_name: Dobrev - first_name: Kateřina full_name: Schwarzerová, Kateřina last_name: Schwarzerová - first_name: Jakub full_name: Rolčík, Jakub last_name: Rolčík - first_name: Daniela full_name: Seifertová, Daniela last_name: Seifertová - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Mravec J, Skůpa P, Bailly A, et al. Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter. Nature. 2009;459(7250):1136-1140. doi:10.1038/nature08066 apa: Mravec, J., Skůpa, P., Bailly, A., Hoyerová, K., Křeček, P., Bielach, A., … Friml, J. (2009). Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter. Nature. Nature Publishing Group. https://doi.org/10.1038/nature08066 chicago: Mravec, Jozef, Petr Skůpa, Aurélien Bailly, Klára Hoyerová, Pavel Křeček, Agnieszka Bielach, Jan Petrášek, et al. “Subcellular Homeostasis of Phytohormone Auxin Is Mediated by the ER Localized PIN5 Transporter.” Nature. Nature Publishing Group, 2009. https://doi.org/10.1038/nature08066. ieee: J. Mravec et al., “Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter,” Nature, vol. 459, no. 7250. Nature Publishing Group, pp. 1136–1140, 2009. ista: Mravec J, Skůpa P, Bailly A, Hoyerová K, Křeček P, Bielach A, Petrášek J, Zhang J, Gaykova V, Stierhof Y, Dobrev P, Schwarzerová K, Rolčík J, Seifertová D, Luschnig C, Benková E, Zažímalová E, Geisler M, Friml J. 2009. Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter. Nature. 459(7250), 1136–1140. mla: Mravec, Jozef, et al. “Subcellular Homeostasis of Phytohormone Auxin Is Mediated by the ER Localized PIN5 Transporter.” Nature, vol. 459, no. 7250, Nature Publishing Group, 2009, pp. 1136–40, doi:10.1038/nature08066. short: J. Mravec, P. Skůpa, A. Bailly, K. Hoyerová, P. Křeček, A. Bielach, J. Petrášek, J. Zhang, V. Gaykova, Y. Stierhof, P. Dobrev, K. Schwarzerová, J. Rolčík, D. Seifertová, C. Luschnig, E. Benková, E. Zažímalová, M. Geisler, J. Friml, Nature 459 (2009) 1136–1140. date_created: 2018-12-11T12:01:07Z date_published: 2009-06-25T00:00:00Z date_updated: 2021-01-12T07:40:45Z day: '25' doi: 10.1038/nature08066 extern: 1 intvolume: ' 459' issue: '7250' month: '06' page: 1136 - 1140 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3645' quality_controlled: 0 status: public title: Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter type: journal_article volume: 459 year: '2009' ... --- _id: '3055' abstract: - lang: eng text: 'ACAP-type ARF GTPase activating proteins (ARF-GAPs) regulate multiple cellular processes, including endocytosis, secretion, phagocytosis, cell adhesion and cell migration. However, the regulation of ACAP functions by other cellular proteins is poorly understood. We have reported previously that a plant ACAP, VAN3, plays a pivotal role in plant venation continuity. Here, we report on newly identified VAN3 regulators: the CVP2 (cotyledon vascular pattern 2) 5 PTase, which is considered to degrade IP3 and also to produce PtdIns(4)P from PtdIns(4,5)P2; and a PH domain-containing protein, VAB (VAN3 binding protein). Combinational mutations of both CVP2 and its closest homologue CVL1 (CVP2 like 1) phenocopied the strong allele of van3 mutants, showing severe vascular continuity. The phenotype of double mutants between van3, cvp2 and vab suggested that VAN3, CVP2 and VAB function in vascular pattern formation in the same pathway. Localization analysis revealed that both CVP2 and VAB colocalize with VAN3 in the trans- Golgi network (TGN), supporting their functions in the same pathway. The subcellular localization of VAN3 was dependent on its PH domain, and mislocalization of VAN3 was induced in cvp2 or vab mutants. These results suggest that CVP2 and VAB cooperatively regulate the subcellular localization of VAN3 through the interaction between its PH domain and phosphoinositides and/or inositol phosphates. In addition, PtdIns(4)P, to which VAN3 binds preferentially, enhanced the ARF-GAP activity of VAN3, whereas IP3 inhibited it. These results suggest the existence of PtdIns(4)P and/or IP3-dependent subcellular targeting and regulation of VAN3 ACAP activity that governs plant vascular tissue continuity.' author: - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Shinichiro full_name: Sawa, Shinichiro last_name: Sawa - first_name: Koji full_name: Koizumi, Koji last_name: Koizumi - first_name: Tomohiro full_name: Uemura, Tomohiro last_name: Uemura - first_name: Takashi full_name: Ueda, Takashi last_name: Ueda - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Akihiko full_name: Nakano, Akihiko last_name: Nakano - first_name: Hiroo full_name: Fukuda, Hiroo last_name: Fukuda citation: ama: Naramoto S, Sawa S, Koizumi K, et al. Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants. Development. 2009;136(9):1529-1538. doi:10.1242/dev.030098 apa: Naramoto, S., Sawa, S., Koizumi, K., Uemura, T., Ueda, T., Friml, J., … Fukuda, H. (2009). Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants. Development. Company of Biologists. https://doi.org/10.1242/dev.030098 chicago: Naramoto, Satoshi, Shinichiro Sawa, Koji Koizumi, Tomohiro Uemura, Takashi Ueda, Jiří Friml, Akihiko Nakano, and Hiroo Fukuda. “Phosphoinositide-Dependent Regulation of VAN3 ARF-GAP Localization and Activity Essential for Vascular Tissue Continuity in Plants.” Development. Company of Biologists, 2009. https://doi.org/10.1242/dev.030098. ieee: S. Naramoto et al., “Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants,” Development, vol. 136, no. 9. Company of Biologists, pp. 1529–1538, 2009. ista: Naramoto S, Sawa S, Koizumi K, Uemura T, Ueda T, Friml J, Nakano A, Fukuda H. 2009. Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants. Development. 136(9), 1529–1538. mla: Naramoto, Satoshi, et al. “Phosphoinositide-Dependent Regulation of VAN3 ARF-GAP Localization and Activity Essential for Vascular Tissue Continuity in Plants.” Development, vol. 136, no. 9, Company of Biologists, 2009, pp. 1529–38, doi:10.1242/dev.030098. short: S. Naramoto, S. Sawa, K. Koizumi, T. Uemura, T. Ueda, J. Friml, A. Nakano, H. Fukuda, Development 136 (2009) 1529–1538. date_created: 2018-12-11T12:01:06Z date_published: 2009-05-01T00:00:00Z date_updated: 2021-01-12T07:40:44Z day: '01' doi: 10.1242/dev.030098 extern: 1 intvolume: ' 136' issue: '9' month: '05' page: 1529 - 1538 publication: Development publication_status: published publisher: Company of Biologists publist_id: '3647' quality_controlled: 0 status: public title: Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants type: journal_article volume: 136 year: '2009' ... --- _id: '3059' abstract: - lang: eng text: The phytohormone auxin plays a major role in embryonic and postembryonic plant development. The temporal and spatial distribution of auxin largely depends on the subcellular polar localization of members of the PIN-FORMED (PIN) auxin efflux carrier family. The Ser/Thr protein kinase PINOID (PID) catalyzes PIN phosphorylation and crucially contributes to the regulation of apical-basal PIN polarity. The GTP exchange factor on ADP-ribosylation factors (ARF-GEF), GNOM preferentially mediates PIN recycling at the basal side of the cell. Interference with GNOM activity leads to dynamic PIN transcytosis between different sides of the cell. Our genetic, pharmacological, and cell biological approaches illustrate that PID and GNOM influence PIN polarity and plant development in an antagonistic manner and that the PID-dependent PIN phosphorylation results in GNOM-independent polar PIN targeting. The data suggest that PID and the protein phosphatase 2A not only regulate the static PIN polarity, but also act antagonistically on the rate of GNOM-dependent polar PIN transcytosis. We propose a model that includes PID-dependent PIN phosphorylation at the plasma membrane and the subsequent sorting of PIN proteins to a GNOM-independent pathway for polarity alterations during developmental processes, such as lateral root formation and leaf vasculature development. author: - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Fang full_name: Huang, Fang last_name: Huang - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Jing full_name: Zhang, Jing last_name: Zhang - first_name: Marta full_name: Michniewicz, Marta last_name: Michniewicz - first_name: Remko full_name: Offringa, Remko last_name: Offringa - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kleine Vehn J, Huang F, Naramoto S, et al. PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis. Plant Cell. 2009;21(12):3839-3849. doi:10.1105/tpc.109.071639 apa: Kleine Vehn, J., Huang, F., Naramoto, S., Zhang, J., Michniewicz, M., Offringa, R., & Friml, J. (2009). PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.109.071639 chicago: Kleine Vehn, Jürgen, Fang Huang, Satoshi Naramoto, Jing Zhang, Marta Michniewicz, Remko Offringa, and Jiří Friml. “PIN Auxin Efflux Carrier Polarity Is Regulated by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2009. https://doi.org/10.1105/tpc.109.071639. ieee: J. Kleine Vehn et al., “PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis,” Plant Cell, vol. 21, no. 12. American Society of Plant Biologists, pp. 3839–3849, 2009. ista: Kleine Vehn J, Huang F, Naramoto S, Zhang J, Michniewicz M, Offringa R, Friml J. 2009. PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis. Plant Cell. 21(12), 3839–3849. mla: Kleine Vehn, Jürgen, et al. “PIN Auxin Efflux Carrier Polarity Is Regulated by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.” Plant Cell, vol. 21, no. 12, American Society of Plant Biologists, 2009, pp. 3839–49, doi:10.1105/tpc.109.071639. short: J. Kleine Vehn, F. Huang, S. Naramoto, J. Zhang, M. Michniewicz, R. Offringa, J. Friml, Plant Cell 21 (2009) 3839–3849. date_created: 2018-12-11T12:01:07Z date_published: 2009-12-01T00:00:00Z date_updated: 2021-01-12T07:40:45Z day: '01' doi: 10.1105/tpc.109.071639 extern: 1 intvolume: ' 21' issue: '12' month: '12' page: 3839 - 3849 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3643' quality_controlled: 0 status: public title: PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis type: journal_article volume: 21 year: '2009' ... --- _id: '3056' abstract: - lang: eng text: Local hormone maxima are essential for the development of multicellular structures and organs. For example, steroid hormones accumulate in specific cell types of the animal fetus to induce sexual differentiation and concentration peaks of the plant hormone auxin direct organ initiation and mediate tissue patterning. Here we provide an example of a regulated local hormone minimum required during organogenesis. Our results demonstrate that formation of a local auxin minimum is necessary for specification of the valve margin separation layer where Arabidopsis fruit opening takes place. Consequently, ectopic production of auxin, specifically in valve margin cells, leads to a complete loss of proper cell fate determination. The valve margin identity factor INDEHISCENT (IND) is responsible for forming the auxin minimum by coordinating auxin efflux in separation-layer cells. We propose that the simplicity of formation and maintenance make local hormone minima particularly well suited to specify a small number of cells such as the stripes at the valve margins. author: - first_name: Karim full_name: Sorefan, Karim last_name: Sorefan - first_name: Thomas full_name: Girin, Thomas last_name: Girin - first_name: Sarah full_name: Liljegren, Sarah J last_name: Liljegren - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Pedro full_name: Robles, Pedro last_name: Robles - first_name: Carlos full_name: Galván-Ampudia, Carlos S last_name: Galván Ampudia - first_name: Remko full_name: Offringa, Remko last_name: Offringa - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Martin full_name: Yanofsky, Martin F last_name: Yanofsky - first_name: Lars full_name: Østergaard, Lars last_name: Østergaard citation: ama: Sorefan K, Girin T, Liljegren S, et al. A regulated auxin minimum is required for seed dispersal in Arabidopsis. Nature. 2009;459(7246):583-586. doi:10.1038/nature07875 apa: Sorefan, K., Girin, T., Liljegren, S., Ljung, K., Robles, P., Galván Ampudia, C., … Østergaard, L. (2009). A regulated auxin minimum is required for seed dispersal in Arabidopsis. Nature. Nature Publishing Group. https://doi.org/10.1038/nature07875 chicago: Sorefan, Karim, Thomas Girin, Sarah Liljegren, Karin Ljung, Pedro Robles, Carlos Galván Ampudia, Remko Offringa, Jiří Friml, Martin Yanofsky, and Lars Østergaard. “A Regulated Auxin Minimum Is Required for Seed Dispersal in Arabidopsis.” Nature. Nature Publishing Group, 2009. https://doi.org/10.1038/nature07875. ieee: K. Sorefan et al., “A regulated auxin minimum is required for seed dispersal in Arabidopsis,” Nature, vol. 459, no. 7246. Nature Publishing Group, pp. 583–586, 2009. ista: Sorefan K, Girin T, Liljegren S, Ljung K, Robles P, Galván Ampudia C, Offringa R, Friml J, Yanofsky M, Østergaard L. 2009. A regulated auxin minimum is required for seed dispersal in Arabidopsis. Nature. 459(7246), 583–586. mla: Sorefan, Karim, et al. “A Regulated Auxin Minimum Is Required for Seed Dispersal in Arabidopsis.” Nature, vol. 459, no. 7246, Nature Publishing Group, 2009, pp. 583–86, doi:10.1038/nature07875. short: K. Sorefan, T. Girin, S. Liljegren, K. Ljung, P. Robles, C. Galván Ampudia, R. Offringa, J. Friml, M. Yanofsky, L. Østergaard, Nature 459 (2009) 583–586. date_created: 2018-12-11T12:01:06Z date_published: 2009-05-28T00:00:00Z date_updated: 2021-01-12T07:40:44Z day: '28' doi: 10.1038/nature07875 extern: 1 intvolume: ' 459' issue: '7246' month: '05' page: 583 - 586 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3646' quality_controlled: 0 status: public title: A regulated auxin minimum is required for seed dispersal in Arabidopsis type: journal_article volume: 459 year: '2009' ... --- _id: '3057' abstract: - lang: eng text: The differential distribution of the plant signaling molecule auxin is required for many aspects of plant development. Local auxin maxima and gradients arise as a result of local auxin metabolism and, predominantly, from directional cell-to-cell transport. In this primer, we discuss how the coordinated activity of several auxin influx and efflux systems, which transport auxin across the plasma membrane, mediates directional auxin flow. This activity crucially contributes to the correct setting of developmental cues in embryogenesis, organogenesis, vascular tissue formation and directional growth in response to environmental stimuli. author: - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Petrášek J, Friml J. Auxin transport routes in plant development. Development. 2009;136(16):2675-2688. doi:10.1242/dev.030353 apa: Petrášek, J., & Friml, J. (2009). Auxin transport routes in plant development. Development. Company of Biologists. https://doi.org/10.1242/dev.030353 chicago: Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.” Development. Company of Biologists, 2009. https://doi.org/10.1242/dev.030353. ieee: J. Petrášek and J. Friml, “Auxin transport routes in plant development,” Development, vol. 136, no. 16. Company of Biologists, pp. 2675–2688, 2009. ista: Petrášek J, Friml J. 2009. Auxin transport routes in plant development. Development. 136(16), 2675–2688. mla: Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.” Development, vol. 136, no. 16, Company of Biologists, 2009, pp. 2675–88, doi:10.1242/dev.030353. short: J. Petrášek, J. Friml, Development 136 (2009) 2675–2688. date_created: 2018-12-11T12:01:07Z date_published: 2009-08-15T00:00:00Z date_updated: 2021-01-12T07:40:45Z day: '15' doi: 10.1242/dev.030353 extern: '1' external_id: pmid: - ' 19633168' intvolume: ' 136' issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/19633168 month: '08' oa: 1 oa_version: Published Version page: 2675 - 2688 pmid: 1 publication: Development publication_status: published publisher: Company of Biologists publist_id: '3644' quality_controlled: '1' status: public title: Auxin transport routes in plant development type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2009' ... --- _id: '3060' article_type: letter_note author: - first_name: Karin full_name: Schumacher, Karin last_name: Schumacher - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Schumacher K, Friml J. Cell biology. Current Opinion in Plant Biology. 2009;12(6):651-652. doi:10.1016/j.pbi.2009.10.009 apa: Schumacher, K., & Friml, J. (2009). Cell biology. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2009.10.009 chicago: Schumacher, Karin, and Jiří Friml. “Cell Biology.” Current Opinion in Plant Biology. Elsevier, 2009. https://doi.org/10.1016/j.pbi.2009.10.009. ieee: K. Schumacher and J. Friml, “Cell biology,” Current Opinion in Plant Biology, vol. 12, no. 6. Elsevier, pp. 651–652, 2009. ista: Schumacher K, Friml J. 2009. Cell biology. Current Opinion in Plant Biology. 12(6), 651–652. mla: Schumacher, Karin, and Jiří Friml. “Cell Biology.” Current Opinion in Plant Biology, vol. 12, no. 6, Elsevier, 2009, pp. 651–52, doi:10.1016/j.pbi.2009.10.009. short: K. Schumacher, J. Friml, Current Opinion in Plant Biology 12 (2009) 651–652. date_created: 2018-12-11T12:01:08Z date_published: 2009-12-01T00:00:00Z date_updated: 2021-01-12T07:40:46Z day: '01' doi: 10.1016/j.pbi.2009.10.009 extern: '1' intvolume: ' 12' issue: '6' language: - iso: eng month: '12' oa_version: None page: 651 - 652 publication: Current Opinion in Plant Biology publication_status: published publisher: Elsevier publist_id: '3641' quality_controlled: '1' status: public title: Cell biology type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2009' ... --- _id: '3203' abstract: - lang: eng text: In recent years the Markov Random Field (MRF) has become the de facto probabilistic model for low-level vision applications. However, in a maximum a posteriori (MAP) framework, MRFs inherently encourage delta function marginal statistics. By contrast, many low-level vision problems have heavy tailed marginal statistics, making the MRF model unsuitable. In this paper we introduce a more general Marginal Probability Field (MPF), of which the MRF is a special, linear case, and show that convex energy MPFs can be used to encourage arbitrary marginal statistics. We introduce a flexible, extensible framework for effectively optimizing the resulting NP-hard MAP problem, based around dual-decomposition and a modified mincost flow algorithm, and which achieves global optimality in some instances. We use a range of applications, including image denoising and texture synthesis, to demonstrate the benefits of this class of MPF over MRFs. author: - first_name: Oliver full_name: Woodford, Oliver J last_name: Woodford - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Woodford O, Rother C, Kolmogorov V. A global perspective on MAP inference for low level vision. In: IEEE; 2009:2319-2326. doi:10.1109/ICCV.2009.5459434' apa: 'Woodford, O., Rother, C., & Kolmogorov, V. (2009). A global perspective on MAP inference for low level vision (pp. 2319–2326). Presented at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2009.5459434' chicago: Woodford, Oliver, Carsten Rother, and Vladimir Kolmogorov. “A Global Perspective on MAP Inference for Low Level Vision,” 2319–26. IEEE, 2009. https://doi.org/10.1109/ICCV.2009.5459434. ieee: 'O. Woodford, C. Rother, and V. Kolmogorov, “A global perspective on MAP inference for low level vision,” presented at the ICCV: International Conference on Computer Vision, 2009, pp. 2319–2326.' ista: 'Woodford O, Rother C, Kolmogorov V. 2009. A global perspective on MAP inference for low level vision. ICCV: International Conference on Computer Vision, 2319–2326.' mla: Woodford, Oliver, et al. A Global Perspective on MAP Inference for Low Level Vision. IEEE, 2009, pp. 2319–26, doi:10.1109/ICCV.2009.5459434. short: O. Woodford, C. Rother, V. Kolmogorov, in:, IEEE, 2009, pp. 2319–2326. conference: name: 'ICCV: International Conference on Computer Vision' date_created: 2018-12-11T12:01:59Z date_published: 2009-05-01T00:00:00Z date_updated: 2021-01-12T07:41:46Z day: '01' doi: 10.1109/ICCV.2009.5459434 extern: 1 month: '05' page: 2319 - 2326 publication_status: published publisher: IEEE publist_id: '3481' quality_controlled: 0 status: public title: A global perspective on MAP inference for low level vision type: conference year: '2009' ... --- _id: '3230' abstract: - lang: eng text: 'We present a new approach to the design of IND-CCA2 secure hybrid encryption schemes in the standard model. Our approach provides an efficient generic transformation from 1-universal to 2-universal hash proof systems. The transformation involves a randomness extractor based on a 4-wise independent hash function as the key derivation function. Our methodology can be instantiated with efficient schemes based on standard intractability assumptions such as Decisional Diffie-Hellman, Quadratic Residuosity, and Paillier''s Decisional Composite Residuosity. Interestingly, our framework also allows to prove IND-CCA2 security of a hybrid version of 1991''s Damgård''s ElGamal public-key encryption scheme under the DDH assumption. ' alternative_title: - LNCS author: - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Martijn full_name: Stam, Martijn last_name: Stam - first_name: Moti full_name: Yung, Moti last_name: Yung citation: ama: 'Kiltz E, Pietrzak KZ, Stam M, Yung M. A new randomness extraction paradigm for hybrid encryption. In: Vol 5479. Springer; 2009:590-609. doi:10.1007/978-3-642-01001-9_34' apa: 'Kiltz, E., Pietrzak, K. Z., Stam, M., & Yung, M. (2009). A new randomness extraction paradigm for hybrid encryption (Vol. 5479, pp. 590–609). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/978-3-642-01001-9_34' chicago: Kiltz, Eike, Krzysztof Z Pietrzak, Martijn Stam, and Moti Yung. “A New Randomness Extraction Paradigm for Hybrid Encryption,” 5479:590–609. Springer, 2009. https://doi.org/10.1007/978-3-642-01001-9_34. ieee: 'E. Kiltz, K. Z. Pietrzak, M. Stam, and M. Yung, “A new randomness extraction paradigm for hybrid encryption,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2009, vol. 5479, pp. 590–609.' ista: 'Kiltz E, Pietrzak KZ, Stam M, Yung M. 2009. A new randomness extraction paradigm for hybrid encryption. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 5479, 590–609.' mla: Kiltz, Eike, et al. A New Randomness Extraction Paradigm for Hybrid Encryption. Vol. 5479, Springer, 2009, pp. 590–609, doi:10.1007/978-3-642-01001-9_34. short: E. Kiltz, K.Z. Pietrzak, M. Stam, M. Yung, in:, Springer, 2009, pp. 590–609. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:09Z date_published: 2009-05-28T00:00:00Z date_updated: 2021-01-12T07:41:58Z day: '28' doi: 10.1007/978-3-642-01001-9_34 extern: 1 intvolume: ' 5479' month: '05' page: 590 - 609 publication_status: published publisher: Springer publist_id: '3449' quality_controlled: 0 status: public title: A new randomness extraction paradigm for hybrid encryption type: conference volume: 5479 year: '2009' ... --- _id: '3231' abstract: - lang: eng text: 'We investigate the security of "padding-based" encryption schemes in the standard model. This class contains all public-key encryption schemes where the encryption algorithm first applies some invertible public transformation to the message (the "padding"), followed by a trapdoor permutation. In particular, this class contains OAEP and its variants. Our main result is a black-box impossibility result showing that one cannot prove any such padding-based scheme chosen-ciphertext secure even assuming the existence of ideal trapdoor permutations. The latter is a strong ideal abstraction of trapdoor permutations which inherits all security properties of uniform random permutations. ' alternative_title: - LNCS author: - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Kiltz E, Pietrzak KZ. On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model. In: Vol 5479. Springer; 2009:389-406. doi:10.1007/978-3-642-01001-9_23' apa: 'Kiltz, E., & Pietrzak, K. Z. (2009). On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model (Vol. 5479, pp. 389–406). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/978-3-642-01001-9_23' chicago: Kiltz, Eike, and Krzysztof Z Pietrzak. “On the Security of Padding Based Encryption Schemes Why We Cannot Prove OAEP Secure in the Standard Model,” 5479:389–406. Springer, 2009. https://doi.org/10.1007/978-3-642-01001-9_23. ieee: 'E. Kiltz and K. Z. Pietrzak, “On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2009, vol. 5479, pp. 389–406.' ista: 'Kiltz E, Pietrzak KZ. 2009. On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 5479, 389–406.' mla: Kiltz, Eike, and Krzysztof Z. Pietrzak. On the Security of Padding Based Encryption Schemes Why We Cannot Prove OAEP Secure in the Standard Model. Vol. 5479, Springer, 2009, pp. 389–406, doi:10.1007/978-3-642-01001-9_23. short: E. Kiltz, K.Z. Pietrzak, in:, Springer, 2009, pp. 389–406. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:09Z date_published: 2009-05-28T00:00:00Z date_updated: 2021-01-12T07:41:58Z day: '28' doi: 10.1007/978-3-642-01001-9_23 extern: 1 intvolume: ' 5479' month: '05' page: 389 - 406 publication_status: published publisher: Springer publist_id: '3450' quality_controlled: 0 status: public title: On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model type: conference volume: 5479 year: '2009' ... --- _id: '3232' abstract: - lang: eng text: 'A weak pseudorandom function (wPRF) is a cryptographic primitive similar to - but weaker than - a pseudorandom function: for wPRFs one only requires that the output is pseudorandom when queried on random inputs.We show that unlike "normal" PRFs, wPRFs are seedincompressible, in the sense that the output of a wPRF is pseudorandom even if a bounded amount of information about the key is leaked. As an application of this result we construct a simple mode of operation which - when instantiated with any wPRF - gives a leakage-resilient stream-cipher. The implementation of such a cipher is secure against every side-channel attack, as long as the amount of information leaked per round is bounded, but overall can be arbitrary large. The construction is simpler than the previous one (Dziembowski-Pietrzak FOCS''08) as it only uses a single primitive (a wPRF) in a straight forward manner. ' alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. A leakage resilient mode of operation. In: Vol 5479. Springer; 2009:462-482. doi:10.1007/978-3-642-01001-9_27' apa: 'Pietrzak, K. Z. (2009). A leakage resilient mode of operation (Vol. 5479, pp. 462–482). Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/10.1007/978-3-642-01001-9_27' chicago: Pietrzak, Krzysztof Z. “A Leakage Resilient Mode of Operation,” 5479:462–82. Springer, 2009. https://doi.org/10.1007/978-3-642-01001-9_27. ieee: 'K. Z. Pietrzak, “A leakage resilient mode of operation,” presented at the CRYPTO: International Cryptology Conference, 2009, vol. 5479, pp. 462–482.' ista: 'Pietrzak KZ. 2009. A leakage resilient mode of operation. CRYPTO: International Cryptology Conference, LNCS, vol. 5479, 462–482.' mla: Pietrzak, Krzysztof Z. A Leakage Resilient Mode of Operation. Vol. 5479, Springer, 2009, pp. 462–82, doi:10.1007/978-3-642-01001-9_27. short: K.Z. Pietrzak, in:, Springer, 2009, pp. 462–482. conference: name: 'CRYPTO: International Cryptology Conference' date_created: 2018-12-11T12:02:09Z date_published: 2009-05-28T00:00:00Z date_updated: 2021-01-12T07:41:59Z day: '28' doi: 10.1007/978-3-642-01001-9_27 extern: 1 intvolume: ' 5479' month: '05' page: 462 - 482 publication_status: published publisher: Springer publist_id: '3448' quality_controlled: 0 status: public title: A leakage resilient mode of operation type: conference volume: 5479 year: '2009' ... --- _id: '3304' abstract: - lang: eng text: Complex traits often involve interactions between different genetic loci. This can lead to sign epistasis, whereby mutations that are individually deleterious or neutral combine to confer a fitness benefit. In order to acquire the beneficial genotype, an asexual population must cross a fitness valley or plateau by first acquiring the deleterious or neutral intermediates. Here, we present a complete, intuitive theoretical description of the valley-crossing process across the full spectrum of possible parameter regimes. We calculate the rate at which a population crosses a fitness valley or plateau of arbitrary width, as a function of the mutation rates, the population size, and the fitnesses of the intermediates. We find that when intermediates are close to neutral, a large population can cross even wide fitness valleys remarkably quickly, so that valley-crossing dynamics may be common even when mutations that directly increase fitness are also possible. Thus the evolutionary dynamics of large populations can be sensitive to the structure of an extended region of the fitness landscape — the population may not take directly uphill paths in favor of paths across valleys and plateaus that lead eventually to fitter genotypes. In smaller populations, we find that below a threshold size, which depends on the width of the fitness valley and the strength of selection against intermediate genotypes, valley-crossing is much less likely and hence the evolutionary dynamics are less influenced by distant regions of the fitness landscape. author: - first_name: Daniel full_name: Daniel Weissman id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Michael full_name: Desai, Michael M last_name: Desai - first_name: Daniel full_name: Fisher, Daniel S last_name: Fisher - first_name: Marcus full_name: Feldman, Marcus W last_name: Feldman citation: ama: Weissman D, Desai M, Fisher D, Feldman M. The rate at which asexual populations cross fitness valleys. Theoretical Population Biology. 2009;75(4):286-300. doi:10.1016/j.tpb.2009.02.006 apa: Weissman, D., Desai, M., Fisher, D., & Feldman, M. (2009). The rate at which asexual populations cross fitness valleys. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2009.02.006 chicago: Weissman, Daniel, Michael Desai, Daniel Fisher, and Marcus Feldman. “The Rate at Which Asexual Populations Cross Fitness Valleys.” Theoretical Population Biology. Academic Press, 2009. https://doi.org/10.1016/j.tpb.2009.02.006. ieee: D. Weissman, M. Desai, D. Fisher, and M. Feldman, “The rate at which asexual populations cross fitness valleys,” Theoretical Population Biology, vol. 75, no. 4. Academic Press, pp. 286–300, 2009. ista: Weissman D, Desai M, Fisher D, Feldman M. 2009. The rate at which asexual populations cross fitness valleys. Theoretical Population Biology. 75(4), 286–300. mla: Weissman, Daniel, et al. “The Rate at Which Asexual Populations Cross Fitness Valleys.” Theoretical Population Biology, vol. 75, no. 4, Academic Press, 2009, pp. 286–300, doi:10.1016/j.tpb.2009.02.006. short: D. Weissman, M. Desai, D. Fisher, M. Feldman, Theoretical Population Biology 75 (2009) 286–300. date_created: 2018-12-11T12:02:34Z date_published: 2009-06-01T00:00:00Z date_updated: 2021-01-12T07:42:31Z day: '01' doi: 10.1016/j.tpb.2009.02.006 extern: 1 intvolume: ' 75' issue: '4' month: '06' page: 286 - 300 publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '3336' quality_controlled: 0 status: public title: The rate at which asexual populations cross fitness valleys type: journal_article volume: 75 year: '2009' ... --- _id: '337' abstract: - lang: eng text: 'The formation of hollow vs solid particles by means of the oxidation reaction of solid metal particles depends on the differential self-diffusivities of the reactants through the composite shell, the reaction probabilities at each interface, and the concentration and diffusivity of the element in solution. By means of a kinetic model of the oxidation process, we determine the phase diagrams for the geometry of the oxidized particles and propose four shell growth regimes. We experimentally illustrate the different growth scenarios by changing the conditions of oxidation of cadmium spherical crystals using different chalcogen precursors. ' article_processing_charge: No article_type: original author: - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Pablo full_name: Guardia, Pablo last_name: Guardia - first_name: Paul full_name: Alivisatos, Paul last_name: Alivisatos citation: ama: Cabot A, Ibáñez M, Guardia P, Alivisatos P. Reaction regimes on the synthesis of hollow particles by the Kirkendall effect. Journal of the American Chemical Society. 2009;131(32):11326-11328. doi:10.1021/ja903751p apa: Cabot, A., Ibáñez, M., Guardia, P., & Alivisatos, P. (2009). Reaction regimes on the synthesis of hollow particles by the Kirkendall effect. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja903751p chicago: Cabot, Andreu, Maria Ibáñez, Pablo Guardia, and Paul Alivisatos. “Reaction Regimes on the Synthesis of Hollow Particles by the Kirkendall Effect.” Journal of the American Chemical Society. ACS, 2009. https://doi.org/10.1021/ja903751p. ieee: A. Cabot, M. Ibáñez, P. Guardia, and P. Alivisatos, “Reaction regimes on the synthesis of hollow particles by the Kirkendall effect,” Journal of the American Chemical Society, vol. 131, no. 32. ACS, pp. 11326–11328, 2009. ista: Cabot A, Ibáñez M, Guardia P, Alivisatos P. 2009. Reaction regimes on the synthesis of hollow particles by the Kirkendall effect. Journal of the American Chemical Society. 131(32), 11326–11328. mla: Cabot, Andreu, et al. “Reaction Regimes on the Synthesis of Hollow Particles by the Kirkendall Effect.” Journal of the American Chemical Society, vol. 131, no. 32, ACS, 2009, pp. 11326–28, doi:10.1021/ja903751p. short: A. Cabot, M. Ibáñez, P. Guardia, P. Alivisatos, Journal of the American Chemical Society 131 (2009) 11326–11328. date_created: 2018-12-11T11:45:53Z date_published: 2009-01-01T00:00:00Z date_updated: 2021-01-12T07:43:00Z day: '01' doi: 10.1021/ja903751p extern: '1' intvolume: ' 131' issue: '32' language: - iso: eng month: '01' oa_version: None page: 11326 - 11328 publication: Journal of the American Chemical Society publication_status: published publisher: ACS publist_id: '7494' quality_controlled: '1' status: public title: Reaction regimes on the synthesis of hollow particles by the Kirkendall effect type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 131 year: '2009' ... --- _id: '3408' abstract: - lang: eng text: Mechanical forces govern physiological processes in all living organisms. Many cellular forces, for example, those generated in cyclic conformational changes of biological machines, have repetitive components. In apparent contrast, little is known about how dynamic protein structures respond to periodic mechanical information. Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics simulations to unfold single and multimeric ubiquitins with periodic forces. By using a coarse-grained representation, we were able to model forces with periods about 2 orders of magnitude longer than the protein's relaxation time. We found that even a moderate periodic force weakened the protein and shifted its unfolding pathways in a frequency- and amplitude-dependent manner. A complex dynamic response with secondary structure refolding and an increasing importance of local interactions was revealed. Importantly, repetitive forces with broadly distributed frequencies elicited very similar molecular responses compared to fixed-frequency forces. When testing the influence of pulling geometry on ubiquitin's mechanical stability, it was found that the linkage involved in the mechanical degradation of cellular proteins renders the protein remarkably insensitive to periodic forces. We also devised a complementary kinetic energy landscape model that traces these observations and explains periodic-force, single-molecule measurements. In turn, this analytical model is capable of predicting dynamic protein responses. These results provide new insights into ubiquitin mechanics and a potential mechanical role during protein degradation, as well as first frameworks for dynamic protein stability and the modeling of repetitive mechanical processes. author: - first_name: Piotr full_name: Szymczak, Piotr last_name: Szymczak - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Szymczak P, Janovjak HL. Periodic forces trigger a complex mechanical response in ubiquitin. Journal of Molecular Biology. 2009;390(3):443-456. doi:10.1016/j.jmb.2009.04.071 apa: Szymczak, P., & Janovjak, H. L. (2009). Periodic forces trigger a complex mechanical response in ubiquitin. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2009.04.071 chicago: Szymczak, Piotr, and Harald L Janovjak. “Periodic Forces Trigger a Complex Mechanical Response in Ubiquitin.” Journal of Molecular Biology. Elsevier, 2009. https://doi.org/10.1016/j.jmb.2009.04.071. ieee: P. Szymczak and H. L. Janovjak, “Periodic forces trigger a complex mechanical response in ubiquitin,” Journal of Molecular Biology, vol. 390, no. 3. Elsevier, pp. 443–456, 2009. ista: Szymczak P, Janovjak HL. 2009. Periodic forces trigger a complex mechanical response in ubiquitin. Journal of Molecular Biology. 390(3), 443–456. mla: Szymczak, Piotr, and Harald L. Janovjak. “Periodic Forces Trigger a Complex Mechanical Response in Ubiquitin.” Journal of Molecular Biology, vol. 390, no. 3, Elsevier, 2009, pp. 443–56, doi:10.1016/j.jmb.2009.04.071. short: P. Szymczak, H.L. Janovjak, Journal of Molecular Biology 390 (2009) 443–456. date_created: 2018-12-11T12:03:10Z date_published: 2009-07-17T00:00:00Z date_updated: 2021-01-12T07:43:16Z day: '17' doi: 10.1016/j.jmb.2009.04.071 extern: 1 intvolume: ' 390' issue: '3' month: '07' page: 443 - 456 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '2994' quality_controlled: 0 status: public title: Periodic forces trigger a complex mechanical response in ubiquitin type: journal_article volume: 390 year: '2009' ... --- _id: '3428' abstract: - lang: eng text: In this issue of Molecular Cell, Davies et al. (2009) work out a sequence of active cellular events that lead to the death of Escherichia coli in the presence of the drug hydroxyurea. article_processing_charge: No author: - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Bollenbach MT, Kishony R. Hydroxyurea triggers cellular responses that actively cause bacterial cell death. Molecular Cell. 2009;36(5):728-729. doi:10.1016/j.molcel.2009.11.027 apa: Bollenbach, M. T., & Kishony, R. (2009). Hydroxyurea triggers cellular responses that actively cause bacterial cell death. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2009.11.027 chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Hydroxyurea Triggers Cellular Responses That Actively Cause Bacterial Cell Death.” Molecular Cell. Cell Press, 2009. https://doi.org/10.1016/j.molcel.2009.11.027. ieee: M. T. Bollenbach and R. Kishony, “Hydroxyurea triggers cellular responses that actively cause bacterial cell death,” Molecular Cell, vol. 36, no. 5. Cell Press, pp. 728–729, 2009. ista: Bollenbach MT, Kishony R. 2009. Hydroxyurea triggers cellular responses that actively cause bacterial cell death. Molecular Cell. 36(5), 728–729. mla: Bollenbach, Mark Tobias, and Roy Kishony. “Hydroxyurea Triggers Cellular Responses That Actively Cause Bacterial Cell Death.” Molecular Cell, vol. 36, no. 5, Cell Press, 2009, pp. 728–29, doi:10.1016/j.molcel.2009.11.027. short: M.T. Bollenbach, R. Kishony, Molecular Cell 36 (2009) 728–729. date_created: 2018-12-11T12:03:17Z date_published: 2009-12-11T00:00:00Z date_updated: 2021-01-12T07:43:24Z day: '11' doi: 10.1016/j.molcel.2009.11.027 extern: '1' intvolume: ' 36' issue: '5' language: - iso: eng month: '12' oa_version: None page: 728 - 729 publication: Molecular Cell publication_status: published publisher: Cell Press publist_id: '2972' status: public title: Hydroxyurea triggers cellular responses that actively cause bacterial cell death type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2009' ... --- _id: '3503' abstract: - lang: eng text: 'We give polynomial-time algorithms for computing the values of Markov decision processes (MDPs) with limsup and liminf objectives. A real-valued reward is assigned to each state, and the value of an infinite path in the MDP is the limsup (resp. liminf) of all rewards along the path. The value of an MDP is the maximal expected value of an infinite path that can be achieved by resolving the decisions of the MDP. Using our result on MDPs, we show that turn-based stochastic games with limsup and liminf objectives can be solved in NP ∩ coNP. ' alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Henzinger TA. Probabilistic systems with limsup and liminf objectives. In: Vol 5489. Springer; 2009:32-45. doi:10.1007/978-3-642-03092-5_4' apa: 'Chatterjee, K., & Henzinger, T. A. (2009). Probabilistic systems with limsup and liminf objectives (Vol. 5489, pp. 32–45). Presented at the ILC: Infinity in Logic and Computation, Springer. https://doi.org/10.1007/978-3-642-03092-5_4' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Probabilistic Systems with Limsup and Liminf Objectives,” 5489:32–45. Springer, 2009. https://doi.org/10.1007/978-3-642-03092-5_4. ieee: 'K. Chatterjee and T. A. Henzinger, “Probabilistic systems with limsup and liminf objectives,” presented at the ILC: Infinity in Logic and Computation, 2009, vol. 5489, pp. 32–45.' ista: 'Chatterjee K, Henzinger TA. 2009. Probabilistic systems with limsup and liminf objectives. ILC: Infinity in Logic and Computation, LNCS, vol. 5489, 32–45.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Probabilistic Systems with Limsup and Liminf Objectives. Vol. 5489, Springer, 2009, pp. 32–45, doi:10.1007/978-3-642-03092-5_4. short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2009, pp. 32–45. conference: name: 'ILC: Infinity in Logic and Computation' date_created: 2018-12-11T12:03:40Z date_published: 2009-12-15T00:00:00Z date_updated: 2021-01-12T07:43:54Z day: '15' doi: 10.1007/978-3-642-03092-5_4 extern: 1 intvolume: ' 5489' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0809.1465 month: '12' oa: 1 page: 32 - 45 publication_status: published publisher: Springer publist_id: '2884' quality_controlled: 0 status: public title: Probabilistic systems with limsup and liminf objectives type: conference volume: 5489 year: '2009' ... --- _id: '3699' abstract: - lang: eng text: Kernel Canonical Correlation Analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, CCA learns representations tied more closely to underlying process generating the the data and can ignore high-variance noise directions. However, for data where acquisition in a given modality is expensive or otherwise limited, CCA may suffer from small sample effects. We propose to use semisupervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of CCA on human fMRI data, with regression to single and multivariate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of CCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing. author: - first_name: Matthew full_name: Blaschko,Matthew B last_name: Blaschko - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Andreas full_name: Bartels, Andreas last_name: Bartels citation: ama: Blaschko M, Lampert C, Bartels A. Semi-Supervised Analysis of Human FMRI Data. Berlin Institute of Technology; 2009. apa: 'Blaschko, M., Lampert, C., & Bartels, A. (2009). Semi-supervised analysis of human fMRI data. BBCI: Berlin Brain-Computer Interface Workshop - Advances in Neurotechnology. Berlin Institute of Technology.' chicago: 'Blaschko, Matthew, Christoph Lampert, and Andreas Bartels. Semi-Supervised Analysis of Human FMRI Data. BBCI: Berlin Brain-Computer Interface Workshop - Advances in Neurotechnology. Berlin Institute of Technology, 2009.' ieee: M. Blaschko, C. Lampert, and A. Bartels, Semi-supervised analysis of human fMRI data. Berlin Institute of Technology, 2009. ista: Blaschko M, Lampert C, Bartels A. 2009. Semi-supervised analysis of human fMRI data, Berlin Institute of Technology,p. mla: 'Blaschko, Matthew, et al. “Semi-Supervised Analysis of Human FMRI Data.” BBCI: Berlin Brain-Computer Interface Workshop - Advances in Neurotechnology, Berlin Institute of Technology, 2009.' short: M. Blaschko, C. Lampert, A. Bartels, Semi-Supervised Analysis of Human FMRI Data, Berlin Institute of Technology, 2009. date_created: 2018-12-11T12:04:41Z date_published: 2009-07-10T00:00:00Z date_updated: 2019-04-26T07:22:33Z day: '10' extern: 1 main_file_link: - open_access: '0' url: http://pubman.mpdl.mpg.de/pubman/faces/viewItemOverviewPage.jsp?itemId=escidoc:1789281 month: '07' publication: 'BBCI: Berlin Brain-Computer Interface Workshop - Advances in Neurotechnology' publication_status: published publisher: Berlin Institute of Technology publist_id: '2661' quality_controlled: 0 status: public title: Semi-supervised analysis of human fMRI data type: conference_poster year: '2009' ... --- _id: '3703' abstract: - lang: eng text: Recent research has shown that the use of contextual cues significantly improves performance in sliding window type localization systems. In this work, we propose a method that incorporates both global and local context information through appropriately defined kernel functions. In particular, we make use of a weighted combination of kernels defined over local spatial regions, as well as a global context kernel. The relative importance of the context contributions is learned automatically, and the resulting discriminant function is of a form such that localization at test time can be solved efficiently using a branch and bound optimization scheme. By specifying context directly with a kernel learning approach, we achieve high localization accuracy with a simple and efficient representation. This is in contrast to other systems that incorporate context for which expensive inference needs to be done at test time. We show experimentally on the PASCAL VOC datasets that the inclusion of context can significantly improve localization performance, provided the relative contributions of context cues are learned appropriately. acknowledgement: The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007- 2013) / ERC grant agreement no. 228180. This work was funded in part by the EC project CLASS, IST 027978, and the PASCAL2 network of excellence. The first author is supported by the Royal Academy of Engineering through a Newton International Fellowship. alternative_title: - Proceedings of the BMVC author: - first_name: Matthew full_name: Blaschko,Matthew B last_name: Blaschko - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Blaschko M, Lampert C. Object localization with global and local context kernels. In: BMVA Press; 2009:1-11. doi:10.5244/C.23.63' apa: 'Blaschko, M., & Lampert, C. (2009). Object localization with global and local context kernels (pp. 1–11). Presented at the BMVC: British Machine Vision Conference, BMVA Press. https://doi.org/10.5244/C.23.63' chicago: Blaschko, Matthew, and Christoph Lampert. “Object Localization with Global and Local Context Kernels,” 1–11. BMVA Press, 2009. https://doi.org/10.5244/C.23.63. ieee: 'M. Blaschko and C. Lampert, “Object localization with global and local context kernels,” presented at the BMVC: British Machine Vision Conference, 2009, pp. 1–11.' ista: 'Blaschko M, Lampert C. 2009. Object localization with global and local context kernels. BMVC: British Machine Vision Conference, Proceedings of the BMVC, , 1–11.' mla: Blaschko, Matthew, and Christoph Lampert. Object Localization with Global and Local Context Kernels. BMVA Press, 2009, pp. 1–11, doi:10.5244/C.23.63. short: M. Blaschko, C. Lampert, in:, BMVA Press, 2009, pp. 1–11. conference: name: 'BMVC: British Machine Vision Conference' date_created: 2018-12-11T12:04:42Z date_published: 2009-09-10T00:00:00Z date_updated: 2021-01-12T07:51:36Z day: '10' doi: 10.5244/C.23.63 extern: 1 main_file_link: - open_access: '0' url: http://www.bmva.org/bmvc/2009/Papers/Paper228/Paper228.pdf month: '09' page: 1 - 11 publication_status: published publisher: BMVA Press publist_id: '2655' quality_controlled: 0 status: public title: Object localization with global and local context kernels tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference year: '2009' ...