--- _id: '13422' abstract: - lang: eng text: 'Make like a leaf: The synthesis and characterization of a family of “flowerlike” Au/Fe3O4 nanoparticles is described, whereby Fe3O4 “leaves” adhere to a gold core (see image). The size and numbers of iron oxide domains can be adjusted flexibly by changing the proportion of the starting materials and the reaction time.' article_processing_charge: No article_type: original author: - first_name: Yanhu full_name: Wei, Yanhu last_name: Wei - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Anatoliy O. full_name: Pinchuk, Anatoliy O. last_name: Pinchuk - first_name: Bartosz A. full_name: Grzybowski, Bartosz A. last_name: Grzybowski citation: ama: Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers.” Small. 2008;4(10):1635-1639. doi:10.1002/smll.200800511 apa: Wei, Y., Klajn, R., Pinchuk, A. O., & Grzybowski, B. A. (2008). Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers.” Small. Wiley. https://doi.org/10.1002/smll.200800511 chicago: Wei, Yanhu, Rafal Klajn, Anatoliy O. Pinchuk, and Bartosz A. Grzybowski. “Synthesis, Shape Control, and Optical Properties of Hybrid Au/Fe3O4 ‘Nanoflowers.’” Small. Wiley, 2008. https://doi.org/10.1002/smll.200800511. ieee: Y. Wei, R. Klajn, A. O. Pinchuk, and B. A. Grzybowski, “Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 ‘nanoflowers,’” Small, vol. 4, no. 10. Wiley, pp. 1635–1639, 2008. ista: Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. 2008. Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers”. Small. 4(10), 1635–1639. mla: Wei, Yanhu, et al. “Synthesis, Shape Control, and Optical Properties of Hybrid Au/Fe3O4 ‘Nanoflowers.’” Small, vol. 4, no. 10, Wiley, 2008, pp. 1635–39, doi:10.1002/smll.200800511. short: Y. Wei, R. Klajn, A.O. Pinchuk, B.A. Grzybowski, Small 4 (2008) 1635–1639. date_created: 2023-08-01T10:30:42Z date_published: 2008-10-09T00:00:00Z date_updated: 2023-08-08T11:14:50Z day: '09' doi: 10.1002/smll.200800511 extern: '1' external_id: pmid: - '18636405' intvolume: ' 4' issue: '10' keyword: - Biomaterials - Biotechnology - General Materials Science - General Chemistry language: - iso: eng month: '10' oa_version: None page: 1635-1639 pmid: 1 publication: Small publication_identifier: eissn: - 1613-6829 issn: - 1613-6810 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers” type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2008' ... --- _id: '517' article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics Research. 2008;89(5-6):475-477. doi:10.1017/S0016672308009683' apa: 'Barton, N. H. (2008). Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009683' chicago: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” Genetics Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009683.' ieee: 'N. H. Barton, “Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.' ista: 'Barton NH. 2008. Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics Research. 89(5–6), 475–477.' mla: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” Genetics Research, vol. 89, no. 5–6, Cambridge University Press, 2008, pp. 475–77, doi:10.1017/S0016672308009683.' short: N.H. Barton, Genetics Research 89 (2008) 475–477. date_created: 2018-12-11T11:46:55Z date_published: 2008-10-29T00:00:00Z date_updated: 2024-02-14T09:51:09Z day: '29' department: - _id: NiBa doi: 10.1017/S0016672308009683 intvolume: ' 89' issue: 5-6 language: - iso: eng month: '10' oa_version: None page: 475 - 477 publication: Genetics Research publication_status: published publisher: Cambridge University Press publist_id: '7302' quality_controlled: '1' scopus_import: '1' status: public title: 'Identity and coalescence in structured populations: A commentary on ''Inbreeding coefficients and coalescence times'' by Montgomery Slatkin' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2008' ... --- _id: '1035' abstract: - lang: eng text: We explore the rich internal structure of Cs2 Feshbach molecules. Pure ultracold molecular samples are prepared in a CO2 -laser trap, and a multitude of weakly bound states is populated by elaborate magnetic-field ramping techniques. Our methods use different Feshbach resonances as input ports and various internal level crossings for controlled state transfer. We populate higher partial-wave states of up to eight units of rotational angular momentum (l -wave states). We investigate the molecular structure by measurements of the magnetic moments for various states. Avoided level crossings between different molecular states are characterized through the changes in magnetic moment and by a Landau-Zener tunneling method. Based on microwave spectroscopy, we present a precise measurement of the magnetic-field-dependent binding energy of the weakly bound s -wave state that is responsible for the large background scattering length of Cs. This state is of particular interest because of its quantum-halo character. acknowledgement: The authors thank E. Tiesinga, P. Julienne, and C. Williams for providing invaluable theoretical input and J. Hutson and A. Simoni for helpful discussions. The authors acknowledge support by the Austrian Science Fund (FWF) within SFB 15 (project part 16) and by the European Union within the Cold Molecules TMR Network under Contract No. HPRN-CT-2002-00290. One of the authors (M.M.) acknowledges support within the Ph.D. program DOC of the Austrian Academy of Sciences, and two of the authors (F.F., C.C.) acknowledge support within the Lise Meitner program of the FWF. One of the authors (S.K.) is supported by the European Community, Marie Curie Intra-European program. article_processing_charge: No author: - first_name: Michael full_name: Mark, Michael last_name: Mark - first_name: Francesca full_name: Ferlaino, Francesca last_name: Ferlaino - first_name: Steven full_name: Knoop, Steven last_name: Knoop - 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: Tobias full_name: Kraemer, Tobias last_name: Kraemer - first_name: Cheng full_name: Chin, Cheng last_name: Chin - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl - first_name: Rudolf full_name: Grimm, Rudolf last_name: Grimm citation: ama: Mark M, Ferlaino F, Knoop S, et al. Spectroscopy of ultracold trapped cesium Feshbach molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 2007;76(4). doi:10.1103/PhysRevA.76.042514 apa: Mark, M., Ferlaino, F., Knoop, S., Danzl, J. G., Kraemer, T., Chin, C., … Grimm, R. (2007). Spectroscopy of ultracold trapped cesium Feshbach molecules. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.76.042514 chicago: Mark, Michael, Francesca Ferlaino, Steven Knoop, Johann G Danzl, Tobias Kraemer, Cheng Chin, Hanns Nägerl, and Rudolf Grimm. “Spectroscopy of Ultracold Trapped Cesium Feshbach Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2007. https://doi.org/10.1103/PhysRevA.76.042514. ieee: M. Mark et al., “Spectroscopy of ultracold trapped cesium Feshbach molecules,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 76, no. 4. American Physical Society, 2007. ista: Mark M, Ferlaino F, Knoop S, Danzl JG, Kraemer T, Chin C, Nägerl H, Grimm R. 2007. Spectroscopy of ultracold trapped cesium Feshbach molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 76(4). mla: Mark, Michael, et al. “Spectroscopy of Ultracold Trapped Cesium Feshbach Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 76, no. 4, American Physical Society, 2007, doi:10.1103/PhysRevA.76.042514. short: M. Mark, F. Ferlaino, S. Knoop, J.G. Danzl, T. Kraemer, C. Chin, H. Nägerl, R. Grimm, Physical Review A - Atomic, Molecular, and Optical Physics 76 (2007). date_created: 2018-12-11T11:49:48Z date_published: 2007-10-25T00:00:00Z date_updated: 2021-01-12T06:47:49Z day: '25' doi: 10.1103/PhysRevA.76.042514 extern: '1' intvolume: ' 76' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/0706.1041 month: '10' oa: 1 oa_version: None publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '6354' status: public title: Spectroscopy of ultracold trapped cesium Feshbach molecules type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 76 year: '2007' ... --- _id: '11116' abstract: - lang: eng text: The metazoan nuclear envelope (NE) breaks down and re-forms during each cell cycle. Nuclear pore complexes (NPCs), which allow nucleocytoplasmic transport during interphase, assemble into the re-forming NE at the end of mitosis. Using in vitro NE assembly, we show that the vertebrate homologue of MEL-28 (maternal effect lethal), a recently discovered NE component in Caenorhabditis elegans, functions in postmitotic NPC assembly. MEL-28 interacts with the Nup107–160 complex (Nup for nucleoporin), an important building block of the NPC, and is essential for the recruitment of the Nup107–160 complex to chromatin. We suggest that MEL-28 acts as a seeding point for NPC assembly. article_processing_charge: No article_type: original author: - first_name: Cerstin full_name: Franz, Cerstin last_name: Franz - first_name: Rudolf full_name: Walczak, Rudolf last_name: Walczak - first_name: Sevil full_name: Yavuz, Sevil last_name: Yavuz - first_name: Rachel full_name: Santarella, Rachel last_name: Santarella - first_name: Marc full_name: Gentzel, Marc last_name: Gentzel - first_name: Peter full_name: Askjaer, Peter last_name: Askjaer - first_name: Vincent full_name: Galy, Vincent last_name: Galy - 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: Iain W full_name: Mattaj, Iain W last_name: Mattaj - first_name: Wolfram full_name: Antonin, Wolfram last_name: Antonin citation: ama: Franz C, Walczak R, Yavuz S, et al. MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO reports. 2007;8(2):165-172. doi:10.1038/sj.embor.7400889 apa: Franz, C., Walczak, R., Yavuz, S., Santarella, R., Gentzel, M., Askjaer, P., … Antonin, W. (2007). MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO Reports. EMBO. https://doi.org/10.1038/sj.embor.7400889 chicago: Franz, Cerstin, Rudolf Walczak, Sevil Yavuz, Rachel Santarella, Marc Gentzel, Peter Askjaer, Vincent Galy, Martin Hetzer, Iain W Mattaj, and Wolfram Antonin. “MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins to Chromatin and Postmitotic Nuclear Pore Complex Assembly.” EMBO Reports. EMBO, 2007. https://doi.org/10.1038/sj.embor.7400889. ieee: C. Franz et al., “MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly,” EMBO reports, vol. 8, no. 2. EMBO, pp. 165–172, 2007. ista: Franz C, Walczak R, Yavuz S, Santarella R, Gentzel M, Askjaer P, Galy V, Hetzer M, Mattaj IW, Antonin W. 2007. MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO reports. 8(2), 165–172. mla: Franz, Cerstin, et al. “MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins to Chromatin and Postmitotic Nuclear Pore Complex Assembly.” EMBO Reports, vol. 8, no. 2, EMBO, 2007, pp. 165–72, doi:10.1038/sj.embor.7400889. short: C. Franz, R. Walczak, S. Yavuz, R. Santarella, M. Gentzel, P. Askjaer, V. Galy, M. Hetzer, I.W. Mattaj, W. Antonin, EMBO Reports 8 (2007) 165–172. date_created: 2022-04-07T07:56:13Z date_published: 2007-01-19T00:00:00Z date_updated: 2022-07-18T08:56:40Z day: '19' doi: 10.1038/sj.embor.7400889 extern: '1' external_id: pmid: - '17235358' intvolume: ' 8' issue: '2' keyword: - Genetics - Molecular Biology - Biochemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/sj.embor.7400889 month: '01' oa: 1 oa_version: Published Version page: 165-172 pmid: 1 publication: EMBO reports publication_identifier: eissn: - 1469-3178 issn: - 1469-221X publication_status: published publisher: EMBO quality_controlled: '1' scopus_import: '1' status: public title: MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 8 year: '2007' ... --- _id: '11115' abstract: - lang: eng text: The formation of the nuclear envelope (NE) around chromatin is a major membrane-remodelling event that occurs during cell division of metazoa. It is unclear whether the nuclear membrane reforms by the fusion of NE fragments or if it re-emerges from an intact tubular network of the endoplasmic reticulum (ER). Here, we show that NE formation and expansion requires a tubular ER network and occurs efficiently in the presence of the membrane fusion inhibitor GTPγS. Chromatin recruitment of membranes, which is initiated by tubule-end binding, followed by the formation, expansion and sealing of flat membrane sheets, is mediated by DNA-binding proteins residing in the ER. Thus, chromatin plays an active role in reshaping of the ER during NE formation. article_processing_charge: No article_type: original author: - first_name: Daniel J. full_name: Anderson, Daniel J. last_name: Anderson - 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, Hetzer M. Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nature Cell Biology. 2007;9(10):1160-1166. doi:10.1038/ncb1636 apa: Anderson, D. J., & Hetzer, M. (2007). Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/ncb1636 chicago: Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by Chromatin-Mediated Reorganization of the Endoplasmic Reticulum.” Nature Cell Biology. Springer Nature, 2007. https://doi.org/10.1038/ncb1636. ieee: D. J. Anderson and M. Hetzer, “Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum,” Nature Cell Biology, vol. 9, no. 10. Springer Nature, pp. 1160–1166, 2007. ista: Anderson DJ, Hetzer M. 2007. Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nature Cell Biology. 9(10), 1160–1166. mla: Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by Chromatin-Mediated Reorganization of the Endoplasmic Reticulum.” Nature Cell Biology, vol. 9, no. 10, Springer Nature, 2007, pp. 1160–66, doi:10.1038/ncb1636. short: D.J. Anderson, M. Hetzer, Nature Cell Biology 9 (2007) 1160–1166. date_created: 2022-04-07T07:56:04Z date_published: 2007-09-09T00:00:00Z date_updated: 2022-07-18T08:56:38Z day: '09' doi: 10.1038/ncb1636 extern: '1' external_id: pmid: - '17828249' intvolume: ' 9' issue: '10' keyword: - Cell Biology language: - iso: eng month: '09' oa_version: None page: 1160-1166 pmid: 1 publication: Nature Cell Biology publication_identifier: eissn: - 1476-4679 issn: - 1465-7392 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 9 year: '2007' ... --- _id: '11884' abstract: - lang: eng text: About 20% of the world's population uses the Web, and a large majority thereof uses Web search engines to find information. As a result, many Web researchers are devoting much effort to improving the speed and capability of search technology. article_processing_charge: No article_type: review author: - 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: Henzinger MH. Search technologies for the internet. Science. 2007;317(5837):468-471. doi:10.1126/science.1126557 apa: Henzinger, M. H. (2007). Search technologies for the internet. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1126557 chicago: Henzinger, Monika H. “Search Technologies for the Internet.” Science. American Association for the Advancement of Science, 2007. https://doi.org/10.1126/science.1126557. ieee: M. H. Henzinger, “Search technologies for the internet,” Science, vol. 317, no. 5837. American Association for the Advancement of Science, pp. 468–471, 2007. ista: Henzinger MH. 2007. Search technologies for the internet. Science. 317(5837), 468–471. mla: Henzinger, Monika H. “Search Technologies for the Internet.” Science, vol. 317, no. 5837, American Association for the Advancement of Science, 2007, pp. 468–71, doi:10.1126/science.1126557. short: M.H. Henzinger, Science 317 (2007) 468–471. date_created: 2022-08-17T07:30:07Z date_published: 2007-07-27T00:00:00Z date_updated: 2023-02-17T14:07:49Z day: '27' doi: 10.1126/science.1126557 extern: '1' external_id: pmid: - '17656714' intvolume: ' 317' issue: '5837' language: - iso: eng month: '07' oa_version: None page: 468-471 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Search technologies for the internet type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 317 year: '2007' ... --- _id: '11924' abstract: - lang: eng text: 'How much can smart combinatorial algorithms improve web search engines? To address this question we will describe three algorithms that have had a positive impact on web search engines: The PageRank algorithm, algorithms for finding near-duplicate web pages, and algorithms for index server loadbalancing.' article_processing_charge: No author: - 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: 'Henzinger MH. Combinatorial algorithms for web search engines: three success stories. In: 18th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial & Applied Mathematics; 2007:1022-1026.' apa: 'Henzinger, M. H. (2007). Combinatorial algorithms for web search engines: three success stories. In 18th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1022–1026). New Orleans, LA, United States: Society for Industrial & Applied Mathematics.' chicago: 'Henzinger, Monika H. “Combinatorial Algorithms for Web Search Engines: Three Success Stories.” In 18th Annual ACM-SIAM Symposium on Discrete Algorithms, 1022–26. Society for Industrial & Applied Mathematics, 2007.' ieee: 'M. H. Henzinger, “Combinatorial algorithms for web search engines: three success stories,” in 18th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA, United States, 2007, pp. 1022–1026.' ista: 'Henzinger MH. 2007. Combinatorial algorithms for web search engines: three success stories. 18th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1022–1026.' mla: 'Henzinger, Monika H. “Combinatorial Algorithms for Web Search Engines: Three Success Stories.” 18th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial & Applied Mathematics, 2007, pp. 1022–26.' short: M.H. Henzinger, in:, 18th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial & Applied Mathematics, 2007, pp. 1022–1026. conference: end_date: 2007-01-09 location: New Orleans, LA, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2007-01-07 date_created: 2022-08-18T12:37:03Z date_published: 2007-01-01T00:00:00Z date_updated: 2023-02-17T12:06:29Z day: '01' extern: '1' language: - iso: eng month: '01' oa_version: None page: 1022-1026 publication: 18th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: isbn: - '9780898716245' publication_status: published publisher: Society for Industrial & Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: 'Combinatorial algorithms for web search engines: three success stories' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2007' ... --- _id: '128' abstract: - lang: eng text: 'A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described. This long tuning range is achieved by simultaneously ramping the external cavity length with the laser injection current. The laser output pointing remains fixed, independent of its frequency because of the cover slip cavity design. This system is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate with lithium vapor and lithium atom beam experiments. ' acknowledgement: "National Science Foundation\r\nThis work was supported with NSF Grant No. PHY-0653623. We thank Dr. W. Bickel and Dr. J. Jones for diagnostic equipment, K. Guerin for assistance with mechanical drawings, and M. Parker of Rincon Research Inc. for optics components." article_number: '106108' author: - first_name: Adra full_name: Carr, Adra last_name: Carr - first_name: Yancey full_name: Serchest, Yancey last_name: Serchest - 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: John full_name: Perreault, John last_name: Perreault - first_name: Vincent full_name: Lonij, Vincent last_name: Lonij - first_name: Alexander full_name: Cronin, Alexander last_name: Cronin citation: ama: Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. Cover slip external cavity diode laser. Review of Scientific Instruments. 2007;78(10). doi:10.1063/1.2801006 apa: Carr, A., Serchest, Y., Waitukaitis, S. R., Perreault, J., Lonij, V., & Cronin, A. (2007). Cover slip external cavity diode laser. Review of Scientific Instruments. American Institute of Physics. https://doi.org/10.1063/1.2801006 chicago: Carr, Adra, Yancey Serchest, Scott R Waitukaitis, John Perreault, Vincent Lonij, and Alexander Cronin. “Cover Slip External Cavity Diode Laser.” Review of Scientific Instruments. American Institute of Physics, 2007. https://doi.org/10.1063/1.2801006. ieee: A. Carr, Y. Serchest, S. R. Waitukaitis, J. Perreault, V. Lonij, and A. Cronin, “Cover slip external cavity diode laser,” Review of Scientific Instruments, vol. 78, no. 10. American Institute of Physics, 2007. ista: Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. 2007. Cover slip external cavity diode laser. Review of Scientific Instruments. 78(10), 106108. mla: Carr, Adra, et al. “Cover Slip External Cavity Diode Laser.” Review of Scientific Instruments, vol. 78, no. 10, 106108, American Institute of Physics, 2007, doi:10.1063/1.2801006. short: A. Carr, Y. Serchest, S.R. Waitukaitis, J. Perreault, V. Lonij, A. Cronin, Review of Scientific Instruments 78 (2007). date_created: 2018-12-11T11:44:46Z date_published: 2007-10-29T00:00:00Z date_updated: 2021-01-12T06:49:35Z day: '29' doi: 10.1063/1.2801006 extern: '1' external_id: arxiv: - '0708.0014' intvolume: ' 78' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/0708.0014 month: '10' oa: 1 oa_version: Preprint publication: Review of Scientific Instruments publication_status: published publisher: American Institute of Physics publist_id: '7925' quality_controlled: '1' status: public title: Cover slip external cavity diode laser type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 78 year: '2007' ... --- _id: '1297' abstract: - lang: eng text: In flies, the large tangential cells of the lobula plate represent an important processing center for visual navigation based on optic flow. Although the visual response properties of these cells have been well studied in blowflies, information on their synaptic organization is mostly lacking. Here we study the distribution of presynaptic release and postsynaptic inhibitory sites in the same set of cells in Drosophila melanogaster. By making use of transgenic tools and immunohistochemistry, our results suggest that HS and VS cells of Drosophila express γ-aminobutyric acid (GABA) receptors in their dendritic region within the lobula plate, thus being postsynaptic to inhibitory input there. At their axon terminals in the protocerebrum, both cell types express synaptobrevin, suggesting the presence of presynaptic specializations there. HS- and VS-cell terminals additionally show evidence for postsynaptic GABAergic input, superimposed on this synaptic polarity. Our findings are in line with the general circuit for visual motion detection and receptive field properties as postulated from electrophysiological and optical recordings in blowflies, suggesting a similar functional organization of lobula plate tangential cells in the two species. 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: 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, Borst A, Reiff D. Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. Journal of Comparative Neurology. 2007;502(4):598-610. doi:10.1002/cne.21319' apa: 'Raghu, S., Jösch, M. A., Borst, A., & Reiff, D. (2007). Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.21319' chicago: 'Raghu, Shamprasad, Maximilian A Jösch, Alexander Borst, and Dierk Reiff. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.” Journal of Comparative Neurology. Wiley-Blackwell, 2007. https://doi.org/10.1002/cne.21319.' ieee: 'S. Raghu, M. A. Jösch, A. Borst, and D. Reiff, “Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites,” Journal of Comparative Neurology, vol. 502, no. 4. Wiley-Blackwell, pp. 598–610, 2007.' ista: 'Raghu S, Jösch MA, Borst A, Reiff D. 2007. Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. Journal of Comparative Neurology. 502(4), 598–610.' mla: 'Raghu, Shamprasad, et al. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.” Journal of Comparative Neurology, vol. 502, no. 4, Wiley-Blackwell, 2007, pp. 598–610, doi:10.1002/cne.21319.' short: S. Raghu, M.A. Jösch, A. Borst, D. Reiff, Journal of Comparative Neurology 502 (2007) 598–610. date_created: 2018-12-11T11:51:13Z date_published: 2007-06-01T00:00:00Z date_updated: 2021-01-12T06:49:42Z day: '01' doi: 10.1002/cne.21319 extern: 1 intvolume: ' 502' issue: '4' month: '06' page: 598 - 610 publication: Journal of Comparative Neurology publication_status: published publisher: Wiley-Blackwell publist_id: '5974' quality_controlled: 0 status: public title: 'Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites' type: journal_article volume: 502 year: '2007' ... --- _id: '167' abstract: - lang: eng text: This book contains research articles on Diophantine Geometry, written by participants of a research program held at the Ennio De Giorgi Mathematical Research Center in Pisa, Italy, during the period April – July 2005. The authors are eminent experts in the field. Several subfields of the main topic are presented; the volume thus is particularly useful to get a broad overview of recent research developments. alternative_title: - CRM Series 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. Simultaneous equal sums of three powers. In: Zannier U, ed. Diophantine Geometry. Vol 4. Edizioni della Normale; 2007:93-100.' apa: Browning, T. D., & Heath Brown, R. (2007). Simultaneous equal sums of three powers. In U. Zannier (Ed.), Diophantine Geometry (Vol. 4, pp. 93–100). Edizioni della Normale. chicago: Browning, Timothy D, and Roger Heath Brown. “Simultaneous Equal Sums of Three Powers.” In Diophantine Geometry, edited by Umberto Zannier, 4:93–100. Edizioni della Normale, 2007. ieee: T. D. Browning and R. Heath Brown, “Simultaneous equal sums of three powers,” in Diophantine Geometry, vol. 4, U. Zannier, Ed. Edizioni della Normale, 2007, pp. 93–100. ista: 'Browning TD, Heath Brown R. 2007.Simultaneous equal sums of three powers. In: Diophantine Geometry. CRM Series, vol. 4, 93–100.' mla: Browning, Timothy D., and Roger Heath Brown. “Simultaneous Equal Sums of Three Powers.” Diophantine Geometry, edited by Umberto Zannier, vol. 4, Edizioni della Normale, 2007, pp. 93–100. short: T.D. Browning, R. Heath Brown, in:, U. Zannier (Ed.), Diophantine Geometry, Edizioni della Normale, 2007, pp. 93–100. date_created: 2018-12-11T11:44:59Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T06:52:24Z day: '01' editor: - first_name: Umberto full_name: Zannier, Umberto last_name: Zannier extern: '1' external_id: arxiv: - '0509152' intvolume: ' 4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/math/0509152 month: '01' oa: 1 oa_version: Preprint page: 93 - 100 publication: Diophantine Geometry publication_status: published publisher: Edizioni della Normale publist_id: '7754' quality_controlled: '1' status: public title: Simultaneous equal sums of three powers type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2007' ... --- _id: '1750' abstract: - lang: eng text: The authors investigate the composition profile of SiGe islands after capping with Si to form quantum dots, using a two step etching procedure and atomic force microscopy. Initially, the Si capping layers are removed by etching selectively Si over Ge and then the composition of the disclosed islands is addressed by selectively etching Ge over Si. For samples grown at 580 °C the authors show that even when overgrowth leads to a flat Si surface and the islands undergo strong morphological changes, a Ge-rich core region is still preserved in the dot. At high growth and overgrowth temperatures (740 °C), the experiments show that the newly formed base of the buried islands is more Si rich than their top. Furthermore, the authors find that for the growth conditions used, no lateral motion takes place during capping. author: - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Mathieu full_name: Stoffel, Mathieu last_name: Stoffel - first_name: Armando full_name: Rastelli, Armando last_name: Rastelli - first_name: Oliver full_name: Schmidt, Oliver G last_name: Schmidt - first_name: Klaus full_name: Kern, Klaus last_name: Kern - first_name: Jerry full_name: Tersoff, Jerry last_name: Tersoff citation: ama: Katsaros G, Stoffel M, Rastelli A, Schmidt O, Kern K, Tersoff J. Three-dimensional isocompositional profiles of buried SiGeSi (001) islands. Applied Physics Letters. 2007;91(1). doi:10.1063/1.2752730 apa: Katsaros, G., Stoffel, M., Rastelli, A., Schmidt, O., Kern, K., & Tersoff, J. (2007). Three-dimensional isocompositional profiles of buried SiGeSi (001) islands. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.2752730 chicago: Katsaros, Georgios, Mathieu Stoffel, Armando Rastelli, Oliver Schmidt, Klaus Kern, and Jerry Tersoff. “Three-Dimensional Isocompositional Profiles of Buried SiGeSi (001) Islands.” Applied Physics Letters. American Institute of Physics, 2007. https://doi.org/10.1063/1.2752730. ieee: G. Katsaros, M. Stoffel, A. Rastelli, O. Schmidt, K. Kern, and J. Tersoff, “Three-dimensional isocompositional profiles of buried SiGeSi (001) islands,” Applied Physics Letters, vol. 91, no. 1. American Institute of Physics, 2007. ista: Katsaros G, Stoffel M, Rastelli A, Schmidt O, Kern K, Tersoff J. 2007. Three-dimensional isocompositional profiles of buried SiGeSi (001) islands. Applied Physics Letters. 91(1). mla: Katsaros, Georgios, et al. “Three-Dimensional Isocompositional Profiles of Buried SiGeSi (001) Islands.” Applied Physics Letters, vol. 91, no. 1, American Institute of Physics, 2007, doi:10.1063/1.2752730. short: G. Katsaros, M. Stoffel, A. Rastelli, O. Schmidt, K. Kern, J. Tersoff, Applied Physics Letters 91 (2007). date_created: 2018-12-11T11:53:48Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T06:52:58Z day: '01' doi: 10.1063/1.2752730 extern: 1 intvolume: ' 91' issue: '1' month: '01' publication: Applied Physics Letters publication_status: published publisher: American Institute of Physics publist_id: '5375' quality_controlled: 0 status: public title: Three-dimensional isocompositional profiles of buried SiGeSi (001) islands type: journal_article volume: 91 year: '2007' ... --- _id: '1762' abstract: - lang: eng text: In quantum information science, the phase of a wave function plays an important role in encoding information. Although most experiments in this field rely on dynamic effects to manipulate this information, an alternative approach is to use geometric phase, which has been argued to have potential fault tolerance. We demonstrated the controlled accumulation of a geometric phase, Berry's phase, in a superconducting qubit; we manipulated the qubit geometrically by means of microwave radiation and observed the accumulated phase in an interference experiment. We found excellent agreement with Berry's predictions and also observed a geometry-dependent contribution to dephasing. acknowledgement: Supported by the EC via an Intra-European Marie Curie Fellowship (P.J.L.), the Natural Sciences and Engineering Research Council of Canada, Canadian Institute for Advanced Research, and Fonds Québécois de la Recherche sur la Nature et les Technologies (A.B.), the National Security Agency under the Army Research Office, NSF, and Yale University (D.I.S., L.F., and R.J.S.), Consiglio Nazionale delle Ricerche–Istituto di Cibernetica, Pozzuoli, Italy (L.F.), the Ontario Research Development Challenge Fund and Mathematics of Information Technology and Complex Systems (J.M.G.), the Swiss National Science Foundation, and ETH Zürich author: - first_name: Peter full_name: Leek, Peter J last_name: Leek - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: M full_name: Göppl, M last_name: Göppl - first_name: Jay full_name: Gambetta, Jay M last_name: Gambetta - first_name: David full_name: Schuster, David I last_name: Schuster - first_name: Luigi full_name: Frunzio, Luigi last_name: Frunzio - first_name: Robert full_name: Schoelkopf, Robert J last_name: Schoelkopf - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Leek P, Fink JM, Blais A, et al. Observation of Berry’s phase in a solid-state qubit. Science. 2007;318(5858):1889-1892. doi:10.1126/science.1149858 apa: Leek, P., Fink, J. M., Blais, A., Bianchetti, R., Göppl, M., Gambetta, J., … Wallraff, A. (2007). Observation of Berry’s phase in a solid-state qubit. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1149858 chicago: Leek, Peter, Johannes M Fink, Alexandre Blais, R Bianchetti, M Göppl, Jay Gambetta, David Schuster, Luigi Frunzio, Robert Schoelkopf, and Andreas Wallraff. “Observation of Berry’s Phase in a Solid-State Qubit.” Science. American Association for the Advancement of Science, 2007. https://doi.org/10.1126/science.1149858. ieee: P. Leek et al., “Observation of Berry’s phase in a solid-state qubit,” Science, vol. 318, no. 5858. American Association for the Advancement of Science, pp. 1889–1892, 2007. ista: Leek P, Fink JM, Blais A, Bianchetti R, Göppl M, Gambetta J, Schuster D, Frunzio L, Schoelkopf R, Wallraff A. 2007. Observation of Berry’s phase in a solid-state qubit. Science. 318(5858), 1889–1892. mla: Leek, Peter, et al. “Observation of Berry’s Phase in a Solid-State Qubit.” Science, vol. 318, no. 5858, American Association for the Advancement of Science, 2007, pp. 1889–92, doi:10.1126/science.1149858. short: P. Leek, J.M. Fink, A. Blais, R. Bianchetti, M. Göppl, J. Gambetta, D. Schuster, L. Frunzio, R. Schoelkopf, A. Wallraff, Science 318 (2007) 1889–1892. date_created: 2018-12-11T11:53:52Z date_published: 2007-12-27T00:00:00Z date_updated: 2021-01-12T06:53:02Z day: '27' doi: 10.1126/science.1149858 extern: 1 intvolume: ' 318' issue: '5858' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0711.0218 month: '12' oa: 1 page: 1889 - 1892 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5360' quality_controlled: 0 status: public title: Observation of Berry's phase in a solid-state qubit type: journal_article volume: 318 year: '2007' ... --- _id: '1797' abstract: - lang: eng text: Intrinsically photosensitive melanopsin-containing retinal ganglion cells (ipRGCs) control important physiological processes, including the circadian rhythm, the pupillary reflex, and the suppression of locomotor behavior (reviewed in [1]). ipRGCs are also activated by classical photoreceptors, the rods and cones, through local retinal circuits [2, 3]. ipRGCs can be transsynaptically labeled through the pupillary-reflex circuit with the derivatives of the Bartha strain of the alphaherpesvirus pseudorabies virus(PRV) [4, 5] that express GFP [6-12]. Bartha-strain derivatives spread only in the retrograde direction [13]. There is evidence that infected cells function normally for a while during GFP expression [7]. Here we combine transsynaptic PRV labeling, two-photon laser microscopy, and electrophysiological techniques to trace the local circuit of different ipRGC subtypes in the mouse retina and record light-evoked activity from the transsynaptically labeled ganglion cells. First, we show that ipRGCs are connected by monostratified amacrine cells that provide strong inhibition from classical-photoreceptor-driven circuits. Second, we show evidence that dopaminergic interplexiform cells are synaptically connected to ipRGCs. The latter finding provides a circuitry link between light-dark adaptation and ipRGC function. acknowledgement: This study was supported by Office of Naval Research Multidisciplinary University Research Initiative [ONR MURI] and Naval International Cooperative Opportunities in Science and Technology Program [NICOP] grants, a Marie Curie Excellence Grant, a Human Frontier Science Program [HFSP] Young Investigator grant, and Friedrich Miescher Institute funds to B.R. author: - first_name: Tim full_name: Viney, Tim J last_name: Viney - first_name: Kamill full_name: Bálint, Kamill last_name: Bálint - first_name: Dániel full_name: Hillier, Dániel last_name: Hillier - first_name: Sandra full_name: Sandra Siegert id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 - first_name: Zsolt full_name: Boldogköi, Zsolt S last_name: Boldogköi - first_name: Lynn full_name: Enquist, Lynn W last_name: Enquist - first_name: Markus full_name: Meister, Markus last_name: Meister - first_name: Constance full_name: Cepko, Constance L last_name: Cepko - first_name: Botond full_name: Roska, Botond M last_name: Roska citation: ama: Viney T, Bálint K, Hillier D, et al. Local retinal circuits of melanopsin-containing ganglion cells identified by transsynaptic viral tracing. Current Biology. 2007;17(11):981-988. doi:10.1016/j.cub.2007.04.058 apa: Viney, T., Bálint, K., Hillier, D., Siegert, S., Boldogköi, Z., Enquist, L., … Roska, B. (2007). Local retinal circuits of melanopsin-containing ganglion cells identified by transsynaptic viral tracing. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2007.04.058 chicago: Viney, Tim, Kamill Bálint, Dániel Hillier, Sandra Siegert, Zsolt Boldogköi, Lynn Enquist, Markus Meister, Constance Cepko, and Botond Roska. “Local Retinal Circuits of Melanopsin-Containing Ganglion Cells Identified by Transsynaptic Viral Tracing.” Current Biology. Cell Press, 2007. https://doi.org/10.1016/j.cub.2007.04.058. ieee: T. Viney et al., “Local retinal circuits of melanopsin-containing ganglion cells identified by transsynaptic viral tracing,” Current Biology, vol. 17, no. 11. Cell Press, pp. 981–988, 2007. ista: Viney T, Bálint K, Hillier D, Siegert S, Boldogköi Z, Enquist L, Meister M, Cepko C, Roska B. 2007. Local retinal circuits of melanopsin-containing ganglion cells identified by transsynaptic viral tracing. Current Biology. 17(11), 981–988. mla: Viney, Tim, et al. “Local Retinal Circuits of Melanopsin-Containing Ganglion Cells Identified by Transsynaptic Viral Tracing.” Current Biology, vol. 17, no. 11, Cell Press, 2007, pp. 981–88, doi:10.1016/j.cub.2007.04.058. short: T. Viney, K. Bálint, D. Hillier, S. Siegert, Z. Boldogköi, L. Enquist, M. Meister, C. Cepko, B. Roska, Current Biology 17 (2007) 981–988. date_created: 2018-12-11T11:54:04Z date_published: 2007-06-05T00:00:00Z date_updated: 2021-01-12T06:53:15Z day: '05' doi: 10.1016/j.cub.2007.04.058 extern: 1 intvolume: ' 17' issue: '11' month: '06' page: 981 - 988 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '5313' quality_controlled: 0 status: public title: Local retinal circuits of melanopsin-containing ganglion cells identified by transsynaptic viral tracing type: journal_article volume: 17 year: '2007' ... --- _id: '1965' abstract: - lang: eng text: Respiratory complex I (NADH:ubiquinone oxidoreductase) is an L-shaped multisubunit protein assembly consisting of a hydrophobic membrane arm and a hydrophilic peripheral arm. It catalyses the transfer of two electrons from NADH to quinone coupled to the translocation of four protons across the membrane. Although we have solved recently the crystal structure of the peripheral arm, the structure of the complete enzyme and the coupling mechanism are not yet known. The membrane domain of Escherichia coli complex I consists of seven different subunits with total molecular mass of 258 kDa. It is significantly more stable than the whole enzyme, which allowed us to obtain well-ordered two-dimensional crystals of the domain, belonging to the space group p22121. Comparison of the projection map of negatively stained crystals with previously published low-resolution structures indicated that the characteristic curved shape of the membrane domain is remarkably well conserved between bacterial and mitochondrial enzymes, helping us to interpret projection maps in the context of the intact complex. Two pronounced stain-excluding densities at the distal end of the membrane domain are likely to represent the two large antiporter-like subunits NuoL and NuoM. Cryo-electron microscopy on frozen-hydrated crystals allowed us to calculate a projection map at 8 Å resolution. About 60 transmembrane α-helices, both perpendicular to the membrane plane and tilted, are present within one membrane domain, which is consistent with secondary structure predictions. A possible binding site and access channel for quinone are found at the interface with the peripheral arm. Tentative assignment of individual subunits to the features of the map has been made. The location of subunits NuoL and NuoM at substantial distance from the peripheral arm, which contains all the redox centres of the complex, indicates that conformational changes are likely to play a role in the mechanism of coupling between electron transfer and proton pumping. author: - first_name: Ekaterina full_name: Baranova, Ekaterina A last_name: Baranova - first_name: Peter full_name: Holt, Peter J last_name: Holt - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Baranova E, Holt P, Sazanov LA. Projection structure of the membrane domain of Escherichia coli respiratory Complex I at 8 Å resolution. Journal of Molecular Biology. 2007;366(1):140-154. doi:10.1016/j.jmb.2006.11.026 apa: Baranova, E., Holt, P., & Sazanov, L. A. (2007). Projection structure of the membrane domain of Escherichia coli respiratory Complex I at 8 Å resolution. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2006.11.026 chicago: Baranova, Ekaterina, Peter Holt, and Leonid A Sazanov. “Projection Structure of the Membrane Domain of Escherichia Coli Respiratory Complex I at 8 Å Resolution.” Journal of Molecular Biology. Elsevier, 2007. https://doi.org/10.1016/j.jmb.2006.11.026. ieee: E. Baranova, P. Holt, and L. A. Sazanov, “Projection structure of the membrane domain of Escherichia coli respiratory Complex I at 8 Å resolution,” Journal of Molecular Biology, vol. 366, no. 1. Elsevier, pp. 140–154, 2007. ista: Baranova E, Holt P, Sazanov LA. 2007. Projection structure of the membrane domain of Escherichia coli respiratory Complex I at 8 Å resolution. Journal of Molecular Biology. 366(1), 140–154. mla: Baranova, Ekaterina, et al. “Projection Structure of the Membrane Domain of Escherichia Coli Respiratory Complex I at 8 Å Resolution.” Journal of Molecular Biology, vol. 366, no. 1, Elsevier, 2007, pp. 140–54, doi:10.1016/j.jmb.2006.11.026. short: E. Baranova, P. Holt, L.A. Sazanov, Journal of Molecular Biology 366 (2007) 140–154. date_created: 2018-12-11T11:54:57Z date_published: 2007-02-09T00:00:00Z date_updated: 2021-01-12T06:54:23Z day: '09' doi: 10.1016/j.jmb.2006.11.026 extern: 1 intvolume: ' 366' issue: '1' month: '02' page: 140 - 154 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '5119' quality_controlled: 0 status: public title: Projection structure of the membrane domain of Escherichia coli respiratory Complex I at 8 Å resolution type: journal_article volume: 366 year: '2007' ... --- _id: '1969' abstract: - lang: eng text: Respiratory complex I catalyses the transfer of electrons from NADH to quinone coupled to the translocation of protons across the membrane. The mechanism of coupling and the structure of the complete enzyme are not known. The membrane domain of the complex contains three similar antiporter-like subunits NuoL/M/N, probably involved in proton pumping. We have previously shown that subunits NuoL/M can be removed from the rest of the complex, suggesting their location at the distal end of the membrane domain. Here, using electron microscopy and single particle analysis, we show that subunits NuoL and M jointly occupy a distal half of the membrane domain, separated by about 10 nm from the interface with the peripheral arm. This indicates that coupling mechanism of complex I is likely to involve long range conformational changes. author: - first_name: Ekaterina full_name: Baranova, Ekaterina A last_name: Baranova - first_name: David full_name: Morgan, David J last_name: Morgan - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Baranova E, Morgan D, Sazanov LA. Single particle analysis confirms distal location of subunits NuoL and NuoM in Escherichia coli complex I. Journal of Structural Biology. 2007;159(2 SPEC. ISS.):238-242. doi:10.1016/j.jsb.2007.01.009 apa: Baranova, E., Morgan, D., & Sazanov, L. A. (2007). Single particle analysis confirms distal location of subunits NuoL and NuoM in Escherichia coli complex I. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2007.01.009 chicago: Baranova, Ekaterina, David Morgan, and Leonid A Sazanov. “Single Particle Analysis Confirms Distal Location of Subunits NuoL and NuoM in Escherichia Coli Complex I.” Journal of Structural Biology. Academic Press, 2007. https://doi.org/10.1016/j.jsb.2007.01.009. ieee: E. Baranova, D. Morgan, and L. A. Sazanov, “Single particle analysis confirms distal location of subunits NuoL and NuoM in Escherichia coli complex I,” Journal of Structural Biology, vol. 159, no. 2 SPEC. ISS. Academic Press, pp. 238–242, 2007. ista: Baranova E, Morgan D, Sazanov LA. 2007. Single particle analysis confirms distal location of subunits NuoL and NuoM in Escherichia coli complex I. Journal of Structural Biology. 159(2 SPEC. ISS.), 238–242. mla: Baranova, Ekaterina, et al. “Single Particle Analysis Confirms Distal Location of Subunits NuoL and NuoM in Escherichia Coli Complex I.” Journal of Structural Biology, vol. 159, no. 2 SPEC. ISS., Academic Press, 2007, pp. 238–42, doi:10.1016/j.jsb.2007.01.009. short: E. Baranova, D. Morgan, L.A. Sazanov, Journal of Structural Biology 159 (2007) 238–242. date_created: 2018-12-11T11:54:58Z date_published: 2007-08-01T00:00:00Z date_updated: 2021-01-12T06:54:24Z day: '01' doi: 10.1016/j.jsb.2007.01.009 extern: 1 intvolume: ' 159' issue: 2 SPEC. ISS. month: '08' page: 238 - 242 publication: Journal of Structural Biology publication_status: published publisher: Academic Press publist_id: '5117' quality_controlled: 0 status: public title: Single particle analysis confirms distal location of subunits NuoL and NuoM in Escherichia coli complex I type: journal_article volume: 159 year: '2007' ... --- _id: '1964' abstract: - lang: eng text: Complex I of respiratory chains plays a central role in cellular energy production. Mutations in its subunits lead to many human neurodegenerative diseases. Recently, a first atomic structure of the hydrophilic domain of complex I from Thermus thermophilus was determined. This domain represents a catalytic core of the enzyme. It consists of eight different subunits, contains all the redox centers, and comprises more than half of the entire complex. In this review, novel mechanistic implications of the structure are discussed, and the effects of many known mutations of complex I subunits are interpreted in a structural context. author: - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: 'Sazanov LA. Respiratory complex I: Mechanistic and structural insights provided by the crystal structure of the hydrophilic domain. Biochemistry. 2007;46(9):2275-2288. doi:10.1021/bi602508x' apa: 'Sazanov, L. A. (2007). Respiratory complex I: Mechanistic and structural insights provided by the crystal structure of the hydrophilic domain. Biochemistry. ACS. https://doi.org/10.1021/bi602508x' chicago: 'Sazanov, Leonid A. “Respiratory Complex I: Mechanistic and Structural Insights Provided by the Crystal Structure of the Hydrophilic Domain.” Biochemistry. ACS, 2007. https://doi.org/10.1021/bi602508x.' ieee: 'L. A. Sazanov, “Respiratory complex I: Mechanistic and structural insights provided by the crystal structure of the hydrophilic domain,” Biochemistry, vol. 46, no. 9. ACS, pp. 2275–2288, 2007.' ista: 'Sazanov LA. 2007. Respiratory complex I: Mechanistic and structural insights provided by the crystal structure of the hydrophilic domain. Biochemistry. 46(9), 2275–2288.' mla: 'Sazanov, Leonid A. “Respiratory Complex I: Mechanistic and Structural Insights Provided by the Crystal Structure of the Hydrophilic Domain.” Biochemistry, vol. 46, no. 9, ACS, 2007, pp. 2275–88, doi:10.1021/bi602508x.' short: L.A. Sazanov, Biochemistry 46 (2007) 2275–2288. date_created: 2018-12-11T11:54:57Z date_published: 2007-03-06T00:00:00Z date_updated: 2021-01-12T06:54:23Z day: '06' doi: 10.1021/bi602508x extern: 1 intvolume: ' 46' issue: '9' month: '03' page: 2275 - 2288 publication: Biochemistry publication_status: published publisher: ACS publist_id: '5118' quality_controlled: 0 status: public title: 'Respiratory complex I: Mechanistic and structural insights provided by the crystal structure of the hydrophilic domain' type: journal_article volume: 46 year: '2007' ... --- _id: '2091' abstract: - lang: eng text: 'We present a novel multi-scale representation and acquisition method for the animation of high-resolution facial geometry and wrinkles. We first acquire a static scan of the face including reflectance data at the highest possible quality. We then augment a traditional marker-based facial motion-capture system by two synchronized video cameras to track expression wrinkles. The resulting model consists of high-resolution geometry, motion-capture data, and expression wrinkles in 2D parametric form. This combination represents the facial shape and its salient features at multiple scales. During motion synthesis the motion-capture data deforms the high-resolution geometry using a linear shell-based mesh-deformation method. The wrinkle geometry is added to the facial base mesh using nonlinear energy optimization. We present the results of our approach for performance replay as well as for wrinkle editing. ' acknowledgement: This research has been supported by the NCCR Co-Me of the Swiss National Science Foundation. author: - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Mario full_name: Botsch, Mario last_name: Botsch - first_name: Roland full_name: Angst, Roland last_name: Angst - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Miguel full_name: Otaduy, Miguel A last_name: Otaduy - 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, Botsch M, Angst R, et al. Multi scale capture of facial geometry and motion. In: ACM; 2007. doi:doi:10.1145/1275808.1276419' apa: 'Bickel, B., Botsch, M., Angst, R., Matusik, W., Otaduy, M., Pfister, H., & Groß, M. (2007). Multi scale capture of facial geometry and motion. Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM. https://doi.org/doi:10.1145/1275808.1276419' chicago: Bickel, Bernd, Mario Botsch, Roland Angst, Wojciech Matusik, Miguel Otaduy, Hanspeter Pfister, and Markus Groß. “Multi Scale Capture of Facial Geometry and Motion.” ACM, 2007. https://doi.org/doi:10.1145/1275808.1276419. ieee: 'B. Bickel et al., “Multi scale capture of facial geometry and motion,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 2007.' ista: 'Bickel B, Botsch M, Angst R, Matusik W, Otaduy M, Pfister H, Groß M. 2007. Multi scale capture of facial geometry and motion. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques.' mla: Bickel, Bernd, et al. Multi Scale Capture of Facial Geometry and Motion. ACM, 2007, doi:doi:10.1145/1275808.1276419. short: B. Bickel, M. Botsch, R. Angst, W. Matusik, M. Otaduy, H. Pfister, M. Groß, in:, ACM, 2007. conference: name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' date_created: 2018-12-11T11:55:39Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T06:55:15Z day: '01' doi: doi:10.1145/1275808.1276419 extern: 1 main_file_link: - open_access: '1' url: http://nrs.harvard.edu/urn-3:HUL.InstRepos:4726184 month: '01' oa: 1 publication_status: published publisher: ACM publist_id: '4942' quality_controlled: 0 status: public title: Multi scale capture of facial geometry and motion type: conference year: '2007' ... --- _id: '2093' abstract: - lang: eng text: 'We present a novel multi-scale representation and acquisition method for the animation of high-resolution facial geometry and wrinkles. We first acquire a static scan of the face including reflectance data at the highest possible quality. We then augment a traditional marker-based facial motion-capture system by two synchronized video cameras to track expression wrinkles. The resulting model consists of high-resolution geometry, motion-capture data, and expression wrinkles in 2D parametric form. This combination represents the facial shape and its salient features at multiple scales. During motion synthesis the motion-capture data deforms the high-resolution geometry using a linear shell-based mesh-deformation method. The wrinkle geometry is added to the facial base mesh using nonlinear energy optimization. We present the results of our approach for performance replay as well as for wrinkle editing. ' acknowledgement: This research has been supported by the NCCR Co-Me of the Swiss National Science Foundation author: - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Mario full_name: Botsch, Mario last_name: Botsch - first_name: Roland full_name: Angst, Roland last_name: Angst - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Miguel full_name: Otaduy, Miguel A last_name: Otaduy - 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, Botsch M, Angst R, et al. Multi scale capture of facial geometry and motion. ACM Transactions on Graphics. 2007;26(3). doi:10.1145/1276377.1276419 apa: Bickel, B., Botsch, M., Angst, R., Matusik, W., Otaduy, M., Pfister, H., & Groß, M. (2007). Multi scale capture of facial geometry and motion. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1276377.1276419 chicago: Bickel, Bernd, Mario Botsch, Roland Angst, Wojciech Matusik, Miguel Otaduy, Hanspeter Pfister, and Markus Groß. “Multi Scale Capture of Facial Geometry and Motion.” ACM Transactions on Graphics. ACM, 2007. https://doi.org/10.1145/1276377.1276419. ieee: B. Bickel et al., “Multi scale capture of facial geometry and motion,” ACM Transactions on Graphics, vol. 26, no. 3. ACM, 2007. ista: Bickel B, Botsch M, Angst R, Matusik W, Otaduy M, Pfister H, Groß M. 2007. Multi scale capture of facial geometry and motion. ACM Transactions on Graphics. 26(3). mla: Bickel, Bernd, et al. “Multi Scale Capture of Facial Geometry and Motion.” ACM Transactions on Graphics, vol. 26, no. 3, ACM, 2007, doi:10.1145/1276377.1276419. short: B. Bickel, M. Botsch, R. Angst, W. Matusik, M. Otaduy, H. Pfister, M. Groß, ACM Transactions on Graphics 26 (2007). date_created: 2018-12-11T11:55:40Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T06:55:15Z day: '01' doi: 10.1145/1276377.1276419 extern: 1 intvolume: ' 26' issue: '3' main_file_link: - open_access: '1' url: http://nrs.harvard.edu/urn-3:HUL.InstRepos:4726184 month: '01' oa: 1 publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4944' quality_controlled: 0 status: public title: Multi scale capture of facial geometry and motion type: journal_article volume: 26 year: '2007' ... --- _id: '2092' abstract: - lang: eng text: We introduce a new appearance-modeling paradigm for synthesizing the internal structure of a 3D model from photographs of a few cross-sections of a real object. When the internal surfaces of the 3D model are revealed as it is cut, carved, or simply clipped, we synthesize their texture from the input photographs. Our texture synthesis algorithm is best classified as a morphing technique, which efficiently outputs the texture attributes of each surface point on demand. For determining source points and their weights in the morphing algorithm, we propose an interpolation domain based on BSP trees that naturally resembles planar splitting of real objects. In the context of the interpolation domain, we define efficient warping and morphing operations that allow for real-time synthesis of textures. Overall, our modeling paradigm, together with its realization through our texture morphing algorithm, allow users to author 3D models that reveal highly realistic internal surfaces in a variety of artistic flavors. acknowledgement: 'This research was supported in part by the NCCR Co-Me of the Swiss National Science Foundation. ' author: - first_name: Nico full_name: Pietroni, Nico last_name: Pietroni - first_name: Miguel full_name: Otaduy, Miguel A last_name: Otaduy - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Fabio full_name: Ganovelli, Fabio last_name: Ganovelli - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: Pietroni N, Otaduy M, Bickel B, Ganovelli F, Groß M. Texturing internal surfaces from a few cross-sections. Computer Graphics Forum. 2007;26(3):637-644. doi:10.1111/j.1467-8659.2007.01087.x apa: Pietroni, N., Otaduy, M., Bickel, B., Ganovelli, F., & Groß, M. (2007). Texturing internal surfaces from a few cross-sections. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2007.01087.x chicago: Pietroni, Nico, Miguel Otaduy, Bernd Bickel, Fabio Ganovelli, and Markus Groß. “Texturing Internal Surfaces from a Few Cross-Sections.” Computer Graphics Forum. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1467-8659.2007.01087.x. ieee: N. Pietroni, M. Otaduy, B. Bickel, F. Ganovelli, and M. Groß, “Texturing internal surfaces from a few cross-sections,” Computer Graphics Forum, vol. 26, no. 3. Wiley-Blackwell, pp. 637–644, 2007. ista: Pietroni N, Otaduy M, Bickel B, Ganovelli F, Groß M. 2007. Texturing internal surfaces from a few cross-sections. Computer Graphics Forum. 26(3), 637–644. mla: Pietroni, Nico, et al. “Texturing Internal Surfaces from a Few Cross-Sections.” Computer Graphics Forum, vol. 26, no. 3, Wiley-Blackwell, 2007, pp. 637–44, doi:10.1111/j.1467-8659.2007.01087.x. short: N. Pietroni, M. Otaduy, B. Bickel, F. Ganovelli, M. Groß, Computer Graphics Forum 26 (2007) 637–644. date_created: 2018-12-11T11:55:39Z date_published: 2007-09-01T00:00:00Z date_updated: 2021-01-12T06:55:15Z day: '01' doi: 10.1111/j.1467-8659.2007.01087.x extern: 1 intvolume: ' 26' issue: '3' month: '09' page: 637 - 644 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '4943' quality_controlled: 0 status: public title: Texturing internal surfaces from a few cross-sections type: journal_article volume: 26 year: '2007' ... --- _id: '2118' abstract: - lang: eng text: 'We extend to infinite dimensions an explicit formula of Chill, Fašangová, Metafune, and Pallara for the optimal angle of analyticity of analytic Ornstein-Uhlenbeck semigroups. The main ingredient is an abstract representation of the Ornstein-Uhlenbeck operator in divergence form. ' acknowledgement: The authors are supported by the ‘VIDI subsidie’ 639.032.201 of the Netherlands Organization for Scientific Research (NWO) and by the Research Training Network HPRN-CT-2002-00281. 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. On analytic Ornstein-Uhlenbeck semigroups in infinite dimensions. Archiv der Mathematik. 2007;89(3):226-236. doi:10.1007/s00013-007-2082-x apa: Maas, J., & Van Neerven, J. (2007). On analytic Ornstein-Uhlenbeck semigroups in infinite dimensions. Archiv Der Mathematik. Birkhäuser. https://doi.org/10.1007/s00013-007-2082-x chicago: Maas, Jan, and Jan Van Neerven. “On Analytic Ornstein-Uhlenbeck Semigroups in Infinite Dimensions.” Archiv Der Mathematik. Birkhäuser, 2007. https://doi.org/10.1007/s00013-007-2082-x. ieee: J. Maas and J. Van Neerven, “On analytic Ornstein-Uhlenbeck semigroups in infinite dimensions,” Archiv der Mathematik, vol. 89, no. 3. Birkhäuser, pp. 226–236, 2007. ista: Maas J, Van Neerven J. 2007. On analytic Ornstein-Uhlenbeck semigroups in infinite dimensions. Archiv der Mathematik. 89(3), 226–236. mla: Maas, Jan, and Jan Van Neerven. “On Analytic Ornstein-Uhlenbeck Semigroups in Infinite Dimensions.” Archiv Der Mathematik, vol. 89, no. 3, Birkhäuser, 2007, pp. 226–36, doi:10.1007/s00013-007-2082-x. short: J. Maas, J. Van Neerven, Archiv Der Mathematik 89 (2007) 226–236. date_created: 2018-12-11T11:55:49Z date_published: 2007-08-06T00:00:00Z date_updated: 2021-01-12T06:55:25Z day: '06' doi: 10.1007/s00013-007-2082-x extern: 1 intvolume: ' 89' issue: '3' main_file_link: - open_access: '1' url: http://repository.tudelft.nl/view/ir/uuid:c2cc3bd8-822b-4e72-ae42-1da0424e8a22/ month: '08' oa: 1 page: 226 - 236 publication: Archiv der Mathematik publication_status: published publisher: Birkhäuser publist_id: '4916' quality_controlled: 0 status: public title: On analytic Ornstein-Uhlenbeck semigroups in infinite dimensions type: journal_article volume: 89 year: '2007' ... --- _id: '2135' abstract: - lang: eng text: We use the x-ray absorption fine structure spectroscopy at Nb K edge to reveal the local atomic structure of KxNa1−xNbO3 (PSN) solid solutions. The study is performed over the temperature range 10–1023K for six different x values. We show that only the combined analysis of extended x-ray absorption fine structure and preedge fine structure provides complete and reliable information about the local structure of NbO6 octahedra. Such extensive treatment of the experimental data shows that the local structure of PSN could be described within the spherical model proposed earlier as a hypothesis for perovskite-type ferroelectric zirconates. We reveal that the Nb atoms are localized near their average positions on the sphere surfaces for all temperatures and x values. With regard to previous results we point out the features of microscopic structure common for PSN and perovskite-type zirconates. acknowledgement: This work was partially supported by Russian Foundation for Basic Research Grant No. 07-02-00796a. The authors are indebted to the French Government for financial support of E.S.N. and M.P.L. within the CNOUS program. author: - 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: A.A full_name: Gonchar, A.A last_name: Gonchar - first_name: Larisa full_name: Reznichenko, Larisa A last_name: Reznichenko - first_name: Tatiana full_name: Nedoseykina, Tatiana I last_name: Nedoseykina - first_name: Alexander full_name: Novakovich, Alexander A last_name: Novakovich - first_name: Olivier full_name: Mathon, Olivier last_name: Mathon - first_name: Yves full_name: Joly, Yves last_name: Joly - first_name: Rostislav full_name: Vedrinskiǐ, Rostislav V last_name: Vedrinskiǐ citation: ama: Lemeshko M, Nazarenko E, Gonchar A., et al. EXAFS studies of the local atomic structure of the lead-free piezoelectric ceramics KxNa1−xNbO3 over the temperature range 10–1023K. Physical Review B - Condensed Matter and Materials Physics. 2007;76. doi:http://dx.doi.org/10.1103/PhysRevB.76.134106 apa: Lemeshko, M., Nazarenko, E., Gonchar, A. ., Reznichenko, L., Nedoseykina, T., Novakovich, A., … Vedrinskiǐ, R. (2007). EXAFS studies of the local atomic structure of the lead-free piezoelectric ceramics KxNa1−xNbO3 over the temperature range 10–1023K. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. http://dx.doi.org/10.1103/PhysRevB.76.134106 chicago: Lemeshko, Mikhail, Elena Nazarenko, A.A Gonchar, Larisa Reznichenko, Tatiana Nedoseykina, Alexander Novakovich, Olivier Mathon, Yves Joly, and Rostislav Vedrinskiǐ. “EXAFS Studies of the Local Atomic Structure of the Lead-Free Piezoelectric Ceramics KxNa1−xNbO3 over the Temperature Range 10–1023K.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2007. http://dx.doi.org/10.1103/PhysRevB.76.134106. ieee: M. Lemeshko et al., “EXAFS studies of the local atomic structure of the lead-free piezoelectric ceramics KxNa1−xNbO3 over the temperature range 10–1023K,” Physical Review B - Condensed Matter and Materials Physics, vol. 76. American Physical Society, 2007. ista: Lemeshko M, Nazarenko E, Gonchar A., Reznichenko L, Nedoseykina T, Novakovich A, Mathon O, Joly Y, Vedrinskiǐ R. 2007. EXAFS studies of the local atomic structure of the lead-free piezoelectric ceramics KxNa1−xNbO3 over the temperature range 10–1023K. Physical Review B - Condensed Matter and Materials Physics. 76. mla: Lemeshko, Mikhail, et al. “EXAFS Studies of the Local Atomic Structure of the Lead-Free Piezoelectric Ceramics KxNa1−xNbO3 over the Temperature Range 10–1023K.” Physical Review B - Condensed Matter and Materials Physics, vol. 76, American Physical Society, 2007, doi:http://dx.doi.org/10.1103/PhysRevB.76.134106. short: M. Lemeshko, E. Nazarenko, A.. Gonchar, L. Reznichenko, T. Nedoseykina, A. Novakovich, O. Mathon, Y. Joly, R. Vedrinskiǐ, Physical Review B - Condensed Matter and Materials Physics 76 (2007). date_created: 2018-12-11T11:55:54Z date_published: 2007-10-09T00:00:00Z date_updated: 2021-01-12T06:55:31Z day: '09' doi: http://dx.doi.org/10.1103/PhysRevB.76.134106 extern: 1 intvolume: ' 76' month: '10' publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '4899' quality_controlled: 0 status: public title: EXAFS studies of the local atomic structure of the lead-free piezoelectric ceramics KxNa1−xNbO3 over the temperature range 10–1023K type: journal_article volume: 76 year: '2007' ... --- _id: '2143' abstract: - lang: eng text: 'Local atomic structure of the piezoelectric ceramics KxNa 1-xNbO3 (x≤0.00, 0.05, 0.30, 0.40, 0.50 and 0.65) is studied in all phase regions (10 K-1023 K) using Nb K-edge extended X-ray absorption fine-structure (EXAFS) spectroscopy. We have shown the validity of a new spherical model for phase transitions on the basis of both fitting of EXAFS signal in the R-space and differential EXAFS analysis. Within this model the Nb atoms are located on the surfaces of small spheres of constant radii surrounding centers of NbO6 octahedrons in all phases. The distribution of the Nb atom on this surface changes during phase transitions. Besides, the analysis of local structure reveals that the geometry of NbO6 octahedra does not depend on the x value at each temperature, whereas the octahedra rotation angles do. ' author: - 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: Anastasia full_name: Gonchar, Anastasia A last_name: Gonchar - first_name: Larisa full_name: Reznichenko, Larisa A last_name: Reznichenko - first_name: Olivier full_name: Mathon, Olivier last_name: Mathon - first_name: Yves full_name: Joly, Yves last_name: Joly - first_name: Rostislav full_name: Vedrinskiǐ, Rostislav V last_name: Vedrinskiǐ citation: ama: 'Lemeshko M, Nazarenko E, Gonchar A, et al. Phase transitions in lead-free piezoelectric ceramics: Study of local atomic structure. EPL. 2007;77(2). doi:10.1209/0295-5075/77/26003 ' apa: 'Lemeshko, M., Nazarenko, E., Gonchar, A., Reznichenko, L., Mathon, O., Joly, Y., & Vedrinskiǐ, R. (2007). Phase transitions in lead-free piezoelectric ceramics: Study of local atomic structure. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/77/26003 ' chicago: 'Lemeshko, Mikhail, Elena Nazarenko, Anastasia Gonchar, Larisa Reznichenko, Olivier Mathon, Yves Joly, and Rostislav Vedrinskiǐ. “Phase Transitions in Lead-Free Piezoelectric Ceramics: Study of Local Atomic Structure.” EPL. IOP Publishing Ltd., 2007. https://doi.org/10.1209/0295-5075/77/26003 .' ieee: 'M. Lemeshko et al., “Phase transitions in lead-free piezoelectric ceramics: Study of local atomic structure,” EPL, vol. 77, no. 2. IOP Publishing Ltd., 2007.' ista: 'Lemeshko M, Nazarenko E, Gonchar A, Reznichenko L, Mathon O, Joly Y, Vedrinskiǐ R. 2007. Phase transitions in lead-free piezoelectric ceramics: Study of local atomic structure. EPL. 77(2).' mla: 'Lemeshko, Mikhail, et al. “Phase Transitions in Lead-Free Piezoelectric Ceramics: Study of Local Atomic Structure.” EPL, vol. 77, no. 2, IOP Publishing Ltd., 2007, doi:10.1209/0295-5075/77/26003 .' short: M. Lemeshko, E. Nazarenko, A. Gonchar, L. Reznichenko, O. Mathon, Y. Joly, R. Vedrinskiǐ, EPL 77 (2007). date_created: 2018-12-11T11:55:57Z date_published: 2007-01-11T00:00:00Z date_updated: 2021-01-12T06:55:34Z day: '11' doi: '10.1209/0295-5075/77/26003 ' extern: 1 intvolume: ' 77' issue: '2' month: '01' publication: EPL publication_status: published publisher: IOP Publishing Ltd. publist_id: '4880' quality_controlled: 0 status: public title: 'Phase transitions in lead-free piezoelectric ceramics: Study of local atomic structure' type: journal_article volume: 77 year: '2007' ... --- _id: '2145' abstract: - lang: eng text: 'We use the x-ray absorption fine structure spectroscopy at Nb K edge to reveal the local atomic structure of Kx Na1-x Nb O3 (PSN) solid solutions. The study is performed over the temperature range 10-1023 K for six different x values. We show that only the combined analysis of extended x-ray absorption fine structure and preedge fine structure provides complete and reliable information about the local structure of Nb O6 octahedra. Such extensive treatment of the experimental data shows that the local structure of PSN could be described within the spherical model proposed earlier as a hypothesis for perovskite-type ferroelectric zirconates. We reveal that the Nb atoms are localized near their average positions on the sphere surfaces for all temperatures and x values. With regard to previous results we point out the features of microscopic structure common for PSN and perovskite-type zirconates. ' acknowledgement: This work was partially supported by Russian Foundation for Basic Research Grant No. 07-02-00796a author: - 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: Anastasia full_name: Gonchar, Anastasia A last_name: Gonchar - first_name: Larisa full_name: Reznichenko, Larisa A last_name: Reznichenko - first_name: Tatiana full_name: Nedoseykina, Tatiana I last_name: Nedoseykina - first_name: Alexander full_name: Novakovich, Alexander A last_name: Novakovich - first_name: Olivier full_name: Mathon, Olivier last_name: Mathon - first_name: Yves full_name: Joly, Yves last_name: Joly - first_name: Rostislav full_name: Vedrinskiǐ, Rostislav V last_name: Vedrinskiǐ citation: ama: Lemeshko M, Nazarenko E, Gonchar A, et al. EXAFS studies of the local atomic structure of the lead free piezoelectric ceramics Kx Na1-x Nb O3 over the temperature range 10-1023 K. Physical Review B - Condensed Matter and Materials Physics. 2007;76(13). doi:10.1103/PhysRevB.76.134106 apa: Lemeshko, M., Nazarenko, E., Gonchar, A., Reznichenko, L., Nedoseykina, T., Novakovich, A., … Vedrinskiǐ, R. (2007). EXAFS studies of the local atomic structure of the lead free piezoelectric ceramics Kx Na1-x Nb O3 over the temperature range 10-1023 K. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.76.134106 chicago: Lemeshko, Mikhail, Elena Nazarenko, Anastasia Gonchar, Larisa Reznichenko, Tatiana Nedoseykina, Alexander Novakovich, Olivier Mathon, Yves Joly, and Rostislav Vedrinskiǐ. “EXAFS Studies of the Local Atomic Structure of the Lead Free Piezoelectric Ceramics Kx Na1-x Nb O3 over the Temperature Range 10-1023 K.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2007. https://doi.org/10.1103/PhysRevB.76.134106. ieee: M. Lemeshko et al., “EXAFS studies of the local atomic structure of the lead free piezoelectric ceramics Kx Na1-x Nb O3 over the temperature range 10-1023 K,” Physical Review B - Condensed Matter and Materials Physics, vol. 76, no. 13. American Physical Society, 2007. ista: Lemeshko M, Nazarenko E, Gonchar A, Reznichenko L, Nedoseykina T, Novakovich A, Mathon O, Joly Y, Vedrinskiǐ R. 2007. EXAFS studies of the local atomic structure of the lead free piezoelectric ceramics Kx Na1-x Nb O3 over the temperature range 10-1023 K. Physical Review B - Condensed Matter and Materials Physics. 76(13). mla: Lemeshko, Mikhail, et al. “EXAFS Studies of the Local Atomic Structure of the Lead Free Piezoelectric Ceramics Kx Na1-x Nb O3 over the Temperature Range 10-1023 K.” Physical Review B - Condensed Matter and Materials Physics, vol. 76, no. 13, American Physical Society, 2007, doi:10.1103/PhysRevB.76.134106. short: M. Lemeshko, E. Nazarenko, A. Gonchar, L. Reznichenko, T. Nedoseykina, A. Novakovich, O. Mathon, Y. Joly, R. Vedrinskiǐ, Physical Review B - Condensed Matter and Materials Physics 76 (2007). date_created: 2018-12-11T11:55:58Z date_published: 2007-10-09T00:00:00Z date_updated: 2021-01-12T06:55:35Z day: '09' doi: 10.1103/PhysRevB.76.134106 extern: 1 intvolume: ' 76' issue: '13' month: '10' publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '4879' quality_controlled: 0 status: public title: EXAFS studies of the local atomic structure of the lead free piezoelectric ceramics Kx Na1-x Nb O3 over the temperature range 10-1023 K type: journal_article volume: 76 year: '2007' ... --- _id: '219' abstract: - lang: eng text: This paper contains a proof of the Manin conjecture for the singular cubic surface S ⊂ P3 that is defined by the equation x1 x22 + x2 x02 + x33 = 0. In fact if U ⊂ S is the Zariski open subset obtained by deleting the unique line from S, and H is the usual exponential height on P3 (Q), then the height zeta function ∑x ∈ U (Q) H (x)- s is analytically continued to the half-plane R e (s) > 9 / 10. acknowledgement: EPSRC grant number GR/R93155/01 author: - first_name: Régis full_name: De La Bretèche, Régis last_name: De La Bretèche - 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: Ulrich full_name: Derenthal, Ulrich last_name: Derenthal citation: ama: De La Bretèche R, Browning TD, Derenthal U. On Manin’s conjecture for a certain singular cubic surface. Annales Scientifiques de l’Ecole Normale Superieure. 2007;40(1):1-50. doi:10.1016/j.ansens.2006.12.002 apa: De La Bretèche, R., Browning, T. D., & Derenthal, U. (2007). On Manin’s conjecture for a certain singular cubic surface. Annales Scientifiques de l’Ecole Normale Superieure. Societe Mathematique de France. https://doi.org/10.1016/j.ansens.2006.12.002 chicago: De La Bretèche, Régis, Timothy D Browning, and Ulrich Derenthal. “On Manin’s Conjecture for a Certain Singular Cubic Surface.” Annales Scientifiques de l’Ecole Normale Superieure. Societe Mathematique de France, 2007. https://doi.org/10.1016/j.ansens.2006.12.002. ieee: R. De La Bretèche, T. D. Browning, and U. Derenthal, “On Manin’s conjecture for a certain singular cubic surface,” Annales Scientifiques de l’Ecole Normale Superieure, vol. 40, no. 1. Societe Mathematique de France, pp. 1–50, 2007. ista: De La Bretèche R, Browning TD, Derenthal U. 2007. On Manin’s conjecture for a certain singular cubic surface. Annales Scientifiques de l’Ecole Normale Superieure. 40(1), 1–50. mla: De La Bretèche, Régis, et al. “On Manin’s Conjecture for a Certain Singular Cubic Surface.” Annales Scientifiques de l’Ecole Normale Superieure, vol. 40, no. 1, Societe Mathematique de France, 2007, pp. 1–50, doi:10.1016/j.ansens.2006.12.002. short: R. De La Bretèche, T.D. Browning, U. Derenthal, Annales Scientifiques de l’Ecole Normale Superieure 40 (2007) 1–50. date_created: 2018-12-11T11:45:16Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T06:55:53Z day: '01' doi: 10.1016/j.ansens.2006.12.002 extern: '1' intvolume: ' 40' issue: '1' language: - iso: eng month: '01' oa_version: None page: 1 - 50 publication: Annales Scientifiques de l'Ecole Normale Superieure publication_status: published publisher: Societe Mathematique de France publist_id: '7693' status: public title: On Manin's conjecture for a certain singular cubic surface type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2007' ... --- _id: '220' abstract: - lang: eng text: Let X ⊂ ℙN be a geometrically integral cubic hypersurface defined over ℚ, with singular locus of dimension at most dim X - 4. The main result in this paper is a proof of the fact that X(ℚ) contains OεX,(BdimX+ε) points of height at most B. 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. Counting rational points on cubic hypersurfaces. Mathematika. 2007;54(1-2):93-112. doi:10.1112/S0025579300000243 apa: Browning, T. D. (2007). Counting rational points on cubic hypersurfaces. Mathematika. University College London. https://doi.org/10.1112/S0025579300000243 chicago: Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces.” Mathematika. University College London, 2007. https://doi.org/10.1112/S0025579300000243. ieee: T. D. Browning, “Counting rational points on cubic hypersurfaces,” Mathematika, vol. 54, no. 1–2. University College London, pp. 93–112, 2007. ista: Browning TD. 2007. Counting rational points on cubic hypersurfaces. Mathematika. 54(1–2), 93–112. mla: Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces.” Mathematika, vol. 54, no. 1–2, University College London, 2007, pp. 93–112, doi:10.1112/S0025579300000243. short: T.D. Browning, Mathematika 54 (2007) 93–112. date_created: 2018-12-11T11:45:16Z date_published: 2007-12-21T00:00:00Z date_updated: 2021-01-12T06:55:56Z day: '21' doi: 10.1112/S0025579300000243 extern: 1 intvolume: ' 54' issue: 1-2 month: '12' page: 93 - 112 publication: Mathematika publication_status: published publisher: University College London publist_id: '7692' quality_controlled: 0 status: public title: Counting rational points on cubic hypersurfaces type: journal_article volume: 54 year: '2007' ... --- _id: '221' author: - first_name: Régis full_name: De La Bretèche, Régis last_name: De La Bretèche - 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: De La Bretèche R, Browning TD. On Manin’s conjecture for singular del Pezzo surfaces of degree four, I. Michigan Mathematical Journal. 2007;55(1):51-80. doi:10.1307/mmj/1177681985 apa: De La Bretèche, R., & Browning, T. D. (2007). On Manin’s conjecture for singular del Pezzo surfaces of degree four, I. Michigan Mathematical Journal. Project Euclid. https://doi.org/10.1307/mmj/1177681985 chicago: De La Bretèche, Régis, and Timothy D Browning. “On Manin’s Conjecture for Singular Del Pezzo Surfaces of Degree Four, I.” Michigan Mathematical Journal. Project Euclid, 2007. https://doi.org/10.1307/mmj/1177681985. ieee: R. De La Bretèche and T. D. Browning, “On Manin’s conjecture for singular del Pezzo surfaces of degree four, I,” Michigan Mathematical Journal, vol. 55, no. 1. Project Euclid, pp. 51–80, 2007. ista: De La Bretèche R, Browning TD. 2007. On Manin’s conjecture for singular del Pezzo surfaces of degree four, I. Michigan Mathematical Journal. 55(1), 51–80. mla: De La Bretèche, Régis, and Timothy D. Browning. “On Manin’s Conjecture for Singular Del Pezzo Surfaces of Degree Four, I.” Michigan Mathematical Journal, vol. 55, no. 1, Project Euclid, 2007, pp. 51–80, doi:10.1307/mmj/1177681985. short: R. De La Bretèche, T.D. Browning, Michigan Mathematical Journal 55 (2007) 51–80. date_created: 2018-12-11T11:45:17Z date_published: 2007-04-27T00:00:00Z date_updated: 2021-01-12T06:56:00Z day: '27' ddc: - '510' doi: 10.1307/mmj/1177681985 extern: '1' external_id: arxiv: - math/0412086 file: - access_level: open_access checksum: 37663dde30b00d2af8a2606c6630a82f content_type: application/pdf creator: dernst date_created: 2019-04-30T08:27:34Z date_updated: 2020-07-14T12:45:32Z file_id: '6361' file_name: 2007_MichiganMath_Breteche.pdf file_size: 256111 relation: main_file file_date_updated: 2020-07-14T12:45:32Z has_accepted_license: '1' intvolume: ' 55' issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 51 - 80 publication: Michigan Mathematical Journal publication_status: published publisher: Project Euclid publist_id: '7691' quality_controlled: '1' status: public title: On Manin's conjecture for singular del Pezzo surfaces of degree four, I type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2007' ... --- _id: '222' abstract: - lang: eng text: Acknowledgements. The authors are grateful to Ulrich Derenthal and Brendan Hassett for several useful conversations relating to universal torsors for singular del Pezzo surfaces. Special thanks are due to Roger Heath–Brown whose ideas led us to the proof of Lemma 6. The paper was finalised while the first author was at the École Normale Supérieure, and the second author was at Oxford University supported by EPSRC grant number GR/R93155/01. The hospitality and financial support of these institutions is gratefully acknowledged. Finally, the authors would like to thank the anonymous referee for his careful reading of the manuscript and numerous useful suggestions. acknowledgement: GR/R93155/01 author: - first_name: Régis full_name: de la Bretèche, Régis last_name: De La Bretèche - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: De La Bretèche R, Browning TD. On Manin’s conjecture for singular del Pezzo surfaces of degree four, II. Mathematical Proceedings of the Cambridge Philosophical Society. 2007;143(3):579-605. doi:10.1017/S0305004107000205 apa: De La Bretèche, R., & Browning, T. D. (2007). On Manin’s conjecture for singular del Pezzo surfaces of degree four, II. Mathematical Proceedings of the Cambridge Philosophical Society. Unknown. https://doi.org/10.1017/S0305004107000205 chicago: De La Bretèche, Régis, and Timothy D Browning. “On Manin’s Conjecture for Singular Del Pezzo Surfaces of Degree Four, II.” Mathematical Proceedings of the Cambridge Philosophical Society. Unknown, 2007. https://doi.org/10.1017/S0305004107000205. ieee: R. De La Bretèche and T. D. Browning, “On Manin’s conjecture for singular del Pezzo surfaces of degree four, II,” Mathematical Proceedings of the Cambridge Philosophical Society, vol. 143, no. 3. Unknown, pp. 579–605, 2007. ista: De La Bretèche R, Browning TD. 2007. On Manin’s conjecture for singular del Pezzo surfaces of degree four, II. Mathematical Proceedings of the Cambridge Philosophical Society. 143(3), 579–605. mla: De La Bretèche, Régis, and Timothy D. Browning. “On Manin’s Conjecture for Singular Del Pezzo Surfaces of Degree Four, II.” Mathematical Proceedings of the Cambridge Philosophical Society, vol. 143, no. 3, Unknown, 2007, pp. 579–605, doi:10.1017/S0305004107000205. short: R. De La Bretèche, T.D. Browning, Mathematical Proceedings of the Cambridge Philosophical Society 143 (2007) 579–605. date_created: 2018-12-11T11:45:17Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T06:56:05Z day: '01' doi: 10.1017/S0305004107000205 extern: 1 intvolume: ' 143' issue: '3' main_file_link: - open_access: '1' url: https://arxiv.org/abs/math/0502510v4 month: '01' oa: 1 page: 579 - 605 publication: Mathematical Proceedings of the Cambridge Philosophical Society publication_status: published publisher: Unknown publist_id: '7689' quality_controlled: 0 status: public title: On Manin's conjecture for singular del Pezzo surfaces of degree four, II type: journal_article volume: 143 year: '2007' ... --- _id: '223' abstract: - lang: eng text: Let Q be a non-singular diagonal quadratic form in at least four variables. We provide upper bounds for the number of integer solutions to the equation Q = 0, which lie in a box with sides of length 2B, as B → ∞. The estimates obtained are completely uniform in the coefficients of the form, and become sharper as they grow larger in modulus. 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. Density of integer solutions to diagonal quadratic forms. Monatshefte fur Mathematik. 2007;152(1):13-38. doi:10.1007/s00605-007-0457-5 apa: Browning, T. D. (2007). Density of integer solutions to diagonal quadratic forms. Monatshefte Fur Mathematik. Springer. https://doi.org/10.1007/s00605-007-0457-5 chicago: Browning, Timothy D. “Density of Integer Solutions to Diagonal Quadratic Forms.” Monatshefte Fur Mathematik. Springer, 2007. https://doi.org/10.1007/s00605-007-0457-5. ieee: T. D. Browning, “Density of integer solutions to diagonal quadratic forms,” Monatshefte fur Mathematik, vol. 152, no. 1. Springer, pp. 13–38, 2007. ista: Browning TD. 2007. Density of integer solutions to diagonal quadratic forms. Monatshefte fur Mathematik. 152(1), 13–38. mla: Browning, Timothy D. “Density of Integer Solutions to Diagonal Quadratic Forms.” Monatshefte Fur Mathematik, vol. 152, no. 1, Springer, 2007, pp. 13–38, doi:10.1007/s00605-007-0457-5. short: T.D. Browning, Monatshefte Fur Mathematik 152 (2007) 13–38. date_created: 2018-12-11T11:45:17Z date_published: 2007-09-01T00:00:00Z date_updated: 2021-01-12T06:56:09Z day: '01' doi: 10.1007/s00605-007-0457-5 extern: 1 intvolume: ' 152' issue: '1' main_file_link: - open_access: '1' url: https://arxiv.org/abs/math/0603569 month: '09' oa: 1 page: 13 - 38 publication: Monatshefte fur Mathematik publication_status: published publisher: Springer publist_id: '7690' quality_controlled: 0 status: public title: Density of integer solutions to diagonal quadratic forms type: journal_article volume: 152 year: '2007' ... --- _id: '2367' abstract: - lang: eng text: It was recently shown by Hansen that the Wigner-Yanase entropy is, for general states of quantum systems, not subadditive with respect to decomposition into two subsystems, although this property is known to hold for pure states. We investigate the question whether the weaker property of subadditivity for pure states with respect to decomposition into more than two subsystems holds. This property would have interesting applications in quantum chemistry. We show, however, that it does not hold in general, and provide a counterexample. author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Seiringer R. On the failure of subadditivity of the Wigner-Yanase entropy. Letters in Mathematical Physics. 2007;80(3):285-288. doi:10.1007/s11005-007-0159-x apa: Seiringer, R. (2007). On the failure of subadditivity of the Wigner-Yanase entropy. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-007-0159-x chicago: Seiringer, Robert. “On the Failure of Subadditivity of the Wigner-Yanase Entropy.” Letters in Mathematical Physics. Springer, 2007. https://doi.org/10.1007/s11005-007-0159-x. ieee: R. Seiringer, “On the failure of subadditivity of the Wigner-Yanase entropy,” Letters in Mathematical Physics, vol. 80, no. 3. Springer, pp. 285–288, 2007. ista: Seiringer R. 2007. On the failure of subadditivity of the Wigner-Yanase entropy. Letters in Mathematical Physics. 80(3), 285–288. mla: Seiringer, Robert. “On the Failure of Subadditivity of the Wigner-Yanase Entropy.” Letters in Mathematical Physics, vol. 80, no. 3, Springer, 2007, pp. 285–88, doi:10.1007/s11005-007-0159-x. short: R. Seiringer, Letters in Mathematical Physics 80 (2007) 285–288. date_created: 2018-12-11T11:57:15Z date_published: 2007-06-01T00:00:00Z date_updated: 2021-01-12T06:57:03Z day: '01' doi: 10.1007/s11005-007-0159-x extern: 1 intvolume: ' 80' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0704.1435 month: '06' oa: 1 page: 285 - 288 publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '4557' quality_controlled: 0 status: public title: On the failure of subadditivity of the Wigner-Yanase entropy type: journal_article volume: 80 year: '2007' ... --- _id: '2372' abstract: - lang: eng text: The increasing interest in the Müller density-matrix-functional theory has led us to a systematic mathematical investigation of its properties. This functional is similar to the Hartree-Fock (HF) functional, but with a modified exchange term in which the square of the density matrix γ(x, x′) is replaced by the square of γ1 2 (x, x′). After an extensive introductory discussion of density-matrix-functional theory we show, among other things, that this functional is convex (unlike the HF functional) and that energy minimizing γ 's have unique densities ρ(r), which is a physically desirable property often absent in HF theory. We show that minimizers exist if N≤Z, and derive various properties of the minimal energy and the corresponding minimizers. We also give a precise statement about the equation for the orbitals of γ, which is more complex than for HF theory. We state some open mathematical questions about the theory together with conjectured solutions. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - 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: Heinz full_name: Siedentop, Heinz K last_name: Siedentop citation: ama: Frank R, Lieb É, Seiringer R, Siedentop H. Müller’s exchange-correlation energy in density-matrix-functional theory. Physical Review A - Atomic, Molecular, and Optical Physics. 2007;76(5). doi:10.1103/PhysRevA.76.052517 apa: Frank, R., Lieb, É., Seiringer, R., & Siedentop, H. (2007). Müller’s exchange-correlation energy in density-matrix-functional theory. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.76.052517 chicago: Frank, Rupert, Élliott Lieb, Robert Seiringer, and Heinz Siedentop. “Müller’s Exchange-Correlation Energy in Density-Matrix-Functional Theory.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2007. https://doi.org/10.1103/PhysRevA.76.052517. ieee: R. Frank, É. Lieb, R. Seiringer, and H. Siedentop, “Müller’s exchange-correlation energy in density-matrix-functional theory,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 76, no. 5. American Physical Society, 2007. ista: Frank R, Lieb É, Seiringer R, Siedentop H. 2007. Müller’s exchange-correlation energy in density-matrix-functional theory. Physical Review A - Atomic, Molecular, and Optical Physics. 76(5). mla: Frank, Rupert, et al. “Müller’s Exchange-Correlation Energy in Density-Matrix-Functional Theory.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 76, no. 5, American Physical Society, 2007, doi:10.1103/PhysRevA.76.052517. short: R. Frank, É. Lieb, R. Seiringer, H. Siedentop, Physical Review A - Atomic, Molecular, and Optical Physics 76 (2007). date_created: 2018-12-11T11:57:17Z date_published: 2007-11-30T00:00:00Z date_updated: 2021-01-12T06:57:05Z day: '30' doi: 10.1103/PhysRevA.76.052517 extern: 1 intvolume: ' 76' issue: '5' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0705.1587 month: '11' oa: 1 publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '4554' quality_controlled: 0 status: public title: Müller's exchange-correlation energy in density-matrix-functional theory type: journal_article volume: 76 year: '2007' ... --- _id: '2370' abstract: - lang: eng text: After recalling briefly the connection between spontaneous symmetry breaking and off-diagonal long-range order for models of magnets a general proof of spontaneous breaking of gauge symmetry as a consequence of Bose-Einstein condensation is presented. The proof is based on a rigorous validation of Bogoliubov's c-number substitution for the k = 0 mode operator α0. 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. Bose-Einstein condensation and spontaneous symmetry breaking. Reports on Mathematical Physics. 2007;59(3):389-399. doi:10.1016/S0034-4877(07)80074-7 apa: Lieb, É., Seiringer, R., & Yngvason, J. (2007). Bose-Einstein condensation and spontaneous symmetry breaking. Reports on Mathematical Physics. Elsevier. https://doi.org/10.1016/S0034-4877(07)80074-7 chicago: Lieb, Élliott, Robert Seiringer, and Jakob Yngvason. “Bose-Einstein Condensation and Spontaneous Symmetry Breaking.” Reports on Mathematical Physics. Elsevier, 2007. https://doi.org/10.1016/S0034-4877(07)80074-7. ieee: É. Lieb, R. Seiringer, and J. Yngvason, “Bose-Einstein condensation and spontaneous symmetry breaking,” Reports on Mathematical Physics, vol. 59, no. 3. Elsevier, pp. 389–399, 2007. ista: Lieb É, Seiringer R, Yngvason J. 2007. Bose-Einstein condensation and spontaneous symmetry breaking. Reports on Mathematical Physics. 59(3), 389–399. mla: Lieb, Élliott, et al. “Bose-Einstein Condensation and Spontaneous Symmetry Breaking.” Reports on Mathematical Physics, vol. 59, no. 3, Elsevier, 2007, pp. 389–99, doi:10.1016/S0034-4877(07)80074-7. short: É. Lieb, R. Seiringer, J. Yngvason, Reports on Mathematical Physics 59 (2007) 389–399. date_created: 2018-12-11T11:57:16Z date_published: 2007-06-01T00:00:00Z date_updated: 2021-01-12T06:57:04Z day: '01' doi: 10.1016/S0034-4877(07)80074-7 extern: 1 intvolume: ' 59' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/math-ph/0610034 month: '06' oa: 1 page: 389 - 399 publication: Reports on Mathematical Physics publication_status: published publisher: Elsevier publist_id: '4556' quality_controlled: 0 status: public title: Bose-Einstein condensation and spontaneous symmetry breaking type: journal_article volume: 59 year: '2007' ... --- _id: '2375' abstract: - lang: eng text: We give a Cwikel-Lieb-Rozenblum type bound on the number of bound states of Schrödinger operators with matrix-valued potentials using the functional integral method of Lieb. This significantly improves the constant in this inequality obtained earlier by Hundertmark. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - 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 citation: ama: Frank R, Lieb É, Seiringer R. Number of bound states of Schrödinger operators with matrix-valued potentials. Letters in Mathematical Physics. 2007;82(2-3):107-116. doi:10.1007/s11005-007-0211-x apa: Frank, R., Lieb, É., & Seiringer, R. (2007). Number of bound states of Schrödinger operators with matrix-valued potentials. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-007-0211-x chicago: Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Number of Bound States of Schrödinger Operators with Matrix-Valued Potentials.” Letters in Mathematical Physics. Springer, 2007. https://doi.org/10.1007/s11005-007-0211-x. ieee: R. Frank, É. Lieb, and R. Seiringer, “Number of bound states of Schrödinger operators with matrix-valued potentials,” Letters in Mathematical Physics, vol. 82, no. 2–3. Springer, pp. 107–116, 2007. ista: Frank R, Lieb É, Seiringer R. 2007. Number of bound states of Schrödinger operators with matrix-valued potentials. Letters in Mathematical Physics. 82(2–3), 107–116. mla: Frank, Rupert, et al. “Number of Bound States of Schrödinger Operators with Matrix-Valued Potentials.” Letters in Mathematical Physics, vol. 82, no. 2–3, Springer, 2007, pp. 107–16, doi:10.1007/s11005-007-0211-x. short: R. Frank, É. Lieb, R. Seiringer, Letters in Mathematical Physics 82 (2007) 107–116. date_created: 2018-12-11T11:57:18Z date_published: 2007-12-01T00:00:00Z date_updated: 2021-01-12T06:57:06Z day: '01' doi: 10.1007/s11005-007-0211-x extern: 1 intvolume: ' 82' issue: 2-3 main_file_link: - open_access: '1' url: http://arxiv.org/abs/0710.1877 month: '12' oa: 1 page: 107 - 116 publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '4552' quality_controlled: 0 status: public title: Number of bound states of Schrödinger operators with matrix-valued potentials type: journal_article volume: 82 year: '2007' ... --- _id: '2373' abstract: - lang: eng text: For the BCS equation with local two-body interaction λV(x), we give a rigorous analysis of the asymptotic behavior of the critical temperature as γ"0. We derive necessary and sufficient conditions onV(x) for the existence of a nontrivial solution for all values of γ>0. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Serguei full_name: Naboko, Serguei N last_name: Naboko - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Hainzl C, Naboko S, Seiringer R. The critical temperature for the BCS equation at weak coupling. Journal of Geometric Analysis. 2007;17(4):559-567. doi:10.1007/BF02937429 apa: Frank, R., Hainzl, C., Naboko, S., & Seiringer, R. (2007). The critical temperature for the BCS equation at weak coupling. Journal of Geometric Analysis. Springer. https://doi.org/10.1007/BF02937429 chicago: Frank, Rupert, Christian Hainzl, Serguei Naboko, and Robert Seiringer. “The Critical Temperature for the BCS Equation at Weak Coupling.” Journal of Geometric Analysis. Springer, 2007. https://doi.org/10.1007/BF02937429. ieee: R. Frank, C. Hainzl, S. Naboko, and R. Seiringer, “The critical temperature for the BCS equation at weak coupling,” Journal of Geometric Analysis, vol. 17, no. 4. Springer, pp. 559–567, 2007. ista: Frank R, Hainzl C, Naboko S, Seiringer R. 2007. The critical temperature for the BCS equation at weak coupling. Journal of Geometric Analysis. 17(4), 559–567. mla: Frank, Rupert, et al. “The Critical Temperature for the BCS Equation at Weak Coupling.” Journal of Geometric Analysis, vol. 17, no. 4, Springer, 2007, pp. 559–67, doi:10.1007/BF02937429. short: R. Frank, C. Hainzl, S. Naboko, R. Seiringer, Journal of Geometric Analysis 17 (2007) 559–567. date_created: 2018-12-11T11:57:17Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T06:57:05Z day: '01' doi: 10.1007/BF02937429 extern: 1 intvolume: ' 17' issue: '4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0704.3564 month: '01' oa: 1 page: 559 - 567 publication: Journal of Geometric Analysis publication_status: published publisher: Springer publist_id: '4553' quality_controlled: 0 status: public title: The critical temperature for the BCS equation at weak coupling type: journal_article volume: 17 year: '2007' ... --- _id: '2371' abstract: - lang: eng text: We give a proof of stability of relativistic matter with magnetic fields all the way up to the critical value of the nuclear charge Zα = 2/π. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - 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 citation: ama: Frank R, Lieb É, Seiringer R. Stability of relativistic matter with magnetic fields for nuclear charges up to the critical value. Communications in Mathematical Physics. 2007;275(2):479-489. doi:10.1007/s00220-007-0307-2 apa: Frank, R., Lieb, É., & Seiringer, R. (2007). Stability of relativistic matter with magnetic fields for nuclear charges up to the critical value. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-007-0307-2 chicago: Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Stability of Relativistic Matter with Magnetic Fields for Nuclear Charges up to the Critical Value.” Communications in Mathematical Physics. Springer, 2007. https://doi.org/10.1007/s00220-007-0307-2. ieee: R. Frank, É. Lieb, and R. Seiringer, “Stability of relativistic matter with magnetic fields for nuclear charges up to the critical value,” Communications in Mathematical Physics, vol. 275, no. 2. Springer, pp. 479–489, 2007. ista: Frank R, Lieb É, Seiringer R. 2007. Stability of relativistic matter with magnetic fields for nuclear charges up to the critical value. Communications in Mathematical Physics. 275(2), 479–489. mla: Frank, Rupert, et al. “Stability of Relativistic Matter with Magnetic Fields for Nuclear Charges up to the Critical Value.” Communications in Mathematical Physics, vol. 275, no. 2, Springer, 2007, pp. 479–89, doi:10.1007/s00220-007-0307-2. short: R. Frank, É. Lieb, R. Seiringer, Communications in Mathematical Physics 275 (2007) 479–489. date_created: 2018-12-11T11:57:16Z date_published: 2007-10-01T00:00:00Z date_updated: 2021-01-12T06:57:05Z day: '01' doi: 10.1007/s00220-007-0307-2 extern: 1 intvolume: ' 275' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/math-ph/0610062 month: '10' oa: 1 page: 479 - 489 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4555' quality_controlled: 0 status: public title: Stability of relativistic matter with magnetic fields for nuclear charges up to the critical value type: journal_article volume: 275 year: '2007' ... --- _id: '2451' abstract: - lang: eng text: Signal molecules known as phytohormones play a decisive role in processing signals coming to plants from the surrounding environment. They include auxin — a simple compound with a large range of effects. Auxin is irregularly deposited in plant tissues, it accumulates in certain cellules and through activation of a signal cascade it causes changes in the development programme of these cellules. This article forms a part of the series prepared in honour of the anniversary of the important plant physiologist — Bohumil Němec. author: - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Friml J. Auxin - Universal development signal in plant life. Živa. 2007;1. apa: Friml, J. (2007). Auxin - Universal development signal in plant life. Živa. CSAV. chicago: Friml, Jiří. “Auxin - Universal development signal in plant life.” Živa. CSAV, 2007. ieee: J. Friml, “Auxin - Universal development signal in plant life,” Živa, vol. 1. CSAV, 2007. ista: Friml J. 2007. Auxin - Universal development signal in plant life. Živa. 1. mla: Friml, Jiří. “Auxin - Universal development signal in plant life.” Živa, vol. 1, CSAV, 2007. short: J. Friml, Živa 1 (2007). date_created: 2018-12-11T11:57:44Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T06:57:34Z day: '01' extern: '1' intvolume: ' 1' language: - iso: cze month: '01' oa_version: None publication: Živa publication_status: published publisher: CSAV publist_id: '4452' quality_controlled: '1' status: public title: Auxin - Universal development signal in plant life type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2007' ... --- _id: '2462' author: - first_name: Marta full_name: Michniewicz, Marta last_name: Michniewicz - first_name: Philip full_name: Brewer, Philip B last_name: Brewer - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Michniewicz M, Brewer P, Friml J. Polar auxin transport and asymmetric auxin distribution. The Arabidopsis Book. 2007;5. doi:10.1199/tab.0108 apa: Michniewicz, M., Brewer, P., & Friml, J. (2007). Polar auxin transport and asymmetric auxin distribution. The Arabidopsis Book. The American Society of Plant Biologists. https://doi.org/10.1199/tab.0108 chicago: Michniewicz, Marta, Philip Brewer, and Jiří Friml. “Polar Auxin Transport and Asymmetric Auxin Distribution.” The Arabidopsis Book. The American Society of Plant Biologists, 2007. https://doi.org/10.1199/tab.0108. ieee: M. Michniewicz, P. Brewer, and J. Friml, “Polar auxin transport and asymmetric auxin distribution,” The Arabidopsis Book, vol. 5. The American Society of Plant Biologists, 2007. ista: Michniewicz M, Brewer P, Friml J. 2007. Polar auxin transport and asymmetric auxin distribution. The Arabidopsis Book. 5. mla: Michniewicz, Marta, et al. “Polar Auxin Transport and Asymmetric Auxin Distribution.” The Arabidopsis Book, vol. 5, The American Society of Plant Biologists, 2007, doi:10.1199/tab.0108. short: M. Michniewicz, P. Brewer, J. Friml, The Arabidopsis Book 5 (2007). date_created: 2018-12-11T11:57:48Z date_published: 2007-08-21T00:00:00Z date_updated: 2021-01-12T06:57:38Z day: '21' doi: 10.1199/tab.0108 extern: 1 intvolume: ' 5' month: '08' publication: The Arabidopsis Book publication_status: published publisher: The American Society of Plant Biologists publist_id: '4441' quality_controlled: 0 status: public title: Polar auxin transport and asymmetric auxin distribution type: journal_article volume: 5 year: '2007' ... --- _id: '2495' abstract: - lang: eng text: 'Metabotropic glutamate receptor 4 (mGluR4) is localized mainly to presynaptic membranes in the brain. Rat neostriatum has been reported to contain two types of mGluR4-immunoreactive axon varicosities: small, weakly immunoreactive varicosities that were distributed randomly (type 1) and large, intensely immunoreactive ones that were often aligned linearly (type 2). In the present study, most type 1 terminals formed asymmetric synapses on dendritic spines, whereas type 2 terminals made symmetric synapses on dendritic shafts, showing immunoreactivity for GABAergic markers. After depletion of neostriatal neurons, type 2 but not type 1 varicosities were largely decreased in the damaged region. When medium-sized spiny neurons (MSNs) were labeled with Sindbis virus expressing membrane-targeted green fluorescent protein, mGluR4 immunoreactivity was observed on some varicosities of their axon collaterals in immunofluorescence and immunoelectron microscopies. Furthermore, type 2 varicosities were often positive for substance P but mostly negative for striatal interneuron markers and preproenkephalin. Thus, striatonigral/striato- entopeduncular MSNs are likely to be the largest source of type 2 mGluR4-immunopositive axon terminals in the neostriatum. Next, in the double-immunofluorescence study, almost all choline acetyltransferase (ChAT)-immunopositive and 41% of NK1 receptor-positive dendrites were heavily associated with type 2 mGluR4-immunoreactive varicosities. Neuronal nitric oxide synthase (nNOS)-positive dendrites, in contrast, seemed associated with only a few type 2 varicosities. Conversely, almost all type 2 varicosities were closely apposed to NK1 receptor-positive dendrites that were known to be derived from cholinergic and nNOS-producing interneurons. These findings indicate that the mGluR4-positive terminals of MSN axon collaterals selectively form synapses with neostriatal cholinergic interneurons.' author: - first_name: Eriko full_name: Kuramoto, Eriko last_name: Kuramoto - first_name: Fumino full_name: Fujiyama, Fumino last_name: Fujiyama - first_name: Tomo full_name: Unzai, Tomo last_name: Unzai - first_name: Kouichi full_name: Nakamura, Kouichi last_name: Nakamura - first_name: Hiroyuki full_name: Hioki, Hiroyuki last_name: Hioki - first_name: Takahiro full_name: Furuta, Takahiro last_name: Furuta - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Francesco full_name: Ferraguti, Francesco last_name: Ferraguti - first_name: Takeshi full_name: Kaneko, Takeshi last_name: Kaneko citation: ama: Kuramoto E, Fujiyama F, Unzai T, et al. Metabotropic glutamate receptor 4-immunopositive terminals of medium-sized spiny neurons selectively form synapses with cholinergic interneurons in the rat neostriatum. Journal of Comparative Neurology. 2007;500(5):908-922. doi:10.1002/cne.21216 apa: Kuramoto, E., Fujiyama, F., Unzai, T., Nakamura, K., Hioki, H., Furuta, T., … Kaneko, T. (2007). Metabotropic glutamate receptor 4-immunopositive terminals of medium-sized spiny neurons selectively form synapses with cholinergic interneurons in the rat neostriatum. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.21216 chicago: Kuramoto, Eriko, Fumino Fujiyama, Tomo Unzai, Kouichi Nakamura, Hiroyuki Hioki, Takahiro Furuta, Ryuichi Shigemoto, Francesco Ferraguti, and Takeshi Kaneko. “Metabotropic Glutamate Receptor 4-Immunopositive Terminals of Medium-Sized Spiny Neurons Selectively Form Synapses with Cholinergic Interneurons in the Rat Neostriatum.” Journal of Comparative Neurology. Wiley-Blackwell, 2007. https://doi.org/10.1002/cne.21216. ieee: E. Kuramoto et al., “Metabotropic glutamate receptor 4-immunopositive terminals of medium-sized spiny neurons selectively form synapses with cholinergic interneurons in the rat neostriatum,” Journal of Comparative Neurology, vol. 500, no. 5. Wiley-Blackwell, pp. 908–922, 2007. ista: Kuramoto E, Fujiyama F, Unzai T, Nakamura K, Hioki H, Furuta T, Shigemoto R, Ferraguti F, Kaneko T. 2007. Metabotropic glutamate receptor 4-immunopositive terminals of medium-sized spiny neurons selectively form synapses with cholinergic interneurons in the rat neostriatum. Journal of Comparative Neurology. 500(5), 908–922. mla: Kuramoto, Eriko, et al. “Metabotropic Glutamate Receptor 4-Immunopositive Terminals of Medium-Sized Spiny Neurons Selectively Form Synapses with Cholinergic Interneurons in the Rat Neostriatum.” Journal of Comparative Neurology, vol. 500, no. 5, Wiley-Blackwell, 2007, pp. 908–22, doi:10.1002/cne.21216. short: E. Kuramoto, F. Fujiyama, T. Unzai, K. Nakamura, H. Hioki, T. Furuta, R. Shigemoto, F. Ferraguti, T. Kaneko, Journal of Comparative Neurology 500 (2007) 908–922. date_created: 2018-12-11T11:58:00Z date_published: 2007-02-10T00:00:00Z date_updated: 2021-01-12T06:57:49Z day: '10' doi: 10.1002/cne.21216 extern: 1 intvolume: ' 500' issue: '5' month: '02' page: 908 - 922 publication: Journal of Comparative Neurology publication_status: published publisher: Wiley-Blackwell publist_id: '4406' quality_controlled: 0 status: public title: Metabotropic glutamate receptor 4-immunopositive terminals of medium-sized spiny neurons selectively form synapses with cholinergic interneurons in the rat neostriatum type: journal_article volume: 500 year: '2007' ... --- _id: '2496' abstract: - lang: eng text: 'Glutamate is one candidate for the neurotransmitters and/or neuromodulators involved in taste signaling in taste buds. Group II metabotropic glutamate receptors (mGluRs: mGluR2 and mGluR3) are known to function as presynaptic receptors that regulate the release of glutamate and/or other neurotransmitters in the central nervous system. Group II mGluRs are negatively linked to adenylyl cyclase through Gαi subunits and thereby reduce the turnover of cAMP. In rat taste tissues, a subset of adenylyl-cyclase-8-expressing taste cells coexpress the Gαi subunits gustducin and Gαi2. However, the expression patterns of group II mGluRs in rat taste tissues have not yet been elucidated. We have therefore examined the expression patterns of mGluR2, mGluR3, and gustducin in rat gustatory tissues. Reverse transcription/polymerase chain reaction assays have revealed that mGluR2 and mGluR3 mRNAs are expressed in the circumvallate papillae. In situ hybridization analyses have detected positive signals for mGluR2 and mGluR3 mRNAs only in the circumvallate taste buds. Among the fungiform, foliate, and circumvallate papillae, an antibody against mGluR2/3 labels a subset of taste bud cells and nerve fibers immediately beneath the taste lingual epithelium. Double-labeling experiments have demonstrated that mGluR2/3-positive cells coexpress gustducin. These results indicate that mGluR2 and mGluR3 are coupled to Gαi subunits and play roles in glutamate-mediated signaling in taste transductions.' author: - first_name: Takashi full_name: Toyono, Takashi last_name: Toyono - first_name: Shinji full_name: Kataoka, Shinji last_name: Kataoka - first_name: Yuji full_name: Seta, Yuji last_name: Seta - 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: Toyoshima, Kuniaki last_name: Toyoshima citation: ama: Toyono T, Kataoka S, Seta Y, Shigemoto R, Toyoshima K. Expression of group II metabotropic glutamate receptors in rat gustatory papillae. Cell and Tissue Research. 2007;328(1):57-63. doi:10.1007/s00441-006-0351-9 apa: Toyono, T., Kataoka, S., Seta, Y., Shigemoto, R., & Toyoshima, K. (2007). Expression of group II metabotropic glutamate receptors in rat gustatory papillae. Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-006-0351-9 chicago: Toyono, Takashi, Shinji Kataoka, Yuji Seta, Ryuichi Shigemoto, and Kuniaki Toyoshima. “Expression of Group II Metabotropic Glutamate Receptors in Rat Gustatory Papillae.” Cell and Tissue Research. Springer, 2007. https://doi.org/10.1007/s00441-006-0351-9. ieee: T. Toyono, S. Kataoka, Y. Seta, R. Shigemoto, and K. Toyoshima, “Expression of group II metabotropic glutamate receptors in rat gustatory papillae,” Cell and Tissue Research, vol. 328, no. 1. Springer, pp. 57–63, 2007. ista: Toyono T, Kataoka S, Seta Y, Shigemoto R, Toyoshima K. 2007. Expression of group II metabotropic glutamate receptors in rat gustatory papillae. Cell and Tissue Research. 328(1), 57–63. mla: Toyono, Takashi, et al. “Expression of Group II Metabotropic Glutamate Receptors in Rat Gustatory Papillae.” Cell and Tissue Research, vol. 328, no. 1, Springer, 2007, pp. 57–63, doi:10.1007/s00441-006-0351-9. short: T. Toyono, S. Kataoka, Y. Seta, R. Shigemoto, K. Toyoshima, Cell and Tissue Research 328 (2007) 57–63. date_created: 2018-12-11T11:58:00Z date_published: 2007-04-01T00:00:00Z date_updated: 2021-01-12T06:57:50Z day: '01' doi: 10.1007/s00441-006-0351-9 extern: 1 intvolume: ' 328' issue: '1' month: '04' page: 57 - 63 publication: Cell and Tissue Research publication_status: published publisher: Springer publist_id: '4405' quality_controlled: 0 status: public title: Expression of group II metabotropic glutamate receptors in rat gustatory papillae type: journal_article volume: 328 year: '2007' ... --- _id: '2665' abstract: - lang: eng text: Substance P (SP) is known to be a peptide that facilitates epileptic activity of principal cells in the hippocampus. Paradoxically, in other models, it was found to be protective against seizures by activating substance P receptor (SPR)-expressing interneurons. Thus, these cells appear to play an important role in the generation and regulation of epileptic seizures. The number, distribution, morphological features and input characteristics of SPR-immunoreactive cells were analyzed in surgically removed hippocampi of 28 temporal lobe epileptic patients and eight control hippocampi in order to examine their changes in epileptic tissues. SPR is expressed in a subset of inhibitory cells in the control human hippocampus, they are multipolar interneurons with smooth dendrites, present in all hippocampal subfields. This cell population is considerably different from SPR-positive cells of the rat hippocampus. The CA1 (cornu Ammonis subfield 1) region was chosen for the detailed morphological analysis of the SPR-immunoreactive cells because of its extreme vulnerability in epilepsy. The presence of various neurochemical markers identifies functionally distinct interneuron types, such as those responsible for perisomatic, dendritic or interneuron-selective inhibition. We found considerable colocalization of SPR with calbindin but not with parvalbumin, calretinin, cholecystokinin and somatostatin, therefore we suppose that SPR-positive cells participate mainly in dendritic inhibition. In the non-sclerotic CA1 region they are mainly preserved, whereas their number is decreased in the sclerotic cases. In the epileptic samples their morphology is considerably altered, they possessed more dendritic branches, which often became beaded. Analyses of synaptic coverage revealed that the ratio of symmetric synaptic input of SPR-immunoreactive cells has increased in epileptic samples. Our results suggest that SPR-positive cells are preserved while principal cells are present in the CA1 region, but show reactive changes in epilepsy including intense branching and growth of their dendritic arborization. author: - first_name: Kinga full_name: Tóth, Kinga last_name: Tóth - first_name: Lucia full_name: Wittner, Lucia last_name: Wittner - first_name: Z full_name: Urbán, Z last_name: Urbán - first_name: Werner full_name: Doyle, Werner K last_name: Doyle - first_name: György full_name: Buzsáki, György last_name: Buzsáki - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Tamás full_name: Freund, Tamás F last_name: Freund - first_name: Zsófia full_name: Maglóczky, Zsófia last_name: Maglóczky citation: ama: Tóth K, Wittner L, Urbán Z, et al. Morphology and synaptic input of substance P receptor-immunoreactive interneurons in control and epileptic human hippocampus. Neuroscience. 2007;144(2):495-508. doi:10.1016/j.neuroscience.2006.09.039 apa: Tóth, K., Wittner, L., Urbán, Z., Doyle, W., Buzsáki, G., Shigemoto, R., … Maglóczky, Z. (2007). Morphology and synaptic input of substance P receptor-immunoreactive interneurons in control and epileptic human hippocampus. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2006.09.039 chicago: Tóth, Kinga, Lucia Wittner, Z Urbán, Werner Doyle, György Buzsáki, Ryuichi Shigemoto, Tamás Freund, and Zsófia Maglóczky. “Morphology and Synaptic Input of Substance P Receptor-Immunoreactive Interneurons in Control and Epileptic Human Hippocampus.” Neuroscience. Elsevier, 2007. https://doi.org/10.1016/j.neuroscience.2006.09.039. ieee: K. Tóth et al., “Morphology and synaptic input of substance P receptor-immunoreactive interneurons in control and epileptic human hippocampus,” Neuroscience, vol. 144, no. 2. Elsevier, pp. 495–508, 2007. ista: Tóth K, Wittner L, Urbán Z, Doyle W, Buzsáki G, Shigemoto R, Freund T, Maglóczky Z. 2007. Morphology and synaptic input of substance P receptor-immunoreactive interneurons in control and epileptic human hippocampus. Neuroscience. 144(2), 495–508. mla: Tóth, Kinga, et al. “Morphology and Synaptic Input of Substance P Receptor-Immunoreactive Interneurons in Control and Epileptic Human Hippocampus.” Neuroscience, vol. 144, no. 2, Elsevier, 2007, pp. 495–508, doi:10.1016/j.neuroscience.2006.09.039. short: K. Tóth, L. Wittner, Z. Urbán, W. Doyle, G. Buzsáki, R. Shigemoto, T. Freund, Z. Maglóczky, Neuroscience 144 (2007) 495–508. date_created: 2018-12-11T11:58:57Z date_published: 2007-01-19T00:00:00Z date_updated: 2021-01-12T06:58:55Z day: '19' doi: 10.1016/j.neuroscience.2006.09.039 extern: 1 intvolume: ' 144' issue: '2' month: '01' page: 495 - 508 publication: Neuroscience publication_status: published publisher: Elsevier publist_id: '4232' quality_controlled: 0 status: public title: Morphology and synaptic input of substance P receptor-immunoreactive interneurons in control and epileptic human hippocampus type: journal_article volume: 144 year: '2007' ... --- _id: '2666' abstract: - lang: eng text: GABAB receptors (GABABRs) are involved in early events during neuronal development. The presence of GABABRs in developing oligodendrocytes has not been established. Using immunofluorescent co-localization, we have identified GABABR proteins in O4 marker-positive oligodendrocyte precursor cells (OPCs) in 4-day-old mouse brain periventricular white matter. In culture, OPCs, differentiated oligodendrocytes (DOs) and type 2 astrocytes (ASTs) express both the GABAB1abcdf and GABAB2 subunits of the GABABR. Using semiquantitative PCR analysis with GABABR isoform-selective primers we found that the expression level of GABAB1abd was substantially higher in OPCs or ASTs than in DOs. In contrast, the GABAB2 isoform showed a similar level of expression in OPCs and DOs, and a significantly higher level in ASTs. This indicates that the expression of GABAB1 and GABAB2 subunits are under independent control during oligodendroglial development. Activation of GABABRs using the selective agonist baclofen demonstrated that these receptors are functionally active and negatively coupled to adenylyl cyclase. Manipulation of GABABR activity had no effect on OPC migration in a conventional agarose drop assay, whereas baclofen significantly increased OPC migration in a more sensitive transwell microchamber-based assay. Exposure of cultured OPCs to baclofen increased their proliferation, providing evidence for a functional role of GABABRs in oligodendrocyte development. The presence of GABABRs in developing oligodendrocytes provides a new mechanism for neuronal-glial interactions during development and may offer a novel target for promoting remyelination following white matter injury. author: - first_name: Karen full_name: Luyt, Karen last_name: Luyt - first_name: Timothy full_name: Slade, Timothy P last_name: Slade - first_name: Jienchi full_name: Dorward, Jienchi J last_name: Dorward - first_name: Claire full_name: Durant, Claire F last_name: Durant - first_name: Yue full_name: Wu, Yue last_name: Wu - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Stuart full_name: Mundell, Stuart J last_name: Mundell - first_name: Anikó full_name: Váradi, Anikó last_name: Váradi - first_name: Elek full_name: Molnár, Elek last_name: Molnár citation: ama: Luyt K, Slade T, Dorward J, et al. Developing oligodendrocytes express functional GABAB receptors that stimulate cell proliferation and migration. Journal of Neurochemistry. 2007;100(3):822-840. doi:10.1111/j.1471-4159.2006.04255.x apa: Luyt, K., Slade, T., Dorward, J., Durant, C., Wu, Y., Shigemoto, R., … Molnár, E. (2007). Developing oligodendrocytes express functional GABAB receptors that stimulate cell proliferation and migration. Journal of Neurochemistry. Wiley-Blackwell. https://doi.org/10.1111/j.1471-4159.2006.04255.x chicago: Luyt, Karen, Timothy Slade, Jienchi Dorward, Claire Durant, Yue Wu, Ryuichi Shigemoto, Stuart Mundell, Anikó Váradi, and Elek Molnár. “Developing Oligodendrocytes Express Functional GABAB Receptors That Stimulate Cell Proliferation and Migration.” Journal of Neurochemistry. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1471-4159.2006.04255.x. ieee: K. Luyt et al., “Developing oligodendrocytes express functional GABAB receptors that stimulate cell proliferation and migration,” Journal of Neurochemistry, vol. 100, no. 3. Wiley-Blackwell, pp. 822–840, 2007. ista: Luyt K, Slade T, Dorward J, Durant C, Wu Y, Shigemoto R, Mundell S, Váradi A, Molnár E. 2007. Developing oligodendrocytes express functional GABAB receptors that stimulate cell proliferation and migration. Journal of Neurochemistry. 100(3), 822–840. mla: Luyt, Karen, et al. “Developing Oligodendrocytes Express Functional GABAB Receptors That Stimulate Cell Proliferation and Migration.” Journal of Neurochemistry, vol. 100, no. 3, Wiley-Blackwell, 2007, pp. 822–40, doi:10.1111/j.1471-4159.2006.04255.x. short: K. Luyt, T. Slade, J. Dorward, C. Durant, Y. Wu, R. Shigemoto, S. Mundell, A. Váradi, E. Molnár, Journal of Neurochemistry 100 (2007) 822–840. date_created: 2018-12-11T11:58:57Z date_published: 2007-02-01T00:00:00Z date_updated: 2021-01-12T06:58:55Z day: '01' doi: 10.1111/j.1471-4159.2006.04255.x extern: 1 intvolume: ' 100' issue: '3' month: '02' page: 822 - 840 publication: Journal of Neurochemistry publication_status: published publisher: Wiley-Blackwell publist_id: '4231' quality_controlled: 0 status: public title: Developing oligodendrocytes express functional GABAB receptors that stimulate cell proliferation and migration type: journal_article volume: 100 year: '2007' ... --- _id: '2668' abstract: - lang: eng text: Hyperpolarization-activated, cyclic nucleotide-gated cation (HCN) channels are expressed postsynaptically in the rodent globus pallidus (GP), where they play several important roles in controlling GP neuronal activity. To further elucidate the role of HCN channels in the GP, immunocytochemical and electrophysiological approaches were used to test the hypothesis that HCN channels are also expressed presynaptically on the local axon collaterals of GP neurons. At the electron microscopic level, immunoperoxidase labelling for HCN1 and HCN2 was localized in GP somata and dendritic processes, myelinated and unmyelinated axons, and axon terminals. One population of labelled terminals formed symmetric synapses with somata and proximal dendrites and were immunoreactive for parvalbumin, consistent with the axon collaterals of GABAergic GP projection neurons. In addition, labelling for HCN2 and, to a lesser degree, HCN1 was observed in axon terminals that formed asymmetric synapses and were immunoreactive for the vesicular glutamate transporter 2. Immunogold labelling demonstrated that HCN1 and HCN2 were located predominantly at extrasynaptic sites along the plasma membrane of both types of terminal. To determine the function of presynaptic HCN channels in the GP, we performed whole-cell recordings from GP neurons in vitro. Bath application of the HCN channel blocker ZD7288 resulted in an increase in the frequency of mIPSCs but had no effect on their amplitude, implying that HCN channels tonically regulate the release of GABA. Their presence, and predicted role in modulating transmitter release, represents a hitherto unidentified mechanism whereby HCN channels influence the activity of GP neurons. author: - first_name: Justin full_name: Boyes, Justin last_name: Boyes - first_name: John full_name: Bolam, John P last_name: Bolam - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Ian full_name: Stanford, Ian M last_name: Stanford citation: ama: Boyes J, Bolam J, Shigemoto R, Stanford I. Functional presynaptic HCN channels in the rat globus pallidus. European Journal of Neuroscience. 2007;25(7):2081-2092. doi:10.1111/j.1460-9568.2007.05463.x apa: Boyes, J., Bolam, J., Shigemoto, R., & Stanford, I. (2007). Functional presynaptic HCN channels in the rat globus pallidus. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2007.05463.x chicago: Boyes, Justin, John Bolam, Ryuichi Shigemoto, and Ian Stanford. “Functional Presynaptic HCN Channels in the Rat Globus Pallidus.” European Journal of Neuroscience. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1460-9568.2007.05463.x. ieee: J. Boyes, J. Bolam, R. Shigemoto, and I. Stanford, “Functional presynaptic HCN channels in the rat globus pallidus,” European Journal of Neuroscience, vol. 25, no. 7. Wiley-Blackwell, pp. 2081–2092, 2007. ista: Boyes J, Bolam J, Shigemoto R, Stanford I. 2007. Functional presynaptic HCN channels in the rat globus pallidus. European Journal of Neuroscience. 25(7), 2081–2092. mla: Boyes, Justin, et al. “Functional Presynaptic HCN Channels in the Rat Globus Pallidus.” European Journal of Neuroscience, vol. 25, no. 7, Wiley-Blackwell, 2007, pp. 2081–92, doi:10.1111/j.1460-9568.2007.05463.x. short: J. Boyes, J. Bolam, R. Shigemoto, I. Stanford, European Journal of Neuroscience 25 (2007) 2081–2092. date_created: 2018-12-11T11:58:58Z date_published: 2007-04-01T00:00:00Z date_updated: 2021-01-12T06:58:56Z day: '01' doi: 10.1111/j.1460-9568.2007.05463.x extern: 1 intvolume: ' 25' issue: '7' month: '04' page: 2081 - 2092 publication: European Journal of Neuroscience publication_status: published publisher: Wiley-Blackwell publist_id: '4228' quality_controlled: 0 status: public title: Functional presynaptic HCN channels in the rat globus pallidus type: journal_article volume: 25 year: '2007' ... --- _id: '2667' abstract: - lang: eng text: The number of AMPA receptor (AMPAR) is the major determinant of synaptic strength at glutamatergic synapses, but little is known about the absolute number and density of AMPARs in individual synapses. Using SDS-digested freeze-fracture replica labeling, which has high detection efficiency comparable with electrophysiological noise analysis for functional AMPAR, we analyzed three kinds of excitatory synapses in the molecular layer of the adult rat cerebellum. In parallel fiber (PF)-Purkinje cell (PC) synapses, we found large variability in the number (38.1 ± 34.4 particles per synapse, mean ± SD; range, 2-178 particles per synapse) and density (437 ± 277 particles/μm2; range, 48-1210 particles/μm2) of immunogold-labeled AMPARs. Two-dimensional view and high sensitivity of this method revealed irregular-shaped small AMPAR clusters within synapses. Climbing fiber (CF)-PC synapses had higher number of AMPAR labeling (68.6 ± 34.5 particles per synapse) than PF-PC and PF-interneuron synapses (36.8 ± 14.4 particles per synapse). Furthermore, AMPAR density at CF-PC and PF-interneuron synapses was approximately five times higher and more uniform than that at PF-PC synapses. These results suggest input- and target-dependent regulation of AMPAR-mediated synaptic strength. author: - first_name: Miwako full_name: Masugi-Tokita, Miwako last_name: Masugi Tokita - first_name: Etsuko full_name: Tarusawa, Etsuko last_name: Tarusawa - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Elek full_name: Molnár, Elek last_name: Molnár - first_name: Kazushi full_name: Fujimoto, Kazushi last_name: Fujimoto - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Masugi Tokita M, Tarusawa E, Watanabe M, Molnár E, Fujimoto K, Shigemoto R. Number and density of AMPA receptors in individual synapses in the rat cerebellum as revealed by SDS-digested freeze-fracture replica labeling. Journal of Neuroscience. 2007;27(8):2135-2144. doi:10.1523/JNEUROSCI.2861-06.2007 apa: Masugi Tokita, M., Tarusawa, E., Watanabe, M., Molnár, E., Fujimoto, K., & Shigemoto, R. (2007). Number and density of AMPA receptors in individual synapses in the rat cerebellum as revealed by SDS-digested freeze-fracture replica labeling. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2861-06.2007 chicago: Masugi Tokita, Miwako, Etsuko Tarusawa, Masahiko Watanabe, Elek Molnár, Kazushi Fujimoto, and Ryuichi Shigemoto. “Number and Density of AMPA Receptors in Individual Synapses in the Rat Cerebellum as Revealed by SDS-Digested Freeze-Fracture Replica Labeling.” Journal of Neuroscience. Society for Neuroscience, 2007. https://doi.org/10.1523/JNEUROSCI.2861-06.2007. ieee: M. Masugi Tokita, E. Tarusawa, M. Watanabe, E. Molnár, K. Fujimoto, and R. Shigemoto, “Number and density of AMPA receptors in individual synapses in the rat cerebellum as revealed by SDS-digested freeze-fracture replica labeling,” Journal of Neuroscience, vol. 27, no. 8. Society for Neuroscience, pp. 2135–2144, 2007. ista: Masugi Tokita M, Tarusawa E, Watanabe M, Molnár E, Fujimoto K, Shigemoto R. 2007. Number and density of AMPA receptors in individual synapses in the rat cerebellum as revealed by SDS-digested freeze-fracture replica labeling. Journal of Neuroscience. 27(8), 2135–2144. mla: Masugi Tokita, Miwako, et al. “Number and Density of AMPA Receptors in Individual Synapses in the Rat Cerebellum as Revealed by SDS-Digested Freeze-Fracture Replica Labeling.” Journal of Neuroscience, vol. 27, no. 8, Society for Neuroscience, 2007, pp. 2135–44, doi:10.1523/JNEUROSCI.2861-06.2007. short: M. Masugi Tokita, E. Tarusawa, M. Watanabe, E. Molnár, K. Fujimoto, R. Shigemoto, Journal of Neuroscience 27 (2007) 2135–2144. date_created: 2018-12-11T11:58:58Z date_published: 2007-02-21T00:00:00Z date_updated: 2021-01-12T06:58:55Z day: '21' doi: 10.1523/JNEUROSCI.2861-06.2007 extern: 1 intvolume: ' 27' issue: '8' month: '02' page: 2135 - 2144 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4230' quality_controlled: 0 status: public title: Number and density of AMPA receptors in individual synapses in the rat cerebellum as revealed by SDS-digested freeze-fracture replica labeling type: journal_article volume: 27 year: '2007' ... --- _id: '2669' abstract: - lang: eng text: The properties of the hyperpolarization-activated current (Ih) and its roles in hippocampal network function evolve radically during development. Because Ih is conducted by the hyperpolarization- activated cyclic nucleotide-gated (HCN) cation channels, we tested the hypothesis that understanding the quantitative developmental profiles of HCN1, HCN2, and HCN4 expression, and the isoform- and age-specific progression of their subcellular distribution, should shed light on the established modifications of the properties of Ih throughout development. Combined quantitative in situ hybridization, regional western blots, and high-resolution, dual-label immunocytochemistry revealed striking and novel information about the expression and distribution of the HCN channel isoforms in the developing hippocampal formation. In cornus ammon 1 (CA) pyramidal cell layer, a robust increase of HCN1 mRNA and protein expression occurred with age, with reciprocal reduction of HCN4 and relatively stable HCN2 levels. These distinct expression patterns raised the contribution of HCN1 to the total HCN channel pool from 33% to 65% consonant with acceleration and reduced cyclic adenosine mono phosphate (cAMP) sensitivity of Ih in this region with age. In CA3, strong expression of HCN1 already neonatally supports the recently established role of this conductance in neonatal, age-specific, hippocampal oscillations (giant depolarizing potentials). Notably, HCN1 channels were present and probably transported to dendritic compartments already on postnatal day (P) 2, whereas HCN2 channel protein was not evident in dendrites for the first 2 weeks of life. HCN2 mRNA and protein expression remained fairly constant subsequent to the first week of life in all hippocampal subfields examined, whereas HCN4 mRNA and protein expression declined after maximal neonatal expression, so that the contribution of this isoform to the total HCN channel pool dropped from 43% (CA1) and 34% (CA3) on P11 to 8% (CA1) and 19% (CA3) on P90. Interneuronal expression of all HCN channel isoforms in stratum pyramidale was robust in parvalbumin-but not in cholecystokinin-expressing populations and with a subunit-specific subcellular distribution. Taken together, these data suggest that early in life, HCN4 may contribute significantly to the functions of Ih in specific hippocampal regions. In addition, these evolving, differential quantitative, and subcellular expression patterns of the HCN channel isoforms support age-specific properties and functions of Ih within the developing hippocampal formation. author: - first_name: Amy full_name: Brewster, Amy L last_name: Brewster - first_name: Yuncai full_name: Chen, Yuncai last_name: Chen - first_name: Roland full_name: Bender, Roland A last_name: Bender - first_name: Amy full_name: Yeh, Amy last_name: Yeh - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Tallie full_name: Baram, Tallie Z last_name: Baram citation: ama: Brewster A, Chen Y, Bender R, Yeh A, Shigemoto R, Baram T. Quantitative analysis and subcellular distribution of mRNA and protein expression of the hyperpolarization-activated cyclic nucleotide-gated channels throughout development in rat hippocampus. Cerebral Cortex. 2007;17(3):702-712. doi:10.1093/cercor/bhk021 apa: Brewster, A., Chen, Y., Bender, R., Yeh, A., Shigemoto, R., & Baram, T. (2007). Quantitative analysis and subcellular distribution of mRNA and protein expression of the hyperpolarization-activated cyclic nucleotide-gated channels throughout development in rat hippocampus. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhk021 chicago: Brewster, Amy, Yuncai Chen, Roland Bender, Amy Yeh, Ryuichi Shigemoto, and Tallie Baram. “Quantitative Analysis and Subcellular Distribution of MRNA and Protein Expression of the Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels throughout Development in Rat Hippocampus.” Cerebral Cortex. Oxford University Press, 2007. https://doi.org/10.1093/cercor/bhk021. ieee: A. Brewster, Y. Chen, R. Bender, A. Yeh, R. Shigemoto, and T. Baram, “Quantitative analysis and subcellular distribution of mRNA and protein expression of the hyperpolarization-activated cyclic nucleotide-gated channels throughout development in rat hippocampus,” Cerebral Cortex, vol. 17, no. 3. Oxford University Press, pp. 702–712, 2007. ista: Brewster A, Chen Y, Bender R, Yeh A, Shigemoto R, Baram T. 2007. Quantitative analysis and subcellular distribution of mRNA and protein expression of the hyperpolarization-activated cyclic nucleotide-gated channels throughout development in rat hippocampus. Cerebral Cortex. 17(3), 702–712. mla: Brewster, Amy, et al. “Quantitative Analysis and Subcellular Distribution of MRNA and Protein Expression of the Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels throughout Development in Rat Hippocampus.” Cerebral Cortex, vol. 17, no. 3, Oxford University Press, 2007, pp. 702–12, doi:10.1093/cercor/bhk021. short: A. Brewster, Y. Chen, R. Bender, A. Yeh, R. Shigemoto, T. Baram, Cerebral Cortex 17 (2007) 702–712. date_created: 2018-12-11T11:58:58Z date_published: 2007-03-01T00:00:00Z date_updated: 2021-01-12T06:58:56Z day: '01' doi: 10.1093/cercor/bhk021 extern: 1 intvolume: ' 17' issue: '3' month: '03' page: 702 - 712 publication: Cerebral Cortex publication_status: published publisher: Oxford University Press publist_id: '4229' quality_controlled: 0 status: public title: Quantitative analysis and subcellular distribution of mRNA and protein expression of the hyperpolarization-activated cyclic nucleotide-gated channels throughout development in rat hippocampus type: journal_article volume: 17 year: '2007' ... --- _id: '2673' abstract: - lang: eng text: Excitatory synaptic transmission is inhibited by G protein coupled receptors, including the adenosine A1, GABAB, and metabotropic glutamate receptor 7. These receptors are present in nerve terminals where they reduce the release of glutamate through activating signaling pathways negatively coupled to Ca2+ channels and adenylyl cyclase. However, it is not clear whether these receptors operate in distinct subpopulations of nerve terminals or if they are co-expressed in the same nerve terminals, despite the functional consequences that such distributions may have on synaptic transmission. Applying Ca2+ imaging and immunocytochemistry, we show that these three G protein coupled receptors coexist in a subpopulation of cerebrocortical nerve terminals. The three receptors share an intracellular signaling pathway through which their inhibitory responses are integrated and coactivation of these receptors produced an integrated response. Indeed, this response was highly variable, from a synergistic response at subthreshold agonist concentrations to an occluded response at high agonist concentrations. The presence of multiple receptors in a nerve terminal could be responsible for the physiological effects of neurotransmitter spillover from neighboring synapses or alternatively, the co-release of transmitters by the same nerve terminal. author: - first_name: Carolina full_name: Ladera, Carolina last_name: Ladera - first_name: María full_name: Godino, María D last_name: Godino - first_name: Ricardo full_name: Martín, Ricardo J last_name: Martín - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Francisco full_name: Ciruela, Francisco last_name: Ciruela - first_name: Magdalena full_name: Torres, Magdalena last_name: Torres - first_name: José full_name: Sánchez-Prieto, José last_name: Sánchez Prieto citation: ama: Ladera C, Godino M, Martín R, et al. The coexistence of multiple receptors in a single nerve terminal provides evidence for pre-synaptic integration. Journal of Neurochemistry. 2007;103(6):2314-2326. doi:10.1111/j.1471-4159.2007.04964.x apa: Ladera, C., Godino, M., Martín, R., Luján, R., Shigemoto, R., Ciruela, F., … Sánchez Prieto, J. (2007). The coexistence of multiple receptors in a single nerve terminal provides evidence for pre-synaptic integration. Journal of Neurochemistry. Wiley-Blackwell. https://doi.org/10.1111/j.1471-4159.2007.04964.x chicago: Ladera, Carolina, María Godino, Ricardo Martín, Rafael Luján, Ryuichi Shigemoto, Francisco Ciruela, Magdalena Torres, and José Sánchez Prieto. “ The Coexistence of Multiple Receptors in a Single Nerve Terminal Provides Evidence for Pre-Synaptic Integration.” Journal of Neurochemistry. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1471-4159.2007.04964.x. ieee: C. Ladera et al., “ The coexistence of multiple receptors in a single nerve terminal provides evidence for pre-synaptic integration,” Journal of Neurochemistry, vol. 103, no. 6. Wiley-Blackwell, pp. 2314–2326, 2007. ista: Ladera C, Godino M, Martín R, Luján R, Shigemoto R, Ciruela F, Torres M, Sánchez Prieto J. 2007. The coexistence of multiple receptors in a single nerve terminal provides evidence for pre-synaptic integration. Journal of Neurochemistry. 103(6), 2314–2326. mla: Ladera, Carolina, et al. “ The Coexistence of Multiple Receptors in a Single Nerve Terminal Provides Evidence for Pre-Synaptic Integration.” Journal of Neurochemistry, vol. 103, no. 6, Wiley-Blackwell, 2007, pp. 2314–26, doi:10.1111/j.1471-4159.2007.04964.x. short: C. Ladera, M. Godino, R. Martín, R. Luján, R. Shigemoto, F. Ciruela, M. Torres, J. Sánchez Prieto, Journal of Neurochemistry 103 (2007) 2314–2326. date_created: 2018-12-11T11:58:59Z date_published: 2007-12-01T00:00:00Z date_updated: 2021-01-12T06:58:58Z day: '01' doi: 10.1111/j.1471-4159.2007.04964.x extern: 1 intvolume: ' 103' issue: '6' month: '12' page: 2314 - 2326 publication: Journal of Neurochemistry publication_status: published publisher: Wiley-Blackwell publist_id: '4224' quality_controlled: 0 status: public title: ' The coexistence of multiple receptors in a single nerve terminal provides evidence for pre-synaptic integration' type: journal_article volume: 103 year: '2007' ... --- _id: '2671' abstract: - lang: eng text: 'Increasing evidence supports roles for the current mediated by hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, I h, in hippocampal maturation and specifically in the evolving changes of intrinsic properties as well as network responses of hippocampal neurons. Here, we describe a novel developmental plasticity of HCN channel expression in axonal and presynaptic compartments: HCN1 channels were localized to axon terminals of the perforant path (the major hippocampal afferent pathway) of immature rats, where they modulated synaptic efficacy. However, presynaptic expression and functions of the channels disappeared with maturation. This was a result of altered channel transport to the axons, because HCN1 mRNA and protein levels in entorhinal cortex neurons, where the perforant path axons originate, were stable through adulthood. Blocking action potential firing in vitro increased presynaptic expression of HCN1 channels in the perforant path, suggesting that network activity contributed to regulating this expression. These findings support a novel developmentally regulated axonal transport of functional ion channels and suggest a role for HCN1 channel-mediated presynaptic I h in hippocampal maturation.' author: - first_name: Roland full_name: Bender, Roland A last_name: Bender - first_name: Timo full_name: Kirschstein, Timo last_name: Kirschstein - first_name: Oliver full_name: Kretz, Oliver last_name: Kretz - first_name: Amy full_name: Brewster, Amy L last_name: Brewster - first_name: Cristina full_name: Richichi, Cristina last_name: Richichi - first_name: Christiane full_name: Rüschenschmidt, Christiane last_name: Rüschenschmidt - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Heinz full_name: Beck,Heinz last_name: Beck - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Tallie full_name: Baram, Tallie Z last_name: Baram citation: ama: 'Bender R, Kirschstein T, Kretz O, et al. Localization of HCN1 channels to presynaptic compartments: Novel plasticity that may contribute to hippocampal maturation. Journal of Neuroscience. 2007;27(17):4697-4706. doi:10.1523/JNEUROSCI.4699-06.2007' apa: 'Bender, R., Kirschstein, T., Kretz, O., Brewster, A., Richichi, C., Rüschenschmidt, C., … Baram, T. (2007). Localization of HCN1 channels to presynaptic compartments: Novel plasticity that may contribute to hippocampal maturation. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.4699-06.2007' chicago: 'Bender, Roland, Timo Kirschstein, Oliver Kretz, Amy Brewster, Cristina Richichi, Christiane Rüschenschmidt, Ryuichi Shigemoto, Heinz Beck, Michael Frotscher, and Tallie Baram. “Localization of HCN1 Channels to Presynaptic Compartments: Novel Plasticity That May Contribute to Hippocampal Maturation.” Journal of Neuroscience. Society for Neuroscience, 2007. https://doi.org/10.1523/JNEUROSCI.4699-06.2007.' ieee: 'R. Bender et al., “Localization of HCN1 channels to presynaptic compartments: Novel plasticity that may contribute to hippocampal maturation,” Journal of Neuroscience, vol. 27, no. 17. Society for Neuroscience, pp. 4697–4706, 2007.' ista: 'Bender R, Kirschstein T, Kretz O, Brewster A, Richichi C, Rüschenschmidt C, Shigemoto R, Beck H, Frotscher M, Baram T. 2007. Localization of HCN1 channels to presynaptic compartments: Novel plasticity that may contribute to hippocampal maturation. Journal of Neuroscience. 27(17), 4697–4706.' mla: 'Bender, Roland, et al. “Localization of HCN1 Channels to Presynaptic Compartments: Novel Plasticity That May Contribute to Hippocampal Maturation.” Journal of Neuroscience, vol. 27, no. 17, Society for Neuroscience, 2007, pp. 4697–706, doi:10.1523/JNEUROSCI.4699-06.2007.' short: R. Bender, T. Kirschstein, O. Kretz, A. Brewster, C. Richichi, C. Rüschenschmidt, R. Shigemoto, H. Beck, M. Frotscher, T. Baram, Journal of Neuroscience 27 (2007) 4697–4706. date_created: 2018-12-11T11:58:59Z date_published: 2007-04-25T00:00:00Z date_updated: 2021-01-12T06:58:57Z day: '25' doi: 10.1523/JNEUROSCI.4699-06.2007 extern: 1 intvolume: ' 27' issue: '17' month: '04' page: 4697 - 4706 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4227' quality_controlled: 0 status: public title: 'Localization of HCN1 channels to presynaptic compartments: Novel plasticity that may contribute to hippocampal maturation' type: journal_article volume: 27 year: '2007' ... --- _id: '2672' abstract: - lang: eng text: Hyperpolarization-activated cyclic nucleotide-modulated (HCN) "pacemaker" channel subunits are integral membrane proteins that assemble as tetramers to form channels in cardiac conduction tissue and nerve cells. Previous studies have suggested that the HCN2 and HCN4 channel isoforms physically interact when overexpressed in mammalian cells, but whether they are able to co-assemble and form functional channels remains unclear. The extent to which co-assembly occurs over self-assembly and whether HCN2-HCN4 heteromeric channels are formed in native tissue are not known. In this study, we show co-assembly of HCN2 and HCN4 in live Chinese hamster ovary cells using bioluminescence resonance energy transfer (BRET2), a novel approach for studying tetramerization of ion channel subunits. Together with results from electrophysiological and imaging approaches, the BRET2 data show that HCN2 and HCN4 subunits self-assemble and co-assemble with equal preference. We also demonstrate colocalization of HCN2 and HCN4 and a positive correlation of their intensities in the embryonic mouse heart using immunohistochemistry, as well as physical interactions between these isoforms in the rat thalamus by coimmunoprecipitation. Together, these data support the formation of HCN2-HCN4 heteromeric channels in native tissue. author: - first_name: Gina full_name: Whitaker, Gina M last_name: Whitaker - first_name: Damiano full_name: Angoli, Damiano last_name: Angoli - first_name: Hamed full_name: Nazzari, Hamed last_name: Nazzari - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Eric full_name: Accili, Eric A last_name: Accili citation: ama: Whitaker G, Angoli D, Nazzari H, Shigemoto R, Accili E. HCN2 and HCN4 isoforms self-assemble and co-assemble with equal preference to form functional pacemaker channels. Journal of Biological Chemistry. 2007;282(31):22900-22909. doi:10.1074/jbc.M610978200 apa: Whitaker, G., Angoli, D., Nazzari, H., Shigemoto, R., & Accili, E. (2007). HCN2 and HCN4 isoforms self-assemble and co-assemble with equal preference to form functional pacemaker channels. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M610978200 chicago: Whitaker, Gina, Damiano Angoli, Hamed Nazzari, Ryuichi Shigemoto, and Eric Accili. “HCN2 and HCN4 Isoforms Self-Assemble and Co-Assemble with Equal Preference to Form Functional Pacemaker Channels.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2007. https://doi.org/10.1074/jbc.M610978200. ieee: G. Whitaker, D. Angoli, H. Nazzari, R. Shigemoto, and E. Accili, “HCN2 and HCN4 isoforms self-assemble and co-assemble with equal preference to form functional pacemaker channels,” Journal of Biological Chemistry, vol. 282, no. 31. American Society for Biochemistry and Molecular Biology, pp. 22900–22909, 2007. ista: Whitaker G, Angoli D, Nazzari H, Shigemoto R, Accili E. 2007. HCN2 and HCN4 isoforms self-assemble and co-assemble with equal preference to form functional pacemaker channels. Journal of Biological Chemistry. 282(31), 22900–22909. mla: Whitaker, Gina, et al. “HCN2 and HCN4 Isoforms Self-Assemble and Co-Assemble with Equal Preference to Form Functional Pacemaker Channels.” Journal of Biological Chemistry, vol. 282, no. 31, American Society for Biochemistry and Molecular Biology, 2007, pp. 22900–09, doi:10.1074/jbc.M610978200. short: G. Whitaker, D. Angoli, H. Nazzari, R. Shigemoto, E. Accili, Journal of Biological Chemistry 282 (2007) 22900–22909. date_created: 2018-12-11T11:58:59Z date_published: 2007-08-03T00:00:00Z date_updated: 2021-01-12T06:58:58Z day: '03' doi: 10.1074/jbc.M610978200 extern: 1 intvolume: ' 282' issue: '31' month: '08' page: 22900 - 22909 publication: Journal of Biological Chemistry publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '4225' quality_controlled: 0 status: public title: HCN2 and HCN4 isoforms self-assemble and co-assemble with equal preference to form functional pacemaker channels type: journal_article volume: 282 year: '2007' ... --- _id: '2670' abstract: - lang: eng text: Glutamate and GABA are the main transmitters in the central nervous system and their effects are mediated by ionotropic and metabotropic receptors. Immunogold electron microscopy has revealed the quantitative localization of these receptors at 20-30 nm resolution. SDS-digested freeze-fracture replica labeling (SDS-FRL), a newly developed immunogold method, provides an accurate estimate of molecule numbers. Here, we summarize the recent advances in quantitative receptor localization, including use of SDS-FRL analyses to determine numbers of AMPA-type glutamate receptors in the cerebellum. The two-dimensional view and high sensitivity of SDS-FRL have revealed small, irregularly shaped AMPA receptor clusters within cerebellar synapses. author: - first_name: Miwako full_name: Masugi-Tokita, Miwako last_name: Masugi Tokita - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Masugi Tokita M, Shigemoto R. High-resolution quantitative visualization of glutamate and GABA receptors at central synapses. Current Opinion in Neurobiology. 2007;17(3):387-393. doi:10.1016/j.conb.2007.04.012 apa: Masugi Tokita, M., & Shigemoto, R. (2007). High-resolution quantitative visualization of glutamate and GABA receptors at central synapses. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2007.04.012 chicago: Masugi Tokita, Miwako, and Ryuichi Shigemoto. “High-Resolution Quantitative Visualization of Glutamate and GABA Receptors at Central Synapses.” Current Opinion in Neurobiology. Elsevier, 2007. https://doi.org/10.1016/j.conb.2007.04.012. ieee: M. Masugi Tokita and R. Shigemoto, “High-resolution quantitative visualization of glutamate and GABA receptors at central synapses,” Current Opinion in Neurobiology, vol. 17, no. 3. Elsevier, pp. 387–393, 2007. ista: Masugi Tokita M, Shigemoto R. 2007. High-resolution quantitative visualization of glutamate and GABA receptors at central synapses. Current Opinion in Neurobiology. 17(3), 387–393. mla: Masugi Tokita, Miwako, and Ryuichi Shigemoto. “High-Resolution Quantitative Visualization of Glutamate and GABA Receptors at Central Synapses.” Current Opinion in Neurobiology, vol. 17, no. 3, Elsevier, 2007, pp. 387–93, doi:10.1016/j.conb.2007.04.012. short: M. Masugi Tokita, R. Shigemoto, Current Opinion in Neurobiology 17 (2007) 387–393. date_created: 2018-12-11T11:58:58Z date_published: 2007-06-01T00:00:00Z date_updated: 2020-07-14T12:45:44Z day: '01' doi: 10.1016/j.conb.2007.04.012 extern: 1 intvolume: ' 17' issue: '3' month: '06' page: 387 - 393 publication: Current Opinion in Neurobiology publication_status: published publisher: Elsevier publist_id: '4226' quality_controlled: 0 status: public title: High-resolution quantitative visualization of glutamate and GABA receptors at central synapses type: review volume: 17 year: '2007' ... --- _id: '2705' alternative_title: - Proceedings of Symposia in Pure Mathematics author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: 'Erdös L. Recent developments in quantum mechanics with magnetic fields. In: Gesztesy F, Deift P, Galvez P, Perry P, Schlag W, eds. Spectral Theory and Mathematical Physics: A Festschrift in Honor of Barry Simon’s 60th Birthday . Vol 76. American Mathematical Society; 2007:401-428.' apa: 'Erdös, L. (2007). Recent developments in quantum mechanics with magnetic fields. In F. Gesztesy, P. Deift, P. Galvez, P. Perry, & W. Schlag (Eds.), Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry Simon’s 60th Birthday (Vol. 76, pp. 401–428). American Mathematical Society.' chicago: 'Erdös, László. “Recent Developments in Quantum Mechanics with Magnetic Fields.” In Spectral Theory and Mathematical Physics: A Festschrift in Honor of Barry Simon’s 60th Birthday , edited by Fritz Gesztesy, Percy Deift, Percy Galvez, Peter Perry, and Wilhelm Schlag, 76:401–28. American Mathematical Society, 2007.' ieee: 'L. Erdös, “Recent developments in quantum mechanics with magnetic fields,” in Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry Simon’s 60th Birthday , vol. 76, F. Gesztesy, P. Deift, P. Galvez, P. Perry, and W. Schlag, Eds. American Mathematical Society, 2007, pp. 401–428.' ista: 'Erdös L. 2007.Recent developments in quantum mechanics with magnetic fields. In: Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry Simon’s 60th Birthday . Proceedings of Symposia in Pure Mathematics, vol. 76, 401–428.' mla: 'Erdös, László. “Recent Developments in Quantum Mechanics with Magnetic Fields.” Spectral Theory and Mathematical Physics: A Festschrift in Honor of Barry Simon’s 60th Birthday , edited by Fritz Gesztesy et al., vol. 76, American Mathematical Society, 2007, pp. 401–28.' short: 'L. Erdös, in:, F. Gesztesy, P. Deift, P. Galvez, P. Perry, W. Schlag (Eds.), Spectral Theory and Mathematical Physics: A Festschrift in Honor of Barry Simon’s 60th Birthday , American Mathematical Society, 2007, pp. 401–428.' date_created: 2018-12-11T11:59:10Z date_published: 2007-03-30T00:00:00Z date_updated: 2021-01-12T06:59:10Z day: '30' editor: - first_name: Fritz full_name: Gesztesy, Fritz last_name: Gesztesy - first_name: Percy full_name: Deift, Percy last_name: Deift - first_name: Percy full_name: Galvez, Percy last_name: Galvez - first_name: Peter full_name: Perry, Peter last_name: Perry - first_name: Wilhelm full_name: Schlag, Wilhelm last_name: Schlag extern: 1 intvolume: ' 76' main_file_link: - open_access: '1' url: http://arxiv.org/abs/math-ph/0510055v2 month: '03' oa: 1 page: 401 - 428 publication: 'Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry Simon''s 60th Birthday ' publication_status: published publisher: American Mathematical Society publist_id: '4191' quality_controlled: 0 status: public title: Recent developments in quantum mechanics with magnetic fields type: book_chapter volume: 76 year: '2007' ... --- _id: '2750' abstract: - lang: eng text: We consider random Schrödinger equations on ℝd for d ≥ 3 with a homogeneous Anderson-Poisson type random potential. Denote by λ the coupling constant and ψt the solution with initial data ψ0. The space and time variables scale as χ ≃λ-2-κ/2, t ≃λ-2-κ with 0 < kappa; < kappa;0(d). We prove that, in the limit λ → 0, the expectation of the Wigner distribution of ψt converges weakly to the solution of a heat equation in the space variable x for arbitrary L2 initial data. The proof is based on a rigorous analysis of Feynman diagrams. In the companion paper [10] the analysis of the non-repetition diagrams was presented. In this paper we complete the proof by estimating the recollision diagrams and showing that the main terms, i.e. the ladder diagrams with renormalized propagator, converge to the heat equation. author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Manfred full_name: Salmhofer, Manfred last_name: Salmhofer - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: Erdös L, Salmhofer M, Yau H. Quantum diffusion of the random Schrödinger evolution in the scaling limit II. The recollision diagrams. Communications in Mathematical Physics. 2007;271(1):1-53. doi:10.1007/s00220-006-0158-2 apa: Erdös, L., Salmhofer, M., & Yau, H. (2007). Quantum diffusion of the random Schrödinger evolution in the scaling limit II. The recollision diagrams. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-006-0158-2 chicago: Erdös, László, Manfred Salmhofer, and Horng Yau. “Quantum Diffusion of the Random Schrödinger Evolution in the Scaling Limit II. The Recollision Diagrams.” Communications in Mathematical Physics. Springer, 2007. https://doi.org/10.1007/s00220-006-0158-2. ieee: L. Erdös, M. Salmhofer, and H. Yau, “Quantum diffusion of the random Schrödinger evolution in the scaling limit II. The recollision diagrams,” Communications in Mathematical Physics, vol. 271, no. 1. Springer, pp. 1–53, 2007. ista: Erdös L, Salmhofer M, Yau H. 2007. Quantum diffusion of the random Schrödinger evolution in the scaling limit II. The recollision diagrams. Communications in Mathematical Physics. 271(1), 1–53. mla: Erdös, László, et al. “Quantum Diffusion of the Random Schrödinger Evolution in the Scaling Limit II. The Recollision Diagrams.” Communications in Mathematical Physics, vol. 271, no. 1, Springer, 2007, pp. 1–53, doi:10.1007/s00220-006-0158-2. short: L. Erdös, M. Salmhofer, H. Yau, Communications in Mathematical Physics 271 (2007) 1–53. date_created: 2018-12-11T11:59:24Z date_published: 2007-04-01T00:00:00Z date_updated: 2021-01-12T06:59:27Z day: '01' doi: 10.1007/s00220-006-0158-2 extern: 1 intvolume: ' 271' issue: '1' month: '04' page: 1 - 53 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4142' quality_controlled: 0 status: public title: Quantum diffusion of the random Schrödinger evolution in the scaling limit II. The recollision diagrams type: journal_article volume: 271 year: '2007' ... --- _id: '2751' abstract: - lang: eng text: We consider random Schrödinger equations on ℤd for d ≥ 3 with identically distributed random potential. Denote by λ the coupling constant and ψ t the solution with initial data ψ 0. The space and time variables scale as x ∼ λ -2-κ/2,t ∼ λ-2-κ with 0 < κ < κ0(d). We prove that, in the limit λ → 0, the expectation of the Wigner distribution of ψ t converges weakly to a solution of a heat equation in the space variable x for arbitrary L 2 initial data. The diffusion coefficient is uniquely determined by the kinetic energy associated to the momentum υ. This work is an extension to the lattice case of our previous result in the continuum [8,9]. Due to the non-convexity of the level surfaces of the dispersion relation, the estimates of several Feynman graphs are more involved. author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Manfred full_name: Salmhofer, Manfred last_name: Salmhofer - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: Erdös L, Salmhofer M, Yau H. Quantum diffusion for the Anderson model in the scaling limit. Annales Henri Poincare. 2007;8(4):621-685. doi:10.1007/s00023-006-0318-0 apa: Erdös, L., Salmhofer, M., & Yau, H. (2007). Quantum diffusion for the Anderson model in the scaling limit. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-006-0318-0 chicago: Erdös, László, Manfred Salmhofer, and Horng Yau. “Quantum Diffusion for the Anderson Model in the Scaling Limit.” Annales Henri Poincare. Birkhäuser, 2007. https://doi.org/10.1007/s00023-006-0318-0. ieee: L. Erdös, M. Salmhofer, and H. Yau, “Quantum diffusion for the Anderson model in the scaling limit,” Annales Henri Poincare, vol. 8, no. 4. Birkhäuser, pp. 621–685, 2007. ista: Erdös L, Salmhofer M, Yau H. 2007. Quantum diffusion for the Anderson model in the scaling limit. Annales Henri Poincare. 8(4), 621–685. mla: Erdös, László, et al. “Quantum Diffusion for the Anderson Model in the Scaling Limit.” Annales Henri Poincare, vol. 8, no. 4, Birkhäuser, 2007, pp. 621–85, doi:10.1007/s00023-006-0318-0. short: L. Erdös, M. Salmhofer, H. Yau, Annales Henri Poincare 8 (2007) 621–685. date_created: 2018-12-11T11:59:24Z date_published: 2007-07-01T00:00:00Z date_updated: 2021-01-12T06:59:27Z day: '01' doi: 10.1007/s00023-006-0318-0 extern: 1 intvolume: ' 8' issue: '4' month: '07' page: 621 - 685 publication: Annales Henri Poincare publication_status: published publisher: Birkhäuser publist_id: '4141' quality_controlled: 0 status: public title: Quantum diffusion for the Anderson model in the scaling limit type: journal_article volume: 8 year: '2007' ... --- _id: '2752' abstract: - lang: eng text: We prove L p -bounds on the Fourier transform of measures μ supported on two dimensional surfaces. Our method allows to consider surfaces whose Gauss curvature vanishes on a one-dimensional submanifold. Under a certain non-degeneracy condition, we prove that μ ∧ ε L 4+β, β > 0, and we give a logarithmically divergent bound on the L 4-norm. We use this latter bound to estimate almost singular integrals involving the dispersion relation, e(p)= ∑13 [1-\cos p_j]} , of the discrete Laplace operator on the cubic lattice. We briefly explain our motivation for this bound originating in the theory of random Schrödinger operators. author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Manfred full_name: Salmhofer, Manfred last_name: Salmhofer citation: ama: Erdös L, Salmhofer M. Decay of the Fourier transform of surfaces with vanishing curvature. Mathematische Zeitschrift. 2007;257(2):261-294. doi:10.1007/s00209-007-0125-4 apa: Erdös, L., & Salmhofer, M. (2007). Decay of the Fourier transform of surfaces with vanishing curvature. Mathematische Zeitschrift. Springer. https://doi.org/10.1007/s00209-007-0125-4 chicago: Erdös, László, and Manfred Salmhofer. “Decay of the Fourier Transform of Surfaces with Vanishing Curvature.” Mathematische Zeitschrift. Springer, 2007. https://doi.org/10.1007/s00209-007-0125-4. ieee: L. Erdös and M. Salmhofer, “Decay of the Fourier transform of surfaces with vanishing curvature,” Mathematische Zeitschrift, vol. 257, no. 2. Springer, pp. 261–294, 2007. ista: Erdös L, Salmhofer M. 2007. Decay of the Fourier transform of surfaces with vanishing curvature. Mathematische Zeitschrift. 257(2), 261–294. mla: Erdös, László, and Manfred Salmhofer. “Decay of the Fourier Transform of Surfaces with Vanishing Curvature.” Mathematische Zeitschrift, vol. 257, no. 2, Springer, 2007, pp. 261–94, doi:10.1007/s00209-007-0125-4. short: L. Erdös, M. Salmhofer, Mathematische Zeitschrift 257 (2007) 261–294. date_created: 2018-12-11T11:59:25Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T06:59:28Z day: '01' doi: 10.1007/s00209-007-0125-4 extern: 1 intvolume: ' 257' issue: '2' month: '01' page: 261 - 294 publication: Mathematische Zeitschrift publication_status: published publisher: Springer publist_id: '4140' quality_controlled: 0 status: public title: Decay of the Fourier transform of surfaces with vanishing curvature type: journal_article volume: 257 year: '2007' ... --- _id: '2749' abstract: - lang: eng text: 'We prove rigorously that the one-particle density matrix of three dimensional interacting Bose systems with a short-scale repulsive pair interaction converges to the solution of the cubic non-linear Schrödinger equation in a suitable scaling limit. The result is extended to k-particle density matrices for all positive integer k. ' 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. Derivation of the cubic non linear Schrödinger equation from quantum dynamics of many body systems. Inventiones Mathematicae. 2007;167(3):515-614. doi:10.1007/s00222-006-0022-1 apa: Erdös, L., Schlein, B., & Yau, H. (2007). Derivation of the cubic non linear Schrödinger equation from quantum dynamics of many body systems. Inventiones Mathematicae. Springer. https://doi.org/10.1007/s00222-006-0022-1 chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Derivation of the Cubic Non Linear Schrödinger Equation from Quantum Dynamics of Many Body Systems.” Inventiones Mathematicae. Springer, 2007. https://doi.org/10.1007/s00222-006-0022-1. ieee: L. Erdös, B. Schlein, and H. Yau, “Derivation of the cubic non linear Schrödinger equation from quantum dynamics of many body systems,” Inventiones Mathematicae, vol. 167, no. 3. Springer, pp. 515–614, 2007. ista: Erdös L, Schlein B, Yau H. 2007. Derivation of the cubic non linear Schrödinger equation from quantum dynamics of many body systems. Inventiones Mathematicae. 167(3), 515–614. mla: Erdös, László, et al. “Derivation of the Cubic Non Linear Schrödinger Equation from Quantum Dynamics of Many Body Systems.” Inventiones Mathematicae, vol. 167, no. 3, Springer, 2007, pp. 515–614, doi:10.1007/s00222-006-0022-1. short: L. Erdös, B. Schlein, H. Yau, Inventiones Mathematicae 167 (2007) 515–614. date_created: 2018-12-11T11:59:24Z date_published: 2007-03-01T00:00:00Z date_updated: 2019-04-26T07:22:19Z day: '01' doi: 10.1007/s00222-006-0022-1 extern: 1 intvolume: ' 167' issue: '3' month: '03' page: 515 - 614 publication: Inventiones Mathematicae publication_status: published publisher: Springer publist_id: '4143' quality_controlled: 0 status: public title: Derivation of the cubic non linear Schrödinger equation from quantum dynamics of many body systems type: review volume: 167 year: '2007' ... --- _id: '2748' abstract: - lang: eng text: The time-dependent Gross-Pitaevskii equation describes the dynamics of initially trapped Bose-Einstein condensates. We present a rigorous proof of this fact starting from a many-body bosonic Schrödinger equation with a short-scale repulsive interaction in the dilute limit. Our proof shows the persistence of an explicit short-scale correlation structure in the condensate. 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. Physical Review Letters. 2007;98(4). doi:10.1103/PhysRevLett.98.040404 apa: Erdös, L., Schlein, B., & Yau, H. (2007). Rigorous derivation of the Gross-Pitaevskii equation. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.98.040404 chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Rigorous Derivation of the Gross-Pitaevskii Equation.” Physical Review Letters. American Physical Society, 2007. https://doi.org/10.1103/PhysRevLett.98.040404. ieee: L. Erdös, B. Schlein, and H. Yau, “Rigorous derivation of the Gross-Pitaevskii equation,” Physical Review Letters, vol. 98, no. 4. American Physical Society, 2007. ista: Erdös L, Schlein B, Yau H. 2007. Rigorous derivation of the Gross-Pitaevskii equation. Physical Review Letters. 98(4). mla: Erdös, László, et al. “Rigorous Derivation of the Gross-Pitaevskii Equation.” Physical Review Letters, vol. 98, no. 4, American Physical Society, 2007, doi:10.1103/PhysRevLett.98.040404. short: L. Erdös, B. Schlein, H. Yau, Physical Review Letters 98 (2007). date_created: 2018-12-11T11:59:23Z date_published: 2007-01-26T00:00:00Z date_updated: 2021-01-12T06:59:26Z day: '26' doi: 10.1103/PhysRevLett.98.040404 extern: 1 intvolume: ' 98' issue: '4' month: '01' publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '4144' quality_controlled: 0 status: public title: Rigorous derivation of the Gross-Pitaevskii equation type: journal_article volume: 98 year: '2007' ... --- _id: '2793' abstract: - lang: eng text: Pipe flow is a prominent example among the shear flows that undergo transition to turbulence without mediation by a linear instability of the laminar profile. Experiments on pipe flow, as well as plane Couette and plane Poiseuille flow, show that triggering turbulence depends sensitively on initial conditions, that between the laminar and the turbulent states there exists no intermediate state with simple spatial or temporal characteristics, and that turbulence is not persistent, i.e., it can decay again, if the observation time is long enough. All these features can consistently be explained on the assumption that the turbulent state corresponds to a chaotic saddle in state space. The goal of this review is to explain this concept, summarize the numerical and experimental evidence for pipe flow, and outline the consequences for related flows. author: - first_name: Bruno full_name: Eckhardt, Bruno last_name: Eckhardt - first_name: Tobias full_name: Schneider, Tobias M last_name: Schneider - 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: Eckhardt B, Schneider T, Hof B, Westerweel J. Turbulence transition in pipe flow. Annual Review of Fluid Mechanics. 2007;39:447-468. doi:10.1146/annurev.fluid.39.050905.110308 apa: Eckhardt, B., Schneider, T., Hof, B., & Westerweel, J. (2007). Turbulence transition in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev.fluid.39.050905.110308 chicago: Eckhardt, Bruno, Tobias Schneider, Björn Hof, and Jerry Westerweel. “Turbulence Transition in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2007. https://doi.org/10.1146/annurev.fluid.39.050905.110308. ieee: B. Eckhardt, T. Schneider, B. Hof, and J. Westerweel, “Turbulence transition in pipe flow,” Annual Review of Fluid Mechanics, vol. 39. Annual Reviews, pp. 447–468, 2007. ista: Eckhardt B, Schneider T, Hof B, Westerweel J. 2007. Turbulence transition in pipe flow. Annual Review of Fluid Mechanics. 39, 447–468. mla: Eckhardt, Bruno, et al. “Turbulence Transition in Pipe Flow.” Annual Review of Fluid Mechanics, vol. 39, Annual Reviews, 2007, pp. 447–68, doi:10.1146/annurev.fluid.39.050905.110308. short: B. Eckhardt, T. Schneider, B. Hof, J. Westerweel, Annual Review of Fluid Mechanics 39 (2007) 447–468. date_created: 2018-12-11T11:59:38Z date_published: 2007-01-01T00:00:00Z date_updated: 2019-04-26T07:22:20Z day: '01' doi: 10.1146/annurev.fluid.39.050905.110308 extern: 1 intvolume: ' 39' month: '01' page: 447 - 468 publication: Annual Review of Fluid Mechanics publication_status: published publisher: Annual Reviews publist_id: '4096' quality_controlled: 0 status: public title: Turbulence transition in pipe flow type: review volume: 39 year: '2007' ... --- _id: '2794' alternative_title: - Springer Proceedings in Physics author: - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Wilco full_name: Tax, Wilco last_name: Tax - first_name: Jerry full_name: Westerweel, Jerry last_name: Westerweel citation: ama: 'Hof B, Tax W, Westerweel J. Lifetime of turbulence in pipe flow. In: Vol 117. Springer; 2007:556-558. doi:10.1007/978-3-540-72604-3_177' apa: 'Hof, B., Tax, W., & Westerweel, J. (2007). Lifetime of turbulence in pipe flow (Vol. 117, pp. 556–558). Presented at the EETC11: European Turbulence Conference, Springer. https://doi.org/10.1007/978-3-540-72604-3_177' chicago: Hof, Björn, Wilco Tax, and Jerry Westerweel. “Lifetime of Turbulence in Pipe Flow,” 117:556–58. Springer, 2007. https://doi.org/10.1007/978-3-540-72604-3_177. ieee: 'B. Hof, W. Tax, and J. Westerweel, “Lifetime of turbulence in pipe flow,” presented at the EETC11: European Turbulence Conference, 2007, vol. 117, pp. 556–558.' ista: 'Hof B, Tax W, Westerweel J. 2007. Lifetime of turbulence in pipe flow. EETC11: European Turbulence Conference, Springer Proceedings in Physics, vol. 117, 556–558.' mla: Hof, Björn, et al. Lifetime of Turbulence in Pipe Flow. Vol. 117, Springer, 2007, pp. 556–58, doi:10.1007/978-3-540-72604-3_177. short: B. Hof, W. Tax, J. Westerweel, in:, Springer, 2007, pp. 556–558. conference: name: 'EETC11: European Turbulence Conference' date_created: 2018-12-11T11:59:38Z date_published: 2007-06-01T00:00:00Z date_updated: 2021-01-12T06:59:45Z day: '01' doi: 10.1007/978-3-540-72604-3_177 extern: 1 intvolume: ' 117' month: '06' page: 556 - 558 publication_status: published publisher: Springer publist_id: '4095' quality_controlled: 0 status: public title: Lifetime of turbulence in pipe flow type: conference volume: 117 year: '2007' ... --- _id: '2893' abstract: - lang: eng text: 'Summary: Regulatory CD4+ T cells, enriched in the CD25 pool of healthy individuals, mediate natural tolerance and prevent autoimmune diseases. Despite their fundamental and potential clinical significance, regulatory T (TR) cells have not yet been incorporated in a coherent theory of the immune system. This article reviews experimental evidence and theoretical arguments supporting a model of TR cell dynamics, uncovering some of its most relevant biological implications. According to this model, the persistence and expansion of TR cell populations depend strictly on specific interactions they make with antigen-presenting cells (APCs) and conventional effector T (TE) cells. This three-partner crossregulation imposes that TR cells feed on the specific autoimmune activities they suppress, with implications ranging from their interactions with other cells to their repertoire selection in the periphery and in the thymus, and to the relationship between these cells and the innate immune system. These implications stem from the basic prediction that the peripheral dynamics sort the CD4+ T-cell repertoire into two subsets: a less diverse set of small clones of autoreactive effector and regulatory cells that regulate each other’s growth, and a more diverse set of barely autoreactive TE cell clones, whose expansion is limited only by APC availability. It is argued that such partitioning of the repertoire sets the ground for self–non-self discrimination. ' author: - first_name: Jorge full_name: Carneiro, Jorge last_name: Carneiro - first_name: Kalet full_name: Leon, Kalet last_name: Leon - first_name: Íris full_name: Caramalho, Íris last_name: Caramalho - first_name: Carline full_name: Van Den Dool, Carline last_name: Van Den Dool - first_name: Rui full_name: Gardner, Rui last_name: Gardner - first_name: Vanessa full_name: Oliveira, Vanessa last_name: Oliveira - first_name: Marie full_name: Bergman, Marie L last_name: Bergman - first_name: Nuno full_name: Sepúlveda, Nuno last_name: Sepúlveda - first_name: Tiago full_name: Tiago Paixao id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Jose full_name: Faro, Jose last_name: Faro - first_name: Jocelyne full_name: Demengeot, Jocelyne last_name: Demengeot citation: ama: Carneiro J, Leon K, Caramalho Í, et al. When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological Reviews. 2007;216(1):48-68. doi:10.1111/j.1600-065X.2007.00487.x apa: Carneiro, J., Leon, K., Caramalho, Í., Van Den Dool, C., Gardner, R., Oliveira, V., … Demengeot, J. (2007). When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological Reviews. Wiley-Blackwell. https://doi.org/10.1111/j.1600-065X.2007.00487.x chicago: Carneiro, Jorge, Kalet Leon, Íris Caramalho, Carline Van Den Dool, Rui Gardner, Vanessa Oliveira, Marie Bergman, et al. “When Three Is Not a Crowd a Crossregulation Model of the Dynamics and Repertoire Selection of Regulatory CD4 T Cells.” Immunological Reviews. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1600-065X.2007.00487.x. ieee: J. Carneiro et al., “When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells,” Immunological Reviews, vol. 216, no. 1. Wiley-Blackwell, pp. 48–68, 2007. ista: Carneiro J, Leon K, Caramalho Í, Van Den Dool C, Gardner R, Oliveira V, Bergman M, Sepúlveda N, Paixao T, Faro J, Demengeot J. 2007. When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological Reviews. 216(1), 48–68. mla: Carneiro, Jorge, et al. “When Three Is Not a Crowd a Crossregulation Model of the Dynamics and Repertoire Selection of Regulatory CD4 T Cells.” Immunological Reviews, vol. 216, no. 1, Wiley-Blackwell, 2007, pp. 48–68, doi:10.1111/j.1600-065X.2007.00487.x. short: J. Carneiro, K. Leon, Í. Caramalho, C. Van Den Dool, R. Gardner, V. Oliveira, M. Bergman, N. Sepúlveda, T. Paixao, J. Faro, J. Demengeot, Immunological Reviews 216 (2007) 48–68. date_created: 2018-12-11T12:00:11Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:00:31Z day: '01' doi: 10.1111/j.1600-065X.2007.00487.x extern: 1 intvolume: ' 216' issue: '1' month: '01' page: 48 - 68 publication: Immunological Reviews publication_status: published publisher: Wiley-Blackwell publist_id: '3865' quality_controlled: 0 status: public title: When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells type: journal_article volume: 216 year: '2007' ... --- _id: '2896' abstract: - lang: eng text: Gene expression from both parental alleles is beneficial by masking the effects of deleterious recessive mutations and by reducing the noise in gene expression in diploid organisms. However, a class of genes are expressed preferentially or strictly from a single allele. The selective advantage of avoiding biallelic expression is clear for allelic-excluded antigen receptor and odorant receptor genes, genes undergoing X-chromosome inactivation in females and parental genomic imprinted genes. In contrast, there is no clear biological rationale for the predominant and stochastic monoallelic expression of cytokine genes in the immune system, and the underlying mechanism is elusive and controversial. A clarification of the mechanism of predominant monoallelic expression would be instrumental in better understanding its eventual biological functional. This prompted the development of a quantitative framework that could describe the dynamics of the pattern of allele expression of the IL-10 gene, from which general quantitative insights could be gained. We report that the experimental observations on these patterns of allelic expression cannot be easily reconciled with a simple model of stochastic transcriptional activation, in which the two alleles are, at any time, equally competent for transcription. Instead, these observations call into action a general model of eukaryotic transcriptional regulation according to which the locus competence for transcription is dynamic, involving multiple, cooperative and stochastic modification steps. In this model, the probability that an allele becomes transcriptionally active is a function of the number of chromatin modifications that it accumulated. On the basis of the properties of this model, we argue that predominant monoallelic expression might have had no adaptive role, and may have evolved under indirect selection for low frequency of expressing cells. acknowledgement: Calado and Paixão acknowledge the financial support of Fundação para a Ciência e a Tecnologia (fellowships SFRH/BD/2973/2000 and SFRH/BD/10550/2002, respectively). author: - first_name: Tiago full_name: Tiago Paixao id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Tiago full_name: Carvalho, Tiago P last_name: Carvalho - first_name: Dinis full_name: Calado, Dinis P last_name: Calado - first_name: Jorge full_name: Carneiro, Jorge last_name: Carneiro citation: ama: Paixao T, Carvalho T, Calado D, Carneiro J. Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology. 2007;85(4):315-322. doi:10.1038/sj.icb.7100057 apa: Paixao, T., Carvalho, T., Calado, D., & Carneiro, J. (2007). Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology. Nature Publishing Group. https://doi.org/10.1038/sj.icb.7100057 chicago: Paixao, Tiago, Tiago Carvalho, Dinis Calado, and Jorge Carneiro. “Quantitative Insights into Stochastic Monoallelic Expression of Cytokine Genes.” Immunology and Cell Biology. Nature Publishing Group, 2007. https://doi.org/10.1038/sj.icb.7100057. ieee: T. Paixao, T. Carvalho, D. Calado, and J. Carneiro, “Quantitative insights into stochastic monoallelic expression of cytokine genes,” Immunology and Cell Biology, vol. 85, no. 4. Nature Publishing Group, pp. 315–322, 2007. ista: Paixao T, Carvalho T, Calado D, Carneiro J. 2007. Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology. 85(4), 315–322. mla: Paixao, Tiago, et al. “Quantitative Insights into Stochastic Monoallelic Expression of Cytokine Genes.” Immunology and Cell Biology, vol. 85, no. 4, Nature Publishing Group, 2007, pp. 315–22, doi:10.1038/sj.icb.7100057. short: T. Paixao, T. Carvalho, D. Calado, J. Carneiro, Immunology and Cell Biology 85 (2007) 315–322. date_created: 2018-12-11T12:00:12Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:00:32Z day: '01' doi: 10.1038/sj.icb.7100057 extern: 1 intvolume: ' 85' issue: '4' month: '01' page: 315 - 322 publication: Immunology and Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '3862' quality_controlled: 0 status: public title: Quantitative insights into stochastic monoallelic expression of cytokine genes type: journal_article volume: 85 year: '2007' ... --- _id: '2933' author: - first_name: M Pawan full_name: Kumar, M Pawan last_name: Kumar - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Philip full_name: Torr, Philip H last_name: Torr citation: ama: 'Kumar MP, Kolmogorov V, Torr P. An Analysis of Convex Relaxations for MAP Estimation. In: Neural Information Processing Systems; 2007.' apa: Kumar, M. P., Kolmogorov, V., & Torr, P. (2007). An Analysis of Convex Relaxations for MAP Estimation. Presented at the Neural Information Processing Systems, Neural Information Processing Systems. chicago: Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex Relaxations for MAP Estimation.” Neural Information Processing Systems, 2007. ieee: M. P. Kumar, V. Kolmogorov, and P. Torr, “An Analysis of Convex Relaxations for MAP Estimation,” presented at the Neural Information Processing Systems, 2007. ista: Kumar MP, Kolmogorov V, Torr P. 2007. An Analysis of Convex Relaxations for MAP Estimation. Neural Information Processing Systems. mla: Kumar, M. Pawan, et al. An Analysis of Convex Relaxations for MAP Estimation. Neural Information Processing Systems, 2007. short: M.P. Kumar, V. Kolmogorov, P. Torr, in:, Neural Information Processing Systems, 2007. conference: name: Neural Information Processing Systems date_created: 2018-12-11T12:00:25Z date_published: 2007-12-01T00:00:00Z date_updated: 2021-01-12T07:39:52Z day: '01' extern: 1 month: '12' publication_status: published publisher: Neural Information Processing Systems publist_id: '3803' quality_controlled: 0 status: public title: An Analysis of Convex Relaxations for MAP Estimation type: conference year: '2007' ... --- _id: '3019' abstract: - lang: eng text: |2- Directional transport of the phytohormone auxin is established primarily at the point of cellular afflux and is required for the establishment and maintenance of plant polarity. Studies in whole plants and heterologous systems indicate that PIN-FORMED (PIN) and P-glycoprotein (PGP) transport proteins mediate the cellular efflux of natural and synthetic auxins. However, aromatic anion transport resulting from PGP and PIN expression in nonplant systems was also found to lack tha high level of substrate specificity seen in planta. Furthermore, previous reports that PGP19 stabilizes PIN1 on the plasma membrane suggested that PIN-PGP interactions might regulate polar auxin efflux. Hare, we show that PGP1 and PGP19 colocalized with PIN1 in the shoot apax in Arabidopsis thaliana and with PIN1 and PIN2 in root tissues. Specific PGP-PIN interactions were seen in yeast two-hybrid and colmmunoprecipitation assays. PIN-PGP interactions appeared to enhance transport activity and, to a greater extent, substrate/inhibitor specificities when coexpressed in heterologous systems. By contrast, no interactions between PGPs and the AUXIN1 influx carrier were observed. Phenotypes of pin and pgp mutants suggest discrete functional roles in auxin transport, but pin pgp mutants exhibited phenotypes that are both additive and synergistic. These results suggest that PINs and PGPs characterize coordinated, Independent auxin transport mechanisms but also function interactively in a tissue-specific manner. author: - first_name: Joshua full_name: Blakeslee, Joshua last_name: Blakeslee - first_name: Anindita full_name: Bandyopadhyay, Anindita last_name: Bandyopadhyay - first_name: Ran full_name: Ok, Ran Lee last_name: Ok - first_name: Jozef full_name: Mravec, Jozef last_name: Mravec - first_name: Boosaree full_name: Titapiwatanakun, Boosaree last_name: Titapiwatanakun - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Srinivas full_name: Makam, Srinivas N last_name: Makam - first_name: Yan full_name: Cheng, Yan last_name: Cheng - first_name: Rodolphe full_name: Bouchard, Rodolphe last_name: Bouchard - first_name: Jiří full_name: Adamec, Jiří last_name: Adamec - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Akitomo full_name: Nagashima, Akitomo last_name: Nagashima - first_name: Tatsuya full_name: Sakai, Tatsuya last_name: Sakai - first_name: Enrico full_name: Martinoia, Enrico last_name: Martinoia - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Wendy full_name: Peer, Wendy A last_name: Peer - first_name: Angus full_name: Murphy, Angus S last_name: Murphy citation: ama: Blakeslee J, Bandyopadhyay A, Ok R, et al. Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis. Plant Cell. 2007;19(1):131-147. doi:10.1105/tpc.106.040782 apa: Blakeslee, J., Bandyopadhyay, A., Ok, R., Mravec, J., Titapiwatanakun, B., Sauer, M., … Murphy, A. (2007). Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.106.040782 chicago: Blakeslee, Joshua, Anindita Bandyopadhyay, Ran Ok, Jozef Mravec, Boosaree Titapiwatanakun, Michael Sauer, Srinivas Makam, et al. “Interactions among PIN FORMED and P Glycoprotein Auxin Transporters in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2007. https://doi.org/10.1105/tpc.106.040782. ieee: J. Blakeslee et al., “Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis,” Plant Cell, vol. 19, no. 1. American Society of Plant Biologists, pp. 131–147, 2007. ista: Blakeslee J, Bandyopadhyay A, Ok R, Mravec J, Titapiwatanakun B, Sauer M, Makam S, Cheng Y, Bouchard R, Adamec J, Geisler M, Nagashima A, Sakai T, Martinoia E, Friml J, Peer W, Murphy A. 2007. Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis. Plant Cell. 19(1), 131–147. mla: Blakeslee, Joshua, et al. “Interactions among PIN FORMED and P Glycoprotein Auxin Transporters in Arabidopsis.” Plant Cell, vol. 19, no. 1, American Society of Plant Biologists, 2007, pp. 131–47, doi:10.1105/tpc.106.040782. short: J. Blakeslee, A. Bandyopadhyay, R. Ok, J. Mravec, B. Titapiwatanakun, M. Sauer, S. Makam, Y. Cheng, R. Bouchard, J. Adamec, M. Geisler, A. Nagashima, T. Sakai, E. Martinoia, J. Friml, W. Peer, A. Murphy, Plant Cell 19 (2007) 131–147. date_created: 2018-12-11T12:00:54Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:40:29Z day: '01' doi: 10.1105/tpc.106.040782 extern: 1 intvolume: ' 19' issue: '1' month: '01' page: 131 - 147 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3682' quality_controlled: 0 status: public title: Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis type: journal_article volume: 19 year: '2007' ... --- _id: '3023' abstract: - lang: eng text: 'Cytokinesis ensures proper partitioning of the nucleocytoplasmic contents into two daughter cells. It has generally been thought that cytokinesis is accomplished differently in animals and plants because of the differences in the preparatory phases, into the centrosomal or acentrosomal nature of the process, the presence or absence of rigid cell walls, and on the basis of ‘outside‐in’ or ‘inside‐out’ mechanism. However, this long‐standing paradigm needs further reevaluation based on new findings. Recent advances reveal that plant cells, similarly to animal cells, possess astral microtubules that regulate the cell division plane. Furthermore, endocytosis has been found to be important for cytokinesis in animal and plant cells: vesicles containing endocytosed cargo provide material for the cell plate formation in plants and for closure of the midbody channel in animals. Thus, although the preparatory phases of the cell division process differ between plant and animal cells, the later phases show similarities. We unify these findings in a model that suggests a conserved mode of cytokinesis.' author: - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Jozef full_name: Šamaj, Jozef last_name: Šamaj - first_name: František full_name: Baluška, František last_name: Baluška - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Dhonukshe P, Šamaj J, Baluška F, Friml J. A unifying new model of cytokinesis for the dividing plant and animal cells. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 2007;29(4):371-381. doi:10.1002/bies.20559' apa: 'Dhonukshe, P., Šamaj, J., Baluška, F., & Friml, J. (2007). A unifying new model of cytokinesis for the dividing plant and animal cells. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. Wiley-Blackwell. https://doi.org/10.1002/bies.20559' chicago: 'Dhonukshe, Pankaj, Jozef Šamaj, František Baluška, and Jiří Friml. “A Unifying New Model of Cytokinesis for the Dividing Plant and Animal Cells.” Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. Wiley-Blackwell, 2007. https://doi.org/10.1002/bies.20559.' ieee: 'P. Dhonukshe, J. Šamaj, F. Baluška, and J. Friml, “A unifying new model of cytokinesis for the dividing plant and animal cells,” Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology, vol. 29, no. 4. Wiley-Blackwell, pp. 371–381, 2007.' ista: 'Dhonukshe P, Šamaj J, Baluška F, Friml J. 2007. A unifying new model of cytokinesis for the dividing plant and animal cells. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 29(4), 371–381.' mla: 'Dhonukshe, Pankaj, et al. “A Unifying New Model of Cytokinesis for the Dividing Plant and Animal Cells.” Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology, vol. 29, no. 4, Wiley-Blackwell, 2007, pp. 371–81, doi:10.1002/bies.20559.' short: 'P. Dhonukshe, J. Šamaj, F. Baluška, J. Friml, Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology 29 (2007) 371–381.' date_created: 2018-12-11T12:00:55Z date_published: 2007-04-01T00:00:00Z date_updated: 2021-01-12T07:40:31Z day: '01' doi: 10.1002/bies.20559 extern: '1' external_id: pmid: - ' 17373659' intvolume: ' 29' issue: '4' language: - iso: eng month: '04' oa_version: None page: 371 - 381 pmid: 1 publication: 'Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology' publication_status: published publisher: Wiley-Blackwell publist_id: '3678' quality_controlled: '1' status: public title: A unifying new model of cytokinesis for the dividing plant and animal cells type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2007' ... --- _id: '3021' abstract: - lang: eng text: Polarized transport of the plant hormone auxin influences multiple growth processes in plants and is regulated by plasma-membrane-localized efflux and uptake carriers. The PGP (P-glycoprotein) ABC transporters (ATP-binding-cassette transporters), PIN (pin-formed) subfamily of major facilitator proteins and members of AUX/LAX families have been shown to independently transport auxin both in planta and in heterologous systems. However, PIN- and PGP-mediated transport in heterologous systems exhibits decreased substrate specificity and inhibitor-sensitivity compared with what is seen in plants and plant cells. To determine whether PIN-PGP interactions enhance transport specificity, we analysed interactions of the representative auxin-transporting PGPs with PIN1 and AUX1 in planta and in heterologous systems. Here, we provide evidence that PINs and PGPs interact and function both independently and co-ordinately to control polar auxin transport and impart transport specificity and directionality. These interactions take place in protein complexes stabilized by PGPs in detergent-resistant microdomains. alternative_title: - Biochemical Society Transactions author: - first_name: Anindita full_name: Bandyopadhyay, Anindita last_name: Bandyopadhyay - first_name: Joshua full_name: Blakeslee, Joshua last_name: Blakeslee - first_name: Ok full_name: Lee, Ok Ran last_name: Lee - first_name: Jozef full_name: Mravec, Jozef last_name: Mravec - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Boosaree full_name: Titapiwatanakun, Boosaree last_name: Titapiwatanakun - first_name: Srinivas full_name: Makam, Srinivas N last_name: Makam - first_name: Rodolphe full_name: Bouchard, Rodolphe last_name: Bouchard - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Enrico full_name: Martinoia, Enrico last_name: Martinoia - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Wendy full_name: Peer, Wendy A last_name: Peer - first_name: Angus full_name: Murphy, Angus S last_name: Murphy citation: ama: 'Bandyopadhyay A, Blakeslee J, Lee O, et al. Interactions of PIN and PGP auxin transport mechanisms. In: Vol 35. Portland Press; 2007:137-141. doi:10.1042/BST0350137' apa: Bandyopadhyay, A., Blakeslee, J., Lee, O., Mravec, J., Sauer, M., Titapiwatanakun, B., … Murphy, A. (2007). Interactions of PIN and PGP auxin transport mechanisms (Vol. 35, pp. 137–141). Presented at the Intercellular Signalling in Plants, Portland Press. https://doi.org/10.1042/BST0350137 chicago: Bandyopadhyay, Anindita, Joshua Blakeslee, Ok Lee, Jozef Mravec, Michael Sauer, Boosaree Titapiwatanakun, Srinivas Makam, et al. “Interactions of PIN and PGP Auxin Transport Mechanisms,” 35:137–41. Portland Press, 2007. https://doi.org/10.1042/BST0350137. ieee: A. Bandyopadhyay et al., “Interactions of PIN and PGP auxin transport mechanisms,” presented at the Intercellular Signalling in Plants, 2007, vol. 35, no. 1, pp. 137–141. ista: Bandyopadhyay A, Blakeslee J, Lee O, Mravec J, Sauer M, Titapiwatanakun B, Makam S, Bouchard R, Geisler M, Martinoia E, Friml J, Peer W, Murphy A. 2007. Interactions of PIN and PGP auxin transport mechanisms. Intercellular Signalling in Plants, Biochemical Society Transactions, vol. 35, 137–141. mla: Bandyopadhyay, Anindita, et al. Interactions of PIN and PGP Auxin Transport Mechanisms. Vol. 35, no. 1, Portland Press, 2007, pp. 137–41, doi:10.1042/BST0350137. short: A. Bandyopadhyay, J. Blakeslee, O. Lee, J. Mravec, M. Sauer, B. Titapiwatanakun, S. Makam, R. Bouchard, M. Geisler, E. Martinoia, J. Friml, W. Peer, A. Murphy, in:, Portland Press, 2007, pp. 137–141. conference: name: Intercellular Signalling in Plants date_created: 2018-12-11T12:00:54Z date_published: 2007-02-01T00:00:00Z date_updated: 2021-01-12T07:40:30Z day: '01' doi: 10.1042/BST0350137 extern: 1 intvolume: ' 35' issue: '1' month: '02' page: 137 - 141 publication_status: published publisher: Portland Press publist_id: '3681' quality_controlled: 0 status: public title: Interactions of PIN and PGP auxin transport mechanisms type: conference volume: 35 year: '2007' ... --- _id: '3029' abstract: - lang: eng text: In Arabidopsis thaliana, lateral roots are formed from root pericycle cells adjacent to the xylem poles. Lateral root development is regulated antagonistically by the plant hormones auxin and cytokinin. While a great deal is known about how auxin promotes lateral root development, the mechanism of cytokinin repression is still unclear. Elevating cytokinin levels was observed to disrupt lateral root initiation and the regular pattern of divisions that characterizes lateral root development in Arabidopsis. To identify the stage of lateral root development that is sensitive to cytokinins, we targeted the expression of the Agrobacterium tumefaciens cytokinin biosynthesis enzyme isopentenyltransferase to either xylem-pole pericycle cells or young lateral root primordia using GAL4-GFP enhancer trap lines. Transactivation experiments revealed that xylem-pole pericycle cells are sensitive to cytokinins, whereas young lateral root primordia are not. This effect is physiologically significant because transactivation of the Arabidopsis cytokinin degrading enzyme cytokinin oxidase 1 in lateral root founder cells results in increased lateral root formation. We observed that cytokinins perturb the expression of PIN genes in lateral root founder cells and prevent the formation of an auxin gradient that is required to pattern lateral root primordia. author: - first_name: Laurent full_name: Laplaze, Laurent last_name: Laplaze - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ilda full_name: Casimiro, Ilda last_name: Casimiro - first_name: Lies full_name: Maes, Lies last_name: Maes - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Vanessa full_name: Calvo, Vanessa last_name: Calvo - first_name: Boris full_name: Parizot, Boris last_name: Parizot - first_name: Maria full_name: Herrera-Rodriguez, Maria Begoña last_name: Herrera Rodriguez - first_name: Remko full_name: Offringa, Remko last_name: Offringa - first_name: Neil full_name: Graham, Neil last_name: Graham - first_name: Patrick full_name: Doumas, Patrick last_name: Doumas - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Didier full_name: Bogusz, Didier last_name: Bogusz - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett citation: ama: Laplaze L, Benková E, Casimiro I, et al. Cytokinins act directly on lateral root founder cells to inhibit root initiation. Plant Cell. 2007;19(12):3889-3900. doi:10.1105/tpc.107.055863 apa: Laplaze, L., Benková, E., Casimiro, I., Maes, L., Vanneste, S., Swarup, R., … Bennett, M. (2007). Cytokinins act directly on lateral root founder cells to inhibit root initiation. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.107.055863 chicago: Laplaze, Laurent, Eva Benková, Ilda Casimiro, Lies Maes, Steffen Vanneste, Ranjan Swarup, Dolf Weijers, et al. “Cytokinins Act Directly on Lateral Root Founder Cells to Inhibit Root Initiation.” Plant Cell. American Society of Plant Biologists, 2007. https://doi.org/10.1105/tpc.107.055863. ieee: L. Laplaze et al., “Cytokinins act directly on lateral root founder cells to inhibit root initiation,” Plant Cell, vol. 19, no. 12. American Society of Plant Biologists, pp. 3889–3900, 2007. ista: Laplaze L, Benková E, Casimiro I, Maes L, Vanneste S, Swarup R, Weijers D, Calvo V, Parizot B, Herrera Rodriguez M, Offringa R, Graham N, Doumas P, Friml J, Bogusz D, Beeckman T, Bennett M. 2007. Cytokinins act directly on lateral root founder cells to inhibit root initiation. Plant Cell. 19(12), 3889–3900. mla: Laplaze, Laurent, et al. “Cytokinins Act Directly on Lateral Root Founder Cells to Inhibit Root Initiation.” Plant Cell, vol. 19, no. 12, American Society of Plant Biologists, 2007, pp. 3889–900, doi:10.1105/tpc.107.055863. short: L. Laplaze, E. Benková, I. Casimiro, L. Maes, S. Vanneste, R. Swarup, D. Weijers, V. Calvo, B. Parizot, M. Herrera Rodriguez, R. Offringa, N. Graham, P. Doumas, J. Friml, D. Bogusz, T. Beeckman, M. Bennett, Plant Cell 19 (2007) 3889–3900. date_created: 2018-12-11T12:00:57Z date_published: 2007-12-01T00:00:00Z date_updated: 2021-01-12T07:40:33Z day: '01' doi: 10.1105/tpc.107.055863 extern: 1 intvolume: ' 19' issue: '12' month: '12' page: 3889 - 3900 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3673' quality_controlled: 0 status: public title: Cytokinins act directly on lateral root founder cells to inhibit root initiation type: journal_article volume: 19 year: '2007' ... --- _id: '3026' abstract: - lang: eng text: In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery. author: - first_name: Kamil full_name: Růžička, Kamil last_name: Růžička - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Radka full_name: Podhorská, Radka last_name: Podhorská - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Růžička K, Ljung K, Vanneste S, et al. Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution. Plant Cell. 2007;19(7):2197-2212. doi:10.1105/tpc.107.052126 apa: Růžička, K., Ljung, K., Vanneste, S., Podhorská, R., Beeckman, T., Friml, J., & Benková, E. (2007). Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.107.052126 chicago: Růžička, Kamil, Karin Ljung, Steffen Vanneste, Radka Podhorská, Tom Beeckman, Jiří Friml, and Eva Benková. “Ethylene Regulates Root Growth through Effects on Auxin Biosynthesis and Transport Dependent Auxin Distribution.” Plant Cell. American Society of Plant Biologists, 2007. https://doi.org/10.1105/tpc.107.052126. ieee: K. Růžička et al., “Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution,” Plant Cell, vol. 19, no. 7. American Society of Plant Biologists, pp. 2197–2212, 2007. ista: Růžička K, Ljung K, Vanneste S, Podhorská R, Beeckman T, Friml J, Benková E. 2007. Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution. Plant Cell. 19(7), 2197–2212. mla: Růžička, Kamil, et al. “Ethylene Regulates Root Growth through Effects on Auxin Biosynthesis and Transport Dependent Auxin Distribution.” Plant Cell, vol. 19, no. 7, American Society of Plant Biologists, 2007, pp. 2197–212, doi:10.1105/tpc.107.052126. short: K. Růžička, K. Ljung, S. Vanneste, R. Podhorská, T. Beeckman, J. Friml, E. Benková, Plant Cell 19 (2007) 2197–2212. date_created: 2018-12-11T12:00:56Z date_published: 2007-07-01T00:00:00Z date_updated: 2021-01-12T07:40:32Z day: '01' doi: 10.1105/tpc.107.052126 extern: 1 intvolume: ' 19' issue: '7' month: '07' page: 2197 - 2212 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3676' quality_controlled: 0 status: public title: Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution type: journal_article volume: 19 year: '2007' ... --- _id: '3028' abstract: - lang: eng text: In plants, cell polarity and tissue patterning are connected by intercellular flow of the phytohormone auxin, whose directional signaling depends on polar subcellular localization of PIN auxin transport proteins. The mechanism of polar targeting of PINs or other cargos in plants is largely unidentified, with the PINOID kinase being the only known molecular component. Here, we identify PP2A phosphatase as an important regulator of PIN apical-basal targeting and auxin distribution. Genetic analysis, localization, and phosphorylation studies demonstrate that PP2A and PINOID both partially colocalize with PINs and act antagonistically on the phosphorylation state of their central hydrophilic loop, hence mediating PIN apical-basal polar targeting. Thus, in plants, polar sorting by the reversible phosphorylation of cargos allows for their conditional delivery to specific intracellular destinations. In the case of PIN proteins, this mechanism enables switches in the direction of intercellular auxin fluxes, which mediate differential growth, tissue patterning, and organogenesis. author: - first_name: Marta full_name: Michniewicz, Marta last_name: Michniewicz - first_name: Marcelo full_name: Zago, Marcelo K last_name: Zago - first_name: Lindy full_name: Abas, Lindy last_name: Abas - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Alois full_name: Schweighofer, Alois last_name: Schweighofer - first_name: Irute full_name: Meskiene, Irute last_name: Meskiene - first_name: Marcus full_name: Heisler, Marcus G last_name: Heisler - first_name: Carolyn full_name: Ohno, Carolyn last_name: Ohno - first_name: Jing full_name: Zhang, Jing last_name: Zhang - first_name: Fang full_name: Huang, Fang last_name: Huang - first_name: Rebecca full_name: Schwab, Rebecca last_name: Schwab - first_name: Detlef full_name: Weigel, Detlef last_name: Weigel - first_name: Elliot full_name: Meyerowitz, Elliot M last_name: Meyerowitz - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - 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: Michniewicz M, Zago M, Abas L, et al. Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. Cell. 2007;130(6):1044-1056. doi:10.1016/j.cell.2007.07.033 apa: Michniewicz, M., Zago, M., Abas, L., Weijers, D., Schweighofer, A., Meskiene, I., … Friml, J. (2007). Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. Cell. Cell Press. https://doi.org/10.1016/j.cell.2007.07.033 chicago: Michniewicz, Marta, Marcelo Zago, Lindy Abas, Dolf Weijers, Alois Schweighofer, Irute Meskiene, Marcus Heisler, et al. “Antagonistic Regulation of PIN Phosphorylation by PP2A and PINOID Directs Auxin Flux.” Cell. Cell Press, 2007. https://doi.org/10.1016/j.cell.2007.07.033. ieee: M. Michniewicz et al., “Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux,” Cell, vol. 130, no. 6. Cell Press, pp. 1044–1056, 2007. ista: Michniewicz M, Zago M, Abas L, Weijers D, Schweighofer A, Meskiene I, Heisler M, Ohno C, Zhang J, Huang F, Schwab R, Weigel D, Meyerowitz E, Luschnig C, Offringa R, Friml J. 2007. Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. Cell. 130(6), 1044–1056. mla: Michniewicz, Marta, et al. “Antagonistic Regulation of PIN Phosphorylation by PP2A and PINOID Directs Auxin Flux.” Cell, vol. 130, no. 6, Cell Press, 2007, pp. 1044–56, doi:10.1016/j.cell.2007.07.033. short: M. Michniewicz, M. Zago, L. Abas, D. Weijers, A. Schweighofer, I. Meskiene, M. Heisler, C. Ohno, J. Zhang, F. Huang, R. Schwab, D. Weigel, E. Meyerowitz, C. Luschnig, R. Offringa, J. Friml, Cell 130 (2007) 1044–1056. date_created: 2018-12-11T12:00:57Z date_published: 2007-09-21T00:00:00Z date_updated: 2021-01-12T07:40:33Z day: '21' doi: 10.1016/j.cell.2007.07.033 extern: 1 intvolume: ' 130' issue: '6' month: '09' page: 1044 - 1056 publication: Cell publication_status: published publisher: Cell Press publist_id: '3674' quality_controlled: 0 status: public title: Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux type: journal_article volume: 130 year: '2007' ... --- _id: '3024' abstract: - lang: eng text: The plant hormone auxin is frequently observed to be asymmetrically distributed across adjacent cells during crucial stages of growth and development. These auxin gradients depend on polar transport and regulate a wide variety of processes, including embryogenesis, organogenesis, vascular tissue differentiation, root meristem maintenance and tropic growth. Auxin can mediate such a perplexing array of developmental processes by acting as a general trigger for the change in developmental program in cells where it accumulates and by providing vectorial information to the tissues by its polar intercellular flow. In recent years, a wealth of molecular data on the mechanism of auxin transport and its regulation has been generated, providing significant insights into the action of this versatile coordinative signal. author: - first_name: Anne full_name: Vieten, Anne last_name: Vieten - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Philip full_name: Brewer, Philip last_name: Brewer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Vieten A, Sauer M, Brewer P, Friml J. Molecular and cellular aspects of auxin-transport-mediated development. Trends in Plant Science. 2007;12(4):160-168. doi:10.1016/j.tplants.2007.03.006 apa: Vieten, A., Sauer, M., Brewer, P., & Friml, J. (2007). Molecular and cellular aspects of auxin-transport-mediated development. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2007.03.006 chicago: Vieten, Anne, Michael Sauer, Philip Brewer, and Jiří Friml. “Molecular and Cellular Aspects of Auxin-Transport-Mediated Development.” Trends in Plant Science. Cell Press, 2007. https://doi.org/10.1016/j.tplants.2007.03.006. ieee: A. Vieten, M. Sauer, P. Brewer, and J. Friml, “Molecular and cellular aspects of auxin-transport-mediated development,” Trends in Plant Science, vol. 12, no. 4. Cell Press, pp. 160–168, 2007. ista: Vieten A, Sauer M, Brewer P, Friml J. 2007. Molecular and cellular aspects of auxin-transport-mediated development. Trends in Plant Science. 12(4), 160–168. mla: Vieten, Anne, et al. “Molecular and Cellular Aspects of Auxin-Transport-Mediated Development.” Trends in Plant Science, vol. 12, no. 4, Cell Press, 2007, pp. 160–68, doi:10.1016/j.tplants.2007.03.006. short: A. Vieten, M. Sauer, P. Brewer, J. Friml, Trends in Plant Science 12 (2007) 160–168. date_created: 2018-12-11T12:00:55Z date_published: 2007-04-01T00:00:00Z date_updated: 2021-01-12T07:40:31Z day: '01' doi: 10.1016/j.tplants.2007.03.006 extern: '1' external_id: pmid: - ' 17369077' intvolume: ' 12' issue: '4' language: - iso: eng month: '04' oa_version: None page: 160 - 168 pmid: 1 publication: Trends in Plant Science publication_status: published publisher: Cell Press publist_id: '3679' quality_controlled: '1' status: public title: Molecular and cellular aspects of auxin-transport-mediated development type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2007' ... --- _id: '3192' abstract: - lang: eng text: Many computer vision applications rely on the efficient optimization of challenging, so-called non-submodular, binary pairwise MRFs. A promising graph cut based approach for optimizing such MRFs known as "roof duality" was recently introduced into computer vision. We study two methods which extend this approach. First, we discuss an efficient implementation of the "probing" technique introduced recently by Boros et al. [5]. It simplifies the MRF while preserving the global optimum. Our code is 400-700 faster on some graphs than the implementation of [5]. Second, we present a new technique which takes an arbitrary input labeling and tries to improve its energy. We give theoretical characterizations of local minima of this procedure. We applied both techniques to many applications, including image segmentation, new view synthesis, superresolution, diagram recognition, parameter learning, texture restoration, and image deconvolution. For several applications we see that we are able to find the global minimum very efficiently, and considerably outperform the original roof duality approach. In comparison to existing techniques, such as graph cut, TRW, BP, ICM, and simulated annealing, we nearly always find a lower energy. author: - 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 - first_name: Victor full_name: Lempitsky, Victor last_name: Lempitsky - first_name: Martin full_name: Szummer, Martin last_name: Szummer citation: ama: 'Rother C, Kolmogorov V, Lempitsky V, Szummer M. Optimizing binary MRFs via extended roof duality. In: IEEE; 2007. doi:10.1109/CVPR.2007.383203' apa: 'Rother, C., Kolmogorov, V., Lempitsky, V., & Szummer, M. (2007). Optimizing binary MRFs via extended roof duality. Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2007.383203' chicago: Rother, Carsten, Vladimir Kolmogorov, Victor Lempitsky, and Martin Szummer. “Optimizing Binary MRFs via Extended Roof Duality.” IEEE, 2007. https://doi.org/10.1109/CVPR.2007.383203. ieee: 'C. Rother, V. Kolmogorov, V. Lempitsky, and M. Szummer, “Optimizing binary MRFs via extended roof duality,” presented at the CVPR: Computer Vision and Pattern Recognition, 2007.' ista: 'Rother C, Kolmogorov V, Lempitsky V, Szummer M. 2007. Optimizing binary MRFs via extended roof duality. CVPR: Computer Vision and Pattern Recognition.' mla: Rother, Carsten, et al. Optimizing Binary MRFs via Extended Roof Duality. IEEE, 2007, doi:10.1109/CVPR.2007.383203. short: C. Rother, V. Kolmogorov, V. Lempitsky, M. Szummer, in:, IEEE, 2007. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:55Z date_published: 2007-07-16T00:00:00Z date_updated: 2021-01-12T07:41:42Z day: '16' doi: 10.1109/CVPR.2007.383203 extern: 1 main_file_link: - open_access: '0' url: http://www.robots.ox.ac.uk/~vilem/QPBOPI.pdf month: '07' publication_status: published publisher: IEEE publist_id: '3490' quality_controlled: 0 status: public title: Optimizing binary MRFs via extended roof duality type: conference year: '2007' ... --- _id: '3191' abstract: - lang: eng text: 'The maximum flow algorithm for minimizing energy functions of binary variables has become a standard tool in computer vision. In many cases, unary costs of the energy depend linearly on parameter lambda. In this paper we study vision applications for which it is important to solve the maxflow problem for different lambda''s. An example is a weighting between data and regularization terms in image segmentation or stereo: it is desirable to vary it both during training (to learn lambda from ground truth data) and testing (to select best lambda using high-knowledge constraints, e.g. user input). We review algorithmic aspects of this parametric maximum flow problem previously unknown in vision, such as the ability to compute all breakpoints of lambda and corresponding optimal configurations infinite time. These results allow, in particular, to minimize the ratio of some geometric functional, such as flux of a vector field over length (or area). Previously, such functional were tackled with shortest path techniques applicable only in 2D. We give theoretical improvements for "PDE cuts" [5]. We present experimental results for image segmentation, 3D reconstruction, and the cosegmentation problem.' author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Kolmogorov V, Boykov Y, Rother C. Applications of parametric maxflow in computer vision. In: IEEE; 2007. doi:10.1109/ICCV.2007.4408910' apa: 'Kolmogorov, V., Boykov, Y., & Rother, C. (2007). Applications of parametric maxflow in computer vision. Presented at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2007.4408910' chicago: Kolmogorov, Vladimir, Yuri Boykov, and Carsten Rother. “Applications of Parametric Maxflow in Computer Vision.” IEEE, 2007. https://doi.org/10.1109/ICCV.2007.4408910. ieee: 'V. Kolmogorov, Y. Boykov, and C. Rother, “Applications of parametric maxflow in computer vision,” presented at the ICCV: International Conference on Computer Vision, 2007.' ista: 'Kolmogorov V, Boykov Y, Rother C. 2007. Applications of parametric maxflow in computer vision. ICCV: International Conference on Computer Vision.' mla: Kolmogorov, Vladimir, et al. Applications of Parametric Maxflow in Computer Vision. IEEE, 2007, doi:10.1109/ICCV.2007.4408910. short: V. Kolmogorov, Y. Boykov, C. Rother, in:, IEEE, 2007. conference: name: 'ICCV: International Conference on Computer Vision' date_created: 2018-12-11T12:01:55Z date_published: 2007-12-26T00:00:00Z date_updated: 2021-01-12T07:41:41Z day: '26' doi: 10.1109/ICCV.2007.4408910 extern: 1 main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/70474/iccv07-paramaxflow.pdf month: '12' publication_status: published publisher: IEEE publist_id: '3489' quality_controlled: 0 status: public title: Applications of parametric maxflow in computer vision type: conference year: '2007' ... --- _id: '3193' abstract: - lang: eng text: 'Optimization techniques based on graph cuts have become a standard tool for many vision applications. These techniques allow to minimize efficiently certain energy functions corresponding to pairwise Markov Random Fields (MRFs). Currently, there is an accepted view within the computer vision community that graph cuts can only be used for optimizing a limited class of MRF energies (e.g., submodular functions). In this survey, we review some results that show that graph cuts can be applied to a much larger class of energy functions (in particular, nonsubmodular functions). While these results are well-known in the optimization community, to our knowledge they were not used in the context of computer vision and MRF optimization. We demonstrate the relevance of these results to vision on the problem of binary texture restoration. ' author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: Kolmogorov V, Rother C. Minimizing nonsubmodular functions with graph cuts - A review. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2007;29(7):1274-1279. doi:10.1109/TPAMI.2007.1031 apa: Kolmogorov, V., & Rother, C. (2007). Minimizing nonsubmodular functions with graph cuts - A review. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2007.1031 chicago: Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions with Graph Cuts - A Review.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2007. https://doi.org/10.1109/TPAMI.2007.1031. ieee: V. Kolmogorov and C. Rother, “Minimizing nonsubmodular functions with graph cuts - A review,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 29, no. 7. IEEE, pp. 1274–1279, 2007. ista: Kolmogorov V, Rother C. 2007. Minimizing nonsubmodular functions with graph cuts - A review. IEEE Transactions on Pattern Analysis and Machine Intelligence. 29(7), 1274–1279. mla: Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions with Graph Cuts - A Review.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 29, no. 7, IEEE, 2007, pp. 1274–79, doi:10.1109/TPAMI.2007.1031. short: V. Kolmogorov, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 29 (2007) 1274–1279. date_created: 2018-12-11T12:01:56Z date_published: 2007-07-01T00:00:00Z date_updated: 2021-01-12T07:41:42Z day: '01' doi: 10.1109/TPAMI.2007.1031 extern: 1 intvolume: ' 29' issue: '7' month: '07' page: 1274 - 1279 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '3491' quality_controlled: 0 status: public title: Minimizing nonsubmodular functions with graph cuts - A review type: journal_article volume: 29 year: '2007' ... --- _id: '3187' abstract: - lang: eng text: Stereo vision has numerous applications in robotics, graphics, inspection and other areas. A prime application, one which has driven work on stereo in our laboratory, is teleconferencing in which the use of a stereo webcam already makes possible various transformations of the video stream. These include digital camera control, insertion of virtual objects, background substitution, and eye-gaze correction [9, 8]. author: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: Blake A, Criminisi A, Cross G, Kolmogorov V, Rother C. Fusion of stereo colour and contrast. Springer Tracts in Advanced Robotics. 2007;28:295-304. doi:10.1007/978-3-540-48113-3_27 apa: Blake, A., Criminisi, A., Cross, G., Kolmogorov, V., & Rother, C. (2007). Fusion of stereo colour and contrast. Springer Tracts in Advanced Robotics. Springer. https://doi.org/10.1007/978-3-540-48113-3_27 chicago: Blake, Andrew, Antonio Criminisi, Geoffrey Cross, Vladimir Kolmogorov, and Carsten Rother. “Fusion of Stereo Colour and Contrast.” Springer Tracts in Advanced Robotics. Springer, 2007. https://doi.org/10.1007/978-3-540-48113-3_27. ieee: A. Blake, A. Criminisi, G. Cross, V. Kolmogorov, and C. Rother, “Fusion of stereo colour and contrast,” Springer Tracts in Advanced Robotics, vol. 28. Springer, pp. 295–304, 2007. ista: Blake A, Criminisi A, Cross G, Kolmogorov V, Rother C. 2007. Fusion of stereo colour and contrast. Springer Tracts in Advanced Robotics. 28, 295–304. mla: Blake, Andrew, et al. “Fusion of Stereo Colour and Contrast.” Springer Tracts in Advanced Robotics, vol. 28, Springer, 2007, pp. 295–304, doi:10.1007/978-3-540-48113-3_27. short: A. Blake, A. Criminisi, G. Cross, V. Kolmogorov, C. Rother, Springer Tracts in Advanced Robotics 28 (2007) 295–304. date_created: 2018-12-11T12:01:54Z date_published: 2007-02-05T00:00:00Z date_updated: 2021-01-12T07:41:40Z day: '05' doi: 10.1007/978-3-540-48113-3_27 extern: 1 intvolume: ' 28' main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67417/criminisi_isrr2005.pdf month: '02' page: 295 - 304 publication: Springer Tracts in Advanced Robotics publication_status: published publisher: Springer publist_id: '3492' quality_controlled: 0 status: public title: Fusion of stereo colour and contrast type: journal_article volume: 28 year: '2007' ... --- _id: '3218' abstract: - lang: eng text: 'A (k, ℓ)-robust combiner for collision-resistant hash-functions is a construction which from ℓ hash-functions constructs a hash-function which is collision-resistant if at least k of the components are collision-resistant. One trivially gets a (k, ℓ)-robust combiner by concatenating the output of any ℓ - k + 1 of the components, unfortunately this is not very practical as the length of the output of the combiner is quite large. We show that this is unavoidable as no black-box (k, ℓ)-robust combiner whose output is significantly shorter than what can be achieved by concatenation exists. This answers a question of Boneh and Boyen (Crypto''06). ' acknowledgement: Supported by DIAMANT, the Dutch national mathematics cluster for discrete interactive and algorithmic algebra and number theory. 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. Non-trivial black-box combiners for collision-resistant hash-functions don’t exist. In: Vol 4515. Springer; 2007:23-33. doi:10.1007/978-3-540-72540-4_2' apa: 'Pietrzak, K. Z. (2007). Non-trivial black-box combiners for collision-resistant hash-functions don’t exist (Vol. 4515, pp. 23–33). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/978-3-540-72540-4_2' chicago: Pietrzak, Krzysztof Z. “Non-Trivial Black-Box Combiners for Collision-Resistant Hash-Functions Don’t Exist,” 4515:23–33. Springer, 2007. https://doi.org/10.1007/978-3-540-72540-4_2. ieee: 'K. Z. Pietrzak, “Non-trivial black-box combiners for collision-resistant hash-functions don’t exist,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2007, vol. 4515, pp. 23–33.' ista: 'Pietrzak KZ. 2007. Non-trivial black-box combiners for collision-resistant hash-functions don’t exist. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4515, 23–33.' mla: Pietrzak, Krzysztof Z. Non-Trivial Black-Box Combiners for Collision-Resistant Hash-Functions Don’t Exist. Vol. 4515, Springer, 2007, pp. 23–33, doi:10.1007/978-3-540-72540-4_2. short: K.Z. Pietrzak, in:, Springer, 2007, pp. 23–33. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:05Z date_published: 2007-06-12T00:00:00Z date_updated: 2021-01-12T07:41:52Z day: '12' doi: 10.1007/978-3-540-72540-4_2 extern: 1 intvolume: ' 4515' month: '06' page: 23 - 33 publication_status: published publisher: Springer publist_id: '3461' quality_controlled: 0 status: public title: Non-trivial black-box combiners for collision-resistant hash-functions don't exist type: conference volume: 4515 year: '2007' ... --- _id: '3305' abstract: - lang: eng text: The accumulation of deleterious mutations plays a major role in evolution, and key to this are the interactions between their fitness effects, known as epistasis. Whether mutations tend to interact synergistically (with multiple mutations being more deleterious than would be expected from their individual fitness effects) or antagonistically is important for a variety of evolutionary questions, particularly the evolution of sex. Unfortunately, the experimental evidence on the prevalence and strength of epistasis is mixed and inconclusive. Here we study theoretically whether synergistic or antagonistic epistasis is likely to be favored by evolution and by how much. We find that in the presence of recombination, evolution favors less synergistic or more antagonistic epistasis whenever mutations that change the epistasis in this direction are possible. This is because evolution favors increased buffering against the effects of deleterious mutations. This suggests that we should not expect synergistic epistasis to be widespread in nature and hence that the mutational deterministic hypothesis for the advantage of sex may not apply widely. author: - first_name: Michael full_name: Desai, Michael M last_name: Desai - first_name: Daniel full_name: Daniel Weissman id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Marcus full_name: Feldman, Marcus W last_name: Feldman citation: ama: Desai M, Weissman D, Feldman M. Evolution can favor antagonistic epistasis. Genetics. 2007;177(2):1001-1010. doi:10.1534/genetics.107.075812 apa: Desai, M., Weissman, D., & Feldman, M. (2007). Evolution can favor antagonistic epistasis. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.107.075812 chicago: Desai, Michael, Daniel Weissman, and Marcus Feldman. “Evolution Can Favor Antagonistic Epistasis.” Genetics. Genetics Society of America, 2007. https://doi.org/10.1534/genetics.107.075812. ieee: M. Desai, D. Weissman, and M. Feldman, “Evolution can favor antagonistic epistasis,” Genetics, vol. 177, no. 2. Genetics Society of America, pp. 1001–10, 2007. ista: Desai M, Weissman D, Feldman M. 2007. Evolution can favor antagonistic epistasis. Genetics. 177(2), 1001–10. mla: Desai, Michael, et al. “Evolution Can Favor Antagonistic Epistasis.” Genetics, vol. 177, no. 2, Genetics Society of America, 2007, pp. 1001–10, doi:10.1534/genetics.107.075812. short: M. Desai, D. Weissman, M. Feldman, Genetics 177 (2007) 1001–10. date_created: 2018-12-11T12:02:34Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:42:32Z day: '01' doi: 10.1534/genetics.107.075812 extern: 1 intvolume: ' 177' issue: '2' month: '01' page: 1001 - 10 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3335' quality_controlled: 0 status: public title: Evolution can favor antagonistic epistasis type: journal_article volume: 177 year: '2007' ... --- _id: '3411' abstract: - lang: eng text: Mechanical single-molecule techniques offer exciting possibilities to investigate protein folding and stability in native environments at submolecular resolution. By applying a free-energy reconstruction procedure developed by Hummer and Szabo, which is based on a statistical theorem introduced by Jarzynski, we determined the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin, and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium unfolding free energy was independent of pulling rate and temperature ranging between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties in individual transmembrane helices. In halorhodopsin, the stabilization of a short helical segment yielded a characteristic signature in the energy profile. In NhaA, a pronounced peak was observed at a functionally important site in the protein. Since a large variety of single- and multispan membrane proteins can be tackled in mechanical unfolding experiments, our approach provides a basis for systematically elucidating energetic properties of membrane proteins with the resolution of individual secondary-structure elements. author: - first_name: Johannes full_name: Preiner, Johannes last_name: Preiner - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Christian full_name: Rankl, Christian last_name: Rankl - first_name: Helene full_name: Knaus, Helene last_name: Knaus - first_name: David full_name: Cisneros, David A last_name: Cisneros - first_name: Alexej full_name: Kedrov, Alexej last_name: Kedrov - first_name: Ferry full_name: Kienberger, Ferry last_name: Kienberger - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller - first_name: Peter full_name: Hinterdorfer, Peter last_name: Hinterdorfer citation: ama: Preiner J, Janovjak HL, Rankl C, et al. Free energy of membrane protein unfolding derived from single-molecule force measurements. Biophysical Journal. 2007;93(3):930-937. doi:10.1529/biophysj.106.096982 apa: Preiner, J., Janovjak, H. L., Rankl, C., Knaus, H., Cisneros, D., Kedrov, A., … Hinterdorfer, P. (2007). Free energy of membrane protein unfolding derived from single-molecule force measurements. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.106.096982 chicago: Preiner, Johannes, Harald L Janovjak, Christian Rankl, Helene Knaus, David Cisneros, Alexej Kedrov, Ferry Kienberger, Daniel Mueller, and Peter Hinterdorfer. “Free Energy of Membrane Protein Unfolding Derived from Single-Molecule Force Measurements.” Biophysical Journal. Biophysical Society, 2007. https://doi.org/10.1529/biophysj.106.096982. ieee: J. Preiner et al., “Free energy of membrane protein unfolding derived from single-molecule force measurements,” Biophysical Journal, vol. 93, no. 3. Biophysical Society, pp. 930–937, 2007. ista: Preiner J, Janovjak HL, Rankl C, Knaus H, Cisneros D, Kedrov A, Kienberger F, Mueller D, Hinterdorfer P. 2007. Free energy of membrane protein unfolding derived from single-molecule force measurements. Biophysical Journal. 93(3), 930–937. mla: Preiner, Johannes, et al. “Free Energy of Membrane Protein Unfolding Derived from Single-Molecule Force Measurements.” Biophysical Journal, vol. 93, no. 3, Biophysical Society, 2007, pp. 930–37, doi:10.1529/biophysj.106.096982. short: J. Preiner, H.L. Janovjak, C. Rankl, H. Knaus, D. Cisneros, A. Kedrov, F. Kienberger, D. Mueller, P. Hinterdorfer, Biophysical Journal 93 (2007) 930–937. date_created: 2018-12-11T12:03:11Z date_published: 2007-08-01T00:00:00Z date_updated: 2021-01-12T07:43:18Z day: '01' doi: 10.1529/biophysj.106.096982 extern: 1 intvolume: ' 93' issue: '3' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913163/ month: '08' oa: 1 page: 930 - 937 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '2990' quality_controlled: 0 status: public title: Free energy of membrane protein unfolding derived from single-molecule force measurements type: journal_article volume: 93 year: '2007' ... --- _id: '3412' abstract: - lang: eng text: |- Molecular interactions are the basic language of biological processes. They establish the forces interacting between the building blocks of proteins and other macromolecules, thus determining their functional roles. Because molecular interactions trigger virtually every biological process, approaches to decipher their language are needed. Single-molecule force spectroscopy (SMFS) has been used to detect and characterize different types of molecular interactions that occur between and within native membrane proteins. The first experiments detected and localized molecular interactions that stabilized membrane proteins, including how these interactions were established during folding of α-helical secondary structure elements into the native protein and how they changed with oligomerization, temperature, and mutations. SMFS also enables investigators to detect and locate molecular interactions established during ligand and inhibitor binding. These exciting applications provide opportunities for studying the molecular forces of life. Further developments will elucidate the origins of molecular interactions encoded in their lifetimes, interaction ranges, interplay, and dynamics characteristic of biological systems. author: - first_name: Alexej full_name: Kedrov, Alexej last_name: Kedrov - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Tanuj full_name: Sapra, Tanuj K last_name: Sapra - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Kedrov A, Janovjak HL, Sapra T, Mueller D. Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy. Annual Review of Biophysics. 2007;36:233-260. doi:10.1146/annurev.biophys.36.040306.132640 apa: Kedrov, A., Janovjak, H. L., Sapra, T., & Mueller, D. (2007). Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev.biophys.36.040306.132640 chicago: Kedrov, Alexej, Harald L Janovjak, Tanuj Sapra, and Daniel Mueller. “Deciphering Molecular Interactions of Native Membrane Proteins by Single-Molecule Force Spectroscopy.” Annual Review of Biophysics. Annual Reviews, 2007. https://doi.org/10.1146/annurev.biophys.36.040306.132640. ieee: A. Kedrov, H. L. Janovjak, T. Sapra, and D. Mueller, “Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy,” Annual Review of Biophysics, vol. 36. Annual Reviews, pp. 233–260, 2007. ista: Kedrov A, Janovjak HL, Sapra T, Mueller D. 2007. Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy. Annual Review of Biophysics. 36, 233–260. mla: Kedrov, Alexej, et al. “Deciphering Molecular Interactions of Native Membrane Proteins by Single-Molecule Force Spectroscopy.” Annual Review of Biophysics, vol. 36, Annual Reviews, 2007, pp. 233–60, doi:10.1146/annurev.biophys.36.040306.132640. short: A. Kedrov, H.L. Janovjak, T. Sapra, D. Mueller, Annual Review of Biophysics 36 (2007) 233–260. date_created: 2018-12-11T12:03:11Z date_published: 2007-06-01T00:00:00Z date_updated: 2019-04-26T07:22:27Z day: '01' doi: 10.1146/annurev.biophys.36.040306.132640 extern: 1 intvolume: ' 36' month: '06' page: 233 - 260 publication: Annual Review of Biophysics publication_status: published publisher: Annual Reviews publist_id: '2989' quality_controlled: 0 status: public title: Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy type: review volume: 36 year: '2007' ... --- _id: '3427' abstract: - lang: eng text: "We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case of transcytosis where morphogens undergo repeated rounds of internalization into cells and recycling. Based on a description on the cellular scale, we derive effective nonlinear transport equations in one and two dimensions which are valid on larger scales. We derive analytic expressions for the concentration dependence of the effective diffusion coefficient and the effective degradation rate. We discuss the effects of a directional bias on morphogen transport and those of the coupling of the morphogen and receptor kinetics. Furthermore, we discuss general properties of cellular transport processes such as the robustness of gradients and relate our results to recent experiments on the morphogen Decapentaplegic (Dpp) that acts in the wing disk of the fruit fly Drosophila.\r\n© 2007 The American Physical Society" 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: Karsten full_name: Kruse, Karsten last_name: Kruse - first_name: Periklis full_name: Pantazis, Periklis last_name: Pantazis - first_name: Marcos full_name: Gonzalez Gaitan, Marcos last_name: Gonzalez Gaitan - first_name: Frank full_name: Julicher, Frank last_name: Julicher citation: ama: Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. Morphogen transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2007;75(1). doi:10.1103/PhysRevE.75.011901 apa: Bollenbach, M. T., Kruse, K., Pantazis, P., Gonzalez Gaitan, M., & Julicher, F. (2007). Morphogen transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.75.011901 chicago: Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos Gonzalez Gaitan, and Frank Julicher. “Morphogen Transport in Epithelia.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2007. https://doi.org/10.1103/PhysRevE.75.011901. ieee: M. T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, and F. Julicher, “Morphogen transport in epithelia,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 75, no. 1. American Institute of Physics, 2007. ista: Bollenbach MT, Kruse K, Pantazis P, Gonzalez Gaitan M, Julicher F. 2007. Morphogen transport in epithelia. Physical Review E Statistical Nonlinear and Soft Matter Physics. 75(1). mla: Bollenbach, Mark Tobias, et al. “Morphogen Transport in Epithelia.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 75, no. 1, American Institute of Physics, 2007, doi:10.1103/PhysRevE.75.011901. short: M.T. Bollenbach, K. Kruse, P. Pantazis, M. Gonzalez Gaitan, F. Julicher, Physical Review E Statistical Nonlinear and Soft Matter Physics 75 (2007). date_created: 2018-12-11T12:03:16Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:43:24Z day: '01' doi: 10.1103/PhysRevE.75.011901 extern: '1' external_id: arxiv: - q-bio/0609011v1 intvolume: ' 75' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/q-bio/0609011v1 month: '01' oa: 1 oa_version: Preprint publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '2974' status: public title: Morphogen transport in epithelia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 75 year: '2007' ... --- _id: '3523' abstract: - lang: eng text: On the linear track, the recent firing sequences of CA1 place cells recur during sharp wave/ripple patterns (SWRs) in a reverse temporal order [Foster & Wilson (2006) Nature, 440, 680-683]. We have found similar reverse-order reactivation during SWRs in open-field exploration where the firing sequence of cells varied before each SWR. Both the onset times and the firing patterns of cells showed a tendency for reversed sequences during SWRs. These effects were observed for SWRs that occurred during exploration, but not for those during longer immobility periods. Additionally, reverse reactivation was stronger when it was preceded by higher speed (> 5 cm/s) run periods. The trend for reverse-order SWR reactivation was not significantly different in familiar and novel environments, even though SWR-associated firing rates of both pyramidal cells and interneurons were reduced in novel environments as compared with familiar. During exploration-associated SWRs (eSWR) place cells retain place-selective firing [O'Neill et al. (2006) Neuron, 49, 143-155]. Here, we have shown that each cell's firing onset was more delayed and firing probability more reduced during eSWRs the further the rat was from the middle of the cell's place field; that is, cells receiving less momentary place-related excitatory drive fired later during SWR events. However, even controlling for place field distance, the recent firing of cells was still significantly correlated with SWR reactivation sequences. We therefore propose that both place-related drive and the firing history of cells contribute to reverse reactivation during eSWRs. author: - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Joseph full_name: Joseph O'Neill id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Kevin full_name: Allen, Kevin last_name: Allen - first_name: Timothy full_name: Senior,Timothy last_name: Senior citation: ama: Csicsvari JL, O’Neill J, Allen K, Senior T. Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration. European Journal of Neuroscience. 2007;26(3):704-716. doi:10.1111/j.1460-9568.2007.05684.x apa: Csicsvari, J. L., O’Neill, J., Allen, K., & Senior, T. (2007). Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2007.05684.x chicago: Csicsvari, Jozsef L, Joseph O’Neill, Kevin Allen, and Timothy Senior. “Place-Selective Firing Contributes to the Reverse-Order Reactivation of CA1 Pyramidal Cells during Sharp Waves in Open-Field Exploration.” European Journal of Neuroscience. Wiley-Blackwell, 2007. https://doi.org/10.1111/j.1460-9568.2007.05684.x. ieee: J. L. Csicsvari, J. O’Neill, K. Allen, and T. Senior, “Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration,” European Journal of Neuroscience, vol. 26, no. 3. Wiley-Blackwell, pp. 704–716, 2007. ista: Csicsvari JL, O’Neill J, Allen K, Senior T. 2007. Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration. European Journal of Neuroscience. 26(3), 704–716. mla: Csicsvari, Jozsef L., et al. “Place-Selective Firing Contributes to the Reverse-Order Reactivation of CA1 Pyramidal Cells during Sharp Waves in Open-Field Exploration.” European Journal of Neuroscience, vol. 26, no. 3, Wiley-Blackwell, 2007, pp. 704–16, doi:10.1111/j.1460-9568.2007.05684.x. short: J.L. Csicsvari, J. O’Neill, K. Allen, T. Senior, European Journal of Neuroscience 26 (2007) 704–716. date_created: 2018-12-11T12:03:46Z date_published: 2007-08-01T00:00:00Z date_updated: 2021-01-12T07:44:03Z day: '01' doi: 10.1111/j.1460-9568.2007.05684.x extern: 1 intvolume: ' 26' issue: '3' month: '08' page: 704 - 716 publication: European Journal of Neuroscience publication_status: published publisher: Wiley-Blackwell publist_id: '2862' quality_controlled: 0 status: public title: Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration type: journal_article volume: 26 year: '2007' ... --- _id: '3601' abstract: - lang: eng text: In this paper, the multiobjective optimal design of space-based reconfigurable sensor networks with novel adaptive MEMS antennas is investigated by using multiobjective evolutionary algorithms. The non-dominated sorting genetic algorithm II (NSGA-II) is employed to obtain multi-criteria Pareto-optimal solutions, which allows system designers to easily make a reasonable trade-off choice from the set of non-dominated solutions according to their preferences and system requirements. As a case study, a cluster-based satellite sensing network is simulated under multiple objectives. Most importantly, this paper also presents the application of our newly designed adaptive MEMS antennas together with the NSGA-II to the multiobjective optimal design of space-based reconfigurable sensor networks. author: - first_name: Erfu full_name: Yang, Erfu last_name: Yang - first_name: Nakul full_name: Haridas, Nakul last_name: Haridas - first_name: Ahmed full_name: El-Rayis, Ahmed O last_name: El Rayis - first_name: Ahmet full_name: Erdogan, Ahmet T last_name: Erdogan - first_name: Tughrul full_name: Arslan, Tughrul last_name: Arslan - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications. In: IEEE; 2007:27-34. doi:10.1109/AHS.2007.76' apa: 'Yang, E., Haridas, N., El Rayis, A., Erdogan, A., Arslan, T., & Barton, N. H. (2007). Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications (pp. 27–34). Presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems, IEEE. https://doi.org/10.1109/AHS.2007.76' chicago: Yang, Erfu, Nakul Haridas, Ahmed El Rayis, Ahmet Erdogan, Tughrul Arslan, and Nicholas H Barton. “Multiobjective Optimal Design of MEMS-Based Reconfigurable and Evolvable Sensor Networks for Space Applications,” 27–34. IEEE, 2007. https://doi.org/10.1109/AHS.2007.76. ieee: 'E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, and N. H. Barton, “Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications,” presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 2007, pp. 27–34.' ista: 'Yang E, Haridas N, El Rayis A, Erdogan A, Arslan T, Barton NH. 2007. Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications. AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 27–34.' mla: Yang, Erfu, et al. Multiobjective Optimal Design of MEMS-Based Reconfigurable and Evolvable Sensor Networks for Space Applications. IEEE, 2007, pp. 27–34, doi:10.1109/AHS.2007.76. short: E. Yang, N. Haridas, A. El Rayis, A. Erdogan, T. Arslan, N.H. Barton, in:, IEEE, 2007, pp. 27–34. conference: name: 'AHS: NASA/ESA Conference on Adaptive Hardware and Systems' date_created: 2018-12-11T12:04:11Z date_published: 2007-08-20T00:00:00Z date_updated: 2021-01-12T07:44:35Z day: '20' doi: 10.1109/AHS.2007.76 extern: 1 month: '08' page: 27 - 34 publication_status: published publisher: IEEE publist_id: '2782' quality_controlled: 0 status: public title: Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications type: conference year: '2007' ... --- _id: '3687' abstract: - lang: eng text: |- Recent years have seen huge advances in object recognition from images. Recognition rates beyond 95% are the rule rather than the exception on many datasets. However, most state-of-the-art methods can only decide if an object is present or not. They are not able to provide information on the object location or extent within in the image. We report on a simple yet powerful scheme that extends many existing recognition methods to also perform localization of object bounding boxes. This is achieved by maximizing the classification score over all possible subrectangles in the image. Despite the impression that this would be computationally intractable, we show that in many situations efficient algorithms exist which solve a generalized maximum subrectangle problem. We show how our method is applicable to a variety object detection frameworks and demonstrate its performance by applying it to the popular bag of visual words model, achieving competitive results on the PASCAL VOC 2006 dataset. author: - first_name: Matthew full_name: Blaschko,Matthew B last_name: Blaschko - first_name: Thomas full_name: Hofmann,Thomas last_name: Hofmann - 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, Hofmann T, Lampert C. Efficient Subwindow Search for Object Localization. Max-Planck-Institute for Biological Cybernetics; 2007. apa: Blaschko, M., Hofmann, T., & Lampert, C. (2007). Efficient subwindow search for object localization. Unknown. Max-Planck-Institute for Biological Cybernetics. chicago: Blaschko, Matthew, Thomas Hofmann, and Christoph Lampert. Efficient Subwindow Search for Object Localization. Unknown. Max-Planck-Institute for Biological Cybernetics, 2007. ieee: M. Blaschko, T. Hofmann, and C. Lampert, Efficient subwindow search for object localization, no. 164. Max-Planck-Institute for Biological Cybernetics, 2007. ista: Blaschko M, Hofmann T, Lampert C. 2007. Efficient subwindow search for object localization, Max-Planck-Institute for Biological Cybernetics,p. mla: Blaschko, Matthew, et al. “Efficient Subwindow Search for Object Localization.” Unknown, no. 164, Max-Planck-Institute for Biological Cybernetics, 2007. short: M. Blaschko, T. Hofmann, C. Lampert, Efficient Subwindow Search for Object Localization, Max-Planck-Institute for Biological Cybernetics, 2007. date_created: 2018-12-11T12:04:37Z date_published: 2007-08-01T00:00:00Z date_updated: 2019-04-26T07:22:33Z day: '01' extern: 1 issue: '164' main_file_link: - open_access: '0' url: http://www.kyb.tuebingen.mpg.de/fileadmin/user_upload/files/publications/TR-164_[0].pdf month: '08' publication: Unknown publication_status: published publisher: Max-Planck-Institute for Biological Cybernetics publist_id: '2681' quality_controlled: 0 status: public title: Efficient subwindow search for object localization type: report year: '2007' ... --- _id: '3701' abstract: - lang: eng text: |- The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms. Our main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior. alternative_title: - LNCS author: - first_name: Adrian full_name: Ulges, Adrian last_name: Ulges - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Daniel full_name: Keysers,Daniel last_name: Keysers - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Ulges A, Lampert C, Keysers D, Breuel T. Optimal dominant motion estimation using adaptive search of transformation space. In: Vol 4713. Springer; 2007:204-213. doi:10.1007/978-3-540-74936-3_21' apa: 'Ulges, A., Lampert, C., Keysers, D., & Breuel, T. (2007). Optimal dominant motion estimation using adaptive search of transformation space (Vol. 4713, pp. 204–213). Presented at the DAGM: German Association For Pattern Recognition, Springer. https://doi.org/10.1007/978-3-540-74936-3_21' chicago: Ulges, Adrian, Christoph Lampert, Daniel Keysers, and Thomas Breuel. “Optimal Dominant Motion Estimation Using Adaptive Search of Transformation Space,” 4713:204–13. Springer, 2007. https://doi.org/10.1007/978-3-540-74936-3_21. ieee: 'A. Ulges, C. Lampert, D. Keysers, and T. Breuel, “Optimal dominant motion estimation using adaptive search of transformation space,” presented at the DAGM: German Association For Pattern Recognition, 2007, vol. 4713, pp. 204–213.' ista: 'Ulges A, Lampert C, Keysers D, Breuel T. 2007. Optimal dominant motion estimation using adaptive search of transformation space. DAGM: German Association For Pattern Recognition, LNCS, vol. 4713, 204–213.' mla: Ulges, Adrian, et al. Optimal Dominant Motion Estimation Using Adaptive Search of Transformation Space. Vol. 4713, Springer, 2007, pp. 204–13, doi:10.1007/978-3-540-74936-3_21. short: A. Ulges, C. Lampert, D. Keysers, T. Breuel, in:, Springer, 2007, pp. 204–213. conference: name: 'DAGM: German Association For Pattern Recognition' date_created: 2018-12-11T12:04:42Z date_published: 2007-11-09T00:00:00Z date_updated: 2021-01-12T07:51:35Z day: '09' doi: 10.1007/978-3-540-74936-3_21 extern: 1 intvolume: ' 4713' month: '11' page: 204 - 213 publication_status: published publisher: Springer publist_id: '2656' quality_controlled: 0 status: public title: Optimal dominant motion estimation using adaptive search of transformation space type: conference volume: 4713 year: '2007' ... --- _id: '3731' abstract: - lang: eng text: A cell's ability to regulate gene transcription depends in large part on the energy with which transcription factors (TFs) bind their DNA regulatory sites. Obtaining accurate models of this binding energy is therefore an important goal for quantitative biology. In this article, we present a principled likelihood-based approach for inferring physical models of TF-DNA binding energy from the data produced by modern high-throughput binding assays. Central to our analysis is the ability to assess the relative likelihood of different model parameters given experimental observations. We take a unique approach to this problem and show how to compute likelihood without any explicit assumptions about the noise that inevitably corrupts such measurements. Sampling possible choices for model parameters according to this likelihood function, we can then make probabilistic predictions for the identities of binding sites and their physical binding energies. Applying this procedure to previously published data on the Saccharomyces cerevisiae TF Abf1p, we find models of TF binding whose parameters are determined with remarkable precision. Evidence for the accuracy of these models is provided by an astonishing level of phylogenetic conservation in the predicted energies of putative binding sites. Results from in vivo and in vitro experiments also provide highly consistent characterizations of Abf1p, a result that contrasts with a previous analysis of the same data. author: - first_name: Justin full_name: Kinney,Justin B last_name: Kinney - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Curtis full_name: Callan,Curtis G last_name: Callan citation: ama: Kinney J, Tkačik G, Callan C. Precise physical models of protein-DNA interaction from high-throughput data. PNAS. 2007;104(2):501-506. doi:10.1073/pnas.0609908104 apa: Kinney, J., Tkačik, G., & Callan, C. (2007). Precise physical models of protein-DNA interaction from high-throughput data. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0609908104 chicago: Kinney, Justin, Gašper Tkačik, and Curtis Callan. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” PNAS. National Academy of Sciences, 2007. https://doi.org/10.1073/pnas.0609908104. ieee: J. Kinney, G. Tkačik, and C. Callan, “Precise physical models of protein-DNA interaction from high-throughput data,” PNAS, vol. 104, no. 2. National Academy of Sciences, pp. 501–506, 2007. ista: Kinney J, Tkačik G, Callan C. 2007. Precise physical models of protein-DNA interaction from high-throughput data. PNAS. 104(2), 501–506. mla: Kinney, Justin, et al. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” PNAS, vol. 104, no. 2, National Academy of Sciences, 2007, pp. 501–06, doi:10.1073/pnas.0609908104. short: J. Kinney, G. Tkačik, C. Callan, PNAS 104 (2007) 501–506. date_created: 2018-12-11T12:04:51Z date_published: 2007-01-09T00:00:00Z date_updated: 2021-01-12T07:51:48Z day: '09' doi: 10.1073/pnas.0609908104 extern: 1 intvolume: ' 104' issue: '2' main_file_link: - open_access: '0' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1766414 month: '01' page: 501 - 506 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '2495' quality_controlled: 0 status: public title: Precise physical models of protein-DNA interaction from high-throughput data type: journal_article volume: 104 year: '2007' ... --- _id: '3765' abstract: - lang: eng text: We present an extension to Lagrangian finite element methods to allow for large plastic deformations of solid materials. These behaviors are seen in such everyday materials as shampoo, dough, and clay as well as in fantastic gooey and blobby creatures in special effects scenes. To account for plastic deformation, we explicitly update the linear basis functions defined over the finite elements during each simulation step. When these updates cause the basis functions to become ill-conditioned, we remesh the simulation domain to produce a new high-quality finite-element mesh, taking care to preserve the original boundary. We also introduce an enhanced plasticity model that preserves volume and includes creep and work hardening/softening. We demonstrate our approach with simulations of synthetic objects that squish, dent, and flow. To validate our methods, we compare simulation results to videos of real materials. article_processing_charge: No author: - first_name: Adam full_name: Bargteil, Adam last_name: Bargteil - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Jessica full_name: Hodgins, Jessica last_name: Hodgins - first_name: Greg full_name: Turk, Greg last_name: Turk citation: ama: Bargteil A, Wojtan C, Hodgins J, Turk G. A finite element method for animating large viscoplastic flow. ACM Transactions on Graphics. 2007;26(3). doi:10.1145/1276377.1276397 apa: Bargteil, A., Wojtan, C., Hodgins, J., & Turk, G. (2007). A finite element method for animating large viscoplastic flow. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1276377.1276397 chicago: Bargteil, Adam, Chris Wojtan, Jessica Hodgins, and Greg Turk. “A Finite Element Method for Animating Large Viscoplastic Flow.” ACM Transactions on Graphics. ACM, 2007. https://doi.org/10.1145/1276377.1276397. ieee: A. Bargteil, C. Wojtan, J. Hodgins, and G. Turk, “A finite element method for animating large viscoplastic flow,” ACM Transactions on Graphics, vol. 26, no. 3. ACM, 2007. ista: Bargteil A, Wojtan C, Hodgins J, Turk G. 2007. A finite element method for animating large viscoplastic flow. ACM Transactions on Graphics. 26(3). mla: Bargteil, Adam, et al. “A Finite Element Method for Animating Large Viscoplastic Flow.” ACM Transactions on Graphics, vol. 26, no. 3, ACM, 2007, doi:10.1145/1276377.1276397. short: A. Bargteil, C. Wojtan, J. Hodgins, G. Turk, ACM Transactions on Graphics 26 (2007). date_created: 2018-12-11T12:05:03Z date_published: 2007-07-29T00:00:00Z date_updated: 2023-02-23T11:41:41Z day: '29' doi: 10.1145/1276377.1276397 extern: '1' intvolume: ' 26' issue: '3' language: - iso: eng month: '07' oa_version: None publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '2462' status: public title: A finite element method for animating large viscoplastic flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2007' ... --- _id: '3762' abstract: - lang: eng text: In this paper, we present a simple method for animating natural phenomena such as erosion, sedimentation, and acidic corrosion. We discretize the appropriate physical or chemical equations using finite differences, and we use the results to modify the shape of a solid body. We remove mass from an object by treating its surface as a level set and advecting it inward, and we deposit the chemical and physical byproducts into simulated fluid. Similarly, our technique deposits sediment onto a surface by advecting the level set outward. Our idea can be used for off-line high quality animations as well as interactive applications such as games, and we demonstrate both in this paper. article_processing_charge: No author: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Mark full_name: Carlson, Mark last_name: Carlson - first_name: Peter full_name: Mucha, Peter last_name: Mucha - first_name: Greg full_name: Turk, Greg last_name: Turk citation: ama: 'Wojtan C, Carlson M, Mucha P, Turk G. Animating corrosion and erosion. In: Eurographics Association; 2007:15-22. doi:10.2312/NPH/NPH07/015-022' apa: 'Wojtan, C., Carlson, M., Mucha, P., & Turk, G. (2007). Animating corrosion and erosion (pp. 15–22). Presented at the EGWNP: Eurographics Workshop on Natural Phenomena, Eurographics Association. https://doi.org/10.2312/NPH/NPH07/015-022' chicago: Wojtan, Chris, Mark Carlson, Peter Mucha, and Greg Turk. “Animating Corrosion and Erosion,” 15–22. Eurographics Association, 2007. https://doi.org/10.2312/NPH/NPH07/015-022. ieee: 'C. Wojtan, M. Carlson, P. Mucha, and G. Turk, “Animating corrosion and erosion,” presented at the EGWNP: Eurographics Workshop on Natural Phenomena, 2007, pp. 15–22.' ista: 'Wojtan C, Carlson M, Mucha P, Turk G. 2007. Animating corrosion and erosion. EGWNP: Eurographics Workshop on Natural Phenomena, 15–22.' mla: Wojtan, Chris, et al. Animating Corrosion and Erosion. Eurographics Association, 2007, pp. 15–22, doi:10.2312/NPH/NPH07/015-022. short: C. Wojtan, M. Carlson, P. Mucha, G. Turk, in:, Eurographics Association, 2007, pp. 15–22. conference: name: 'EGWNP: Eurographics Workshop on Natural Phenomena' date_created: 2018-12-11T12:05:02Z date_published: 2007-09-01T00:00:00Z date_updated: 2023-02-23T11:41:34Z day: '01' doi: 10.2312/NPH/NPH07/015-022 extern: '1' language: - iso: eng main_file_link: - url: http://www.amath.unc.edu/Faculty/mucha/Reprints/EGNPerosion.pdf month: '09' oa_version: None page: 15 - 22 publication_status: published publisher: Eurographics Association publist_id: '2464' status: public title: Animating corrosion and erosion type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2007' ... --- _id: '3816' abstract: - lang: eng text: Gamma frequency oscillations are thought to provide a temporal structure for information processing in the brain. They contribute to cognitive functions, such as memory formation and sensory processing, and are disturbed in some psychiatric disorders. Fast-spiking, parvalbumin-expressing, soma-inhibiting interneurons have a key role in the generation of these oscillations. Experimental analysis in the hippocampus and the neocortex reveals that synapses among these interneurons are highly specialized. Computational analysis further suggests that synaptic specialization turns interneuron networks into robust gamma frequency oscillators. author: - first_name: Marlene full_name: Bartos, Marlene last_name: Bartos - first_name: Imre full_name: Vida, Imre last_name: Vida - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Bartos M, Vida I, Jonas PM. Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron networks (Review). Nature Reviews Neuroscience. 2007;8(1):45-56. doi:10.1038/nrn2044 apa: Bartos, M., Vida, I., & Jonas, P. M. (2007). Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron networks (Review). Nature Reviews Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nrn2044 chicago: Bartos, Marlene, Imre Vida, and Peter M Jonas. “Synaptic Mechanisms of Synchronized Gamma Oscillations in Inhibitory Interneuron Networks (Review).” Nature Reviews Neuroscience. Nature Publishing Group, 2007. https://doi.org/10.1038/nrn2044 . ieee: M. Bartos, I. Vida, and P. M. Jonas, “Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron networks (Review),” Nature Reviews Neuroscience, vol. 8, no. 1. Nature Publishing Group, pp. 45–56, 2007. ista: Bartos M, Vida I, Jonas PM. 2007. Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron networks (Review). Nature Reviews Neuroscience. 8(1), 45–56. mla: Bartos, Marlene, et al. “Synaptic Mechanisms of Synchronized Gamma Oscillations in Inhibitory Interneuron Networks (Review).” Nature Reviews Neuroscience, vol. 8, no. 1, Nature Publishing Group, 2007, pp. 45–56, doi:10.1038/nrn2044 . short: M. Bartos, I. Vida, P.M. Jonas, Nature Reviews Neuroscience 8 (2007) 45–56. date_created: 2018-12-11T12:05:20Z date_published: 2007-01-21T00:00:00Z date_updated: 2021-01-12T07:52:24Z day: '21' doi: '10.1038/nrn2044 ' extern: 1 intvolume: ' 8' issue: '1' month: '01' page: 45 - 56 publication: Nature Reviews Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '2393' quality_controlled: 0 status: public title: Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron networks (Review) type: journal_article volume: 8 year: '2007' ... --- _id: '3911' abstract: - lang: eng text: Life in a social group increases the risk of disease transmission. To counteract this threat, social insects have evolved manifold antiparasite defenses, ranging from social exclusion of infected group members to intensive care. It is generally assumed that individuals performing hygienic behaviors risk infecting themselves, suggesting a high direct cost of helping. Our work instead indicates the opposite for garden ants. Social contact with individual workers, which were experimentally exposed to a fungal parasite, provided a clear survival benefit to nontreated, naive group members upon later challenge with the same parasite. This first demonstration of contact immunity in Social Hymenoptera and complementary results from other animal groups and plants suggest its general importance in both antiparasite and antiherbivore defense. In addition to this physiological prophylaxis of adult ants, infection of the brood was prevented in our experiment by behavioral changes of treated and naive workers. Parasite-treated ants stayed away from the brood chamber, whereas their naive nestmates increased brood-care activities. Our findings reveal a direct benefit for individuals to perform hygienic behaviors toward others, and this might explain the widely observed maintenance of social cohesion under parasite attack in insect societies. author: - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Ugelvig LV, Cremer S. Social prophylaxis: group interaction promotes collective immunity in ant colonies. Current Biology. 2007;17(22):1967-1971. doi:10.1016/j.cub.2007.10.029' apa: 'Ugelvig, L. V., & Cremer, S. (2007). Social prophylaxis: group interaction promotes collective immunity in ant colonies. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2007.10.029' chicago: 'Ugelvig, Line V, and Sylvia Cremer. “Social Prophylaxis: Group Interaction Promotes Collective Immunity in Ant Colonies.” Current Biology. Cell Press, 2007. https://doi.org/10.1016/j.cub.2007.10.029.' ieee: 'L. V. Ugelvig and S. Cremer, “Social prophylaxis: group interaction promotes collective immunity in ant colonies,” Current Biology, vol. 17, no. 22. Cell Press, pp. 1967–1971, 2007.' ista: 'Ugelvig LV, Cremer S. 2007. Social prophylaxis: group interaction promotes collective immunity in ant colonies. Current Biology. 17(22), 1967–1971.' mla: 'Ugelvig, Line V., and Sylvia Cremer. “Social Prophylaxis: Group Interaction Promotes Collective Immunity in Ant Colonies.” Current Biology, vol. 17, no. 22, Cell Press, 2007, pp. 1967–71, doi:10.1016/j.cub.2007.10.029.' short: L.V. Ugelvig, S. Cremer, Current Biology 17 (2007) 1967–1971. date_created: 2018-12-11T12:05:51Z date_published: 2007-11-20T00:00:00Z date_updated: 2021-01-12T07:53:08Z day: '20' doi: 10.1016/j.cub.2007.10.029 extern: '1' intvolume: ' 17' issue: '22' language: - iso: eng month: '11' oa_version: None page: 1967 - 1971 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '2245' status: public title: 'Social prophylaxis: group interaction promotes collective immunity in ant colonies' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2007' ... --- _id: '3909' abstract: - lang: eng text: Social insect colonies have evolved collective immune defences against parasites. These ‘social immune systems’ result from the cooperation of the individual group members to combat the increased risk of disease transmission that arises from sociality and group living. In this review we illustrate the pathways that parasites can take to infect a social insect colony and use these pathways as a framework to predict colony defence mechanisms and present the existing evidence. We find that the collective defences can be both prophylactic and activated on demand and consist of behavioural, physiological and organisational adaptations of the colony that prevent parasite entrance, establishment and spread. We discuss the regulation of collective immunity, which requires complex integration of information about both the parasites and the internal status of the insect colony. Our review concludes with an examination of the evolution of social immunity, which is based on the consequences of selection at both the individual and the colony level. author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Sophie full_name: Armitage, Sophie last_name: Armitage - first_name: Paul full_name: Schmid Hempel, Paul last_name: Schmid Hempel citation: ama: Cremer S, Armitage S, Schmid Hempel P. Social immunity. Current Biology. 2007;17(16):R693-R702. doi:10.1016/j.cub.2007.06.008 apa: Cremer, S., Armitage, S., & Schmid Hempel, P. (2007). Social immunity. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2007.06.008 chicago: Cremer, Sylvia, Sophie Armitage, and Paul Schmid Hempel. “Social Immunity.” Current Biology. Cell Press, 2007. https://doi.org/10.1016/j.cub.2007.06.008. ieee: S. Cremer, S. Armitage, and P. Schmid Hempel, “Social immunity,” Current Biology, vol. 17, no. 16. Cell Press, pp. R693–R702, 2007. ista: Cremer S, Armitage S, Schmid Hempel P. 2007. Social immunity. Current Biology. 17(16), R693–R702. mla: Cremer, Sylvia, et al. “Social Immunity.” Current Biology, vol. 17, no. 16, Cell Press, 2007, pp. R693–702, doi:10.1016/j.cub.2007.06.008. short: S. Cremer, S. Armitage, P. Schmid Hempel, Current Biology 17 (2007) R693–R702. date_created: 2018-12-11T12:05:50Z date_published: 2007-08-21T00:00:00Z date_updated: 2021-01-12T07:53:07Z day: '21' doi: 10.1016/j.cub.2007.06.008 extern: '1' intvolume: ' 17' issue: '16' language: - iso: eng month: '08' oa_version: None page: R693 - R702 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '2243' status: public title: Social immunity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2007' ... --- _id: '3910' author: - first_name: David full_name: Hughes, David last_name: Hughes - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Hughes D, Cremer S. Plasticity in anti-parasite behaviours and its suggested role in invasion biology. Animal Behaviour. 2007;74(5):1593-1599. doi:10.1016/j.anbehav.2006.12.025 apa: Hughes, D., & Cremer, S. (2007). Plasticity in anti-parasite behaviours and its suggested role in invasion biology. Animal Behaviour. Elsevier. https://doi.org/10.1016/j.anbehav.2006.12.025 chicago: Hughes, David, and Sylvia Cremer. “Plasticity in Anti-Parasite Behaviours and Its Suggested Role in Invasion Biology.” Animal Behaviour. Elsevier, 2007. https://doi.org/10.1016/j.anbehav.2006.12.025. ieee: D. Hughes and S. Cremer, “Plasticity in anti-parasite behaviours and its suggested role in invasion biology,” Animal Behaviour, vol. 74, no. 5. Elsevier, pp. 1593–1599, 2007. ista: Hughes D, Cremer S. 2007. Plasticity in anti-parasite behaviours and its suggested role in invasion biology. Animal Behaviour. 74(5), 1593–1599. mla: Hughes, David, and Sylvia Cremer. “Plasticity in Anti-Parasite Behaviours and Its Suggested Role in Invasion Biology.” Animal Behaviour, vol. 74, no. 5, Elsevier, 2007, pp. 1593–99, doi:10.1016/j.anbehav.2006.12.025. short: D. Hughes, S. Cremer, Animal Behaviour 74 (2007) 1593–1599. date_created: 2018-12-11T12:05:50Z date_published: 2007-11-01T00:00:00Z date_updated: 2021-01-12T07:53:08Z day: '01' doi: 10.1016/j.anbehav.2006.12.025 extern: '1' intvolume: ' 74' issue: '5' language: - iso: eng month: '11' oa_version: None page: 1593 - 1599 publication: Animal Behaviour publication_status: published publisher: Elsevier publist_id: '2244' status: public title: Plasticity in anti-parasite behaviours and its suggested role in invasion biology type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2007' ... --- _id: '3976' abstract: - lang: eng text: Herein, we study the interfaces of a set of 146 transient protein-protein interfaces in order to better understand the principles of their interactions. We define and generate the protein interface using tools from computational geometry and topology and then apply statistical analysis to its residue composition. In addition to counting individual occurrences, we evaluate pairing preferences, both across and as neighbors on one side of an interface. Likelihood correction emphasizes novel and unexpected pairs, such as the His-Cys pair found in most complexes of serine proteases with their diverse inhibitors and the Met-Met neighbor pair found in unrelated protein interfaces. We also present a visualization of the protein interface that allows for facile identification of residue-residue contacts and other biochemical properties. author: - first_name: Jeffrey full_name: Headd, Jeffrey J last_name: Headd - first_name: Y E Andrew full_name: Ban, Y E Andrew last_name: Ban - first_name: Paul full_name: Brown, Paul last_name: Brown - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Madhuwanti full_name: Vaidya, Madhuwanti last_name: Vaidya - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph citation: ama: 'Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. Protein-protein interfaces: Properties, preferences, and projections. Journal of Proteome Research. 2007;6(7):2576-2586. doi:10.1021/pr070018+' apa: 'Headd, J., Ban, Y. E. A., Brown, P., Edelsbrunner, H., Vaidya, M., & Rudolph, J. (2007). Protein-protein interfaces: Properties, preferences, and projections. Journal of Proteome Research. American Chemical Society. https://doi.org/10.1021/pr070018+' chicago: 'Headd, Jeffrey, Y E Andrew Ban, Paul Brown, Herbert Edelsbrunner, Madhuwanti Vaidya, and Johannes Rudolph. “Protein-Protein Interfaces: Properties, Preferences, and Projections.” Journal of Proteome Research. American Chemical Society, 2007. https://doi.org/10.1021/pr070018+.' ieee: 'J. Headd, Y. E. A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, and J. Rudolph, “Protein-protein interfaces: Properties, preferences, and projections,” Journal of Proteome Research, vol. 6, no. 7. American Chemical Society, pp. 2576–2586, 2007.' ista: 'Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. 2007. Protein-protein interfaces: Properties, preferences, and projections. Journal of Proteome Research. 6(7), 2576–2586.' mla: 'Headd, Jeffrey, et al. “Protein-Protein Interfaces: Properties, Preferences, and Projections.” Journal of Proteome Research, vol. 6, no. 7, American Chemical Society, 2007, pp. 2576–86, doi:10.1021/pr070018+.' short: J. Headd, Y.E.A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, J. Rudolph, Journal of Proteome Research 6 (2007) 2576–2586. date_created: 2018-12-11T12:06:13Z date_published: 2007-06-02T00:00:00Z date_updated: 2021-01-12T07:53:36Z day: '02' doi: 10.1021/pr070018+ extern: 1 intvolume: ' 6' issue: '7' month: '06' page: 2576 - 2586 publication: Journal of Proteome Research publication_status: published publisher: American Chemical Society publist_id: '2151' quality_controlled: 0 status: public title: 'Protein-protein interfaces: Properties, preferences, and projections' type: journal_article volume: 6 year: '2007' ... --- _id: '3981' abstract: - lang: eng text: Building on the work of Martinetz, Schulten and de Silva, Carlsson, we introduce a 2-parameter family of witness complexes and algorithms for constructing them. This family can be used to determine the gross topology of point cloud data in R-d or other metric spaces. The 2-parameter family is sensitive to differences in sampling density and thus amenable to detecting patterns within the data set. It also lends itself to theoretical analysis. For example, we can prove that in the limit, when the witnesses cover the entire domain, witness complexes in the family that share the first, scale parameter have the same homotopy type. acknowledgement: Research by the authors is partially supported by DARPA under grant HR0011-05-1-0007, by CNRS under grant PICS-3416 and by IST Program of the EU under Contract IST-2002-506766. alternative_title: - LNCS author: - first_name: Dominique full_name: Attali, Dominique last_name: Attali - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Yuriy full_name: Mileyko, Yuriy last_name: Mileyko citation: ama: 'Attali D, Edelsbrunner H, Harer J, Mileyko Y. Alpha-beta witness complexes. In: Vol 4619. Springer; 2007:386-397. doi:10.1007/978-3-540-73951-7_34' apa: 'Attali, D., Edelsbrunner, H., Harer, J., & Mileyko, Y. (2007). Alpha-beta witness complexes (Vol. 4619, pp. 386–397). Presented at the WADS: International Workshop on Algrithms and Data Structures, Springer. https://doi.org/10.1007/978-3-540-73951-7_34' chicago: Attali, Dominique, Herbert Edelsbrunner, John Harer, and Yuriy Mileyko. “Alpha-Beta Witness Complexes,” 4619:386–97. Springer, 2007. https://doi.org/10.1007/978-3-540-73951-7_34. ieee: 'D. Attali, H. Edelsbrunner, J. Harer, and Y. Mileyko, “Alpha-beta witness complexes,” presented at the WADS: International Workshop on Algrithms and Data Structures, 2007, vol. 4619, pp. 386–397.' ista: 'Attali D, Edelsbrunner H, Harer J, Mileyko Y. 2007. Alpha-beta witness complexes. WADS: International Workshop on Algrithms and Data Structures, LNCS, vol. 4619, 386–397.' mla: Attali, Dominique, et al. Alpha-Beta Witness Complexes. Vol. 4619, Springer, 2007, pp. 386–97, doi:10.1007/978-3-540-73951-7_34. short: D. Attali, H. Edelsbrunner, J. Harer, Y. Mileyko, in:, Springer, 2007, pp. 386–397. conference: name: 'WADS: International Workshop on Algrithms and Data Structures' date_created: 2018-12-11T12:06:15Z date_published: 2007-08-21T00:00:00Z date_updated: 2021-01-12T07:53:38Z day: '21' doi: 10.1007/978-3-540-73951-7_34 extern: 1 intvolume: ' 4619' month: '08' page: 386 - 397 publication_status: published publisher: Springer publist_id: '2149' quality_controlled: 0 status: public title: Alpha-beta witness complexes type: conference volume: 4619 year: '2007' ... --- _id: '3975' abstract: - lang: eng text: We study the reconstruction of a stratified space from a possibly noisy point sample. Specifically, we use the vineyard of the distance function restricted to a I-parameter family of neighborhoods of a point to assess the local homology of the stratified space at that point. We prove the correctness of this assessment under the assumption of a sufficiently dense sample. We also give an algorithm that constructs the vineyard and makes the local assessment in time at most cubic in the size of the Delaunay triangulation of the point sample. author: - first_name: Paul full_name: Paul Bendich id: 43F6EC54-F248-11E8-B48F-1D18A9856A87 last_name: Bendich - first_name: David full_name: Cohen-Steiner, David last_name: Cohen Steiner - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov citation: ama: 'Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. Inferring local homology from sampled stratified spaces. In: IEEE; 2007:536-546. doi:10.1109/FOCS.2007.33' apa: 'Bendich, P., Cohen Steiner, D., Edelsbrunner, H., Harer, J., & Morozov, D. (2007). Inferring local homology from sampled stratified spaces (pp. 536–546). Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2007.33' chicago: Bendich, Paul, David Cohen Steiner, Herbert Edelsbrunner, John Harer, and Dmitriy Morozov. “Inferring Local Homology from Sampled Stratified Spaces,” 536–46. IEEE, 2007. https://doi.org/10.1109/FOCS.2007.33. ieee: 'P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, and D. Morozov, “Inferring local homology from sampled stratified spaces,” presented at the FOCS: Foundations of Computer Science, 2007, pp. 536–546.' ista: 'Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. 2007. Inferring local homology from sampled stratified spaces. FOCS: Foundations of Computer Science, 536–546.' mla: Bendich, Paul, et al. Inferring Local Homology from Sampled Stratified Spaces. IEEE, 2007, pp. 536–46, doi:10.1109/FOCS.2007.33. short: P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, D. Morozov, in:, IEEE, 2007, pp. 536–546. conference: name: 'FOCS: Foundations of Computer Science' date_created: 2018-12-11T12:06:13Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:53:35Z day: '01' doi: 10.1109/FOCS.2007.33 extern: 1 month: '01' page: 536 - 546 publication_status: published publisher: IEEE publist_id: '2150' quality_controlled: 0 status: public title: Inferring local homology from sampled stratified spaces type: conference year: '2007' ... --- _id: '3977' abstract: - lang: eng text: Using inclusion-exclusion, we can write the indicator function of a union of finitely many balls as an alternating sum of indicator functions of common intersections of balls. We exhibit abstract simplicial complexes that correspond to minimal inclusion-exclusion formulas. They include the dual complex, as defined in [3], and are characterized by the independence of their simplices and by geometric realizations with the same underlying space as the dual complex. author: - first_name: Dominique full_name: Attali, Dominique last_name: Attali - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Attali D, Edelsbrunner H. Inclusion-exclusion formulas from independent complexes. Discrete & Computational Geometry. 2007;37(1):59-77. doi:10.1007/s00454-006-1274-7 apa: Attali, D., & Edelsbrunner, H. (2007). Inclusion-exclusion formulas from independent complexes. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1274-7 chicago: Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas from Independent Complexes.” Discrete & Computational Geometry. Springer, 2007. https://doi.org/10.1007/s00454-006-1274-7. ieee: D. Attali and H. Edelsbrunner, “Inclusion-exclusion formulas from independent complexes,” Discrete & Computational Geometry, vol. 37, no. 1. Springer, pp. 59–77, 2007. ista: Attali D, Edelsbrunner H. 2007. Inclusion-exclusion formulas from independent complexes. Discrete & Computational Geometry. 37(1), 59–77. mla: Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas from Independent Complexes.” Discrete & Computational Geometry, vol. 37, no. 1, Springer, 2007, pp. 59–77, doi:10.1007/s00454-006-1274-7. short: D. Attali, H. Edelsbrunner, Discrete & Computational Geometry 37 (2007) 59–77. date_created: 2018-12-11T12:06:14Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:53:36Z day: '01' doi: 10.1007/s00454-006-1274-7 extern: 1 intvolume: ' 37' issue: '1' month: '01' page: 59 - 77 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '2152' quality_controlled: 0 status: public title: Inclusion-exclusion formulas from independent complexes type: journal_article volume: 37 year: '2007' ... --- _id: '4152' abstract: - lang: eng text: 'Gastrulation is a morphogenetic process that results in the formation of the embryonic germ layers. Here we detail the major cell movements that occur during zebrafish gastrulation: epiboly, internalization, and convergent extension. Although gastrulation is known to be regulated by signaling pathways such as the Wnt/planar cell polarity pathway, many questions remain about the underlying molecular and cellular mechanisms. Key factors that may play a role in gastrulation cell movements are cell adhesion and cytoskeletal rearrangement. In addition, some of the driving force for gastrulation may derive from tissue interactions such as those described between the enveloping layer and the yolk syncytial layer. Future exploration of gastrulation mechanisms relies on the development of sensitive and quantitative techniques to characterize embryonic germ-layer properties.' author: - first_name: Laurel full_name: Rohde, Laurel last_name: Rohde - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Rohde L, Heisenberg C-PJ. Zebrafish gastrulation: Cell movements, signals, and mechanisms. International Review of Cytology - A Survey of Cell Biology. 2007;261:159-192. doi:10.1016/S0074-7696(07)61004-3' apa: 'Rohde, L., & Heisenberg, C.-P. J. (2007). Zebrafish gastrulation: Cell movements, signals, and mechanisms. International Review of Cytology - A Survey of Cell Biology. Academic Press. https://doi.org/10.1016/S0074-7696(07)61004-3' chicago: 'Rohde, Laurel, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation: Cell Movements, Signals, and Mechanisms.” International Review of Cytology - A Survey of Cell Biology. Academic Press, 2007. https://doi.org/10.1016/S0074-7696(07)61004-3.' ieee: 'L. Rohde and C.-P. J. Heisenberg, “Zebrafish gastrulation: Cell movements, signals, and mechanisms,” International Review of Cytology - A Survey of Cell Biology, vol. 261. Academic Press, pp. 159–192, 2007.' ista: 'Rohde L, Heisenberg C-PJ. 2007. Zebrafish gastrulation: Cell movements, signals, and mechanisms. International Review of Cytology - A Survey of Cell Biology. 261, 159–192.' mla: 'Rohde, Laurel, and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Cell Movements, Signals, and Mechanisms.” International Review of Cytology - A Survey of Cell Biology, vol. 261, Academic Press, 2007, pp. 159–92, doi:10.1016/S0074-7696(07)61004-3.' short: L. Rohde, C.-P.J. Heisenberg, International Review of Cytology - A Survey of Cell Biology 261 (2007) 159–192. date_created: 2018-12-11T12:07:15Z date_published: 2007-06-06T00:00:00Z date_updated: 2021-01-12T07:54:53Z day: '06' doi: 10.1016/S0074-7696(07)61004-3 extern: '1' intvolume: ' 261' language: - iso: eng month: '06' oa_version: None page: 159 - 192 publication: International Review of Cytology - A Survey of Cell Biology publication_status: published publisher: Academic Press publist_id: '1967' status: public title: 'Zebrafish gastrulation: Cell movements, signals, and mechanisms' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 261 year: '2007' ... --- _id: '4182' abstract: - lang: eng text: We are interested in the cellular and molecular mechanisms underlying tissue morphogenesis during zebrafish gastrulation. Both differential cell adhesion and contractility have been proposed to be key mechanisms by which tissues form and rearrange in development. To obtain insight into the potential roles of differential cell adhesion and contraction for germ layer morphogenesis during gastrulation, we are analyzing cell adhesion and contraction of germ layer progenitor cells using atomic force microscopy, primary tissue culture and transplantation assays. I will present and discuss data about the differential adhesiveness and contractility of germ layer progenitor cells in the context of germ layer formation during vertebrate gastrulation. acknowledgement: Abstract for the Annual Meeting of the German Societey for Cell Biology. article_processing_charge: No author: - first_name: Michael full_name: Krieg, Michael last_name: Krieg - first_name: Yohanna full_name: Arboleda, Yohanna last_name: Arboleda - first_name: Daniel full_name: Müller, Daniel last_name: Müller - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation. European Journal of Cell Biology. 2007;86(Supplement 1):39-39. doi:10.1016/j.ejcb.2007.02.002 apa: Krieg, M., Arboleda, Y., Müller, D., & Heisenberg, C.-P. J. (2007). The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2007.02.002 chicago: Krieg, Michael, Yohanna Arboleda, Daniel Müller, and Carl-Philipp J Heisenberg. “The Role of Cell Adhesion and Contractility for Germ Layer Morphogenesis during Zebrafish Gastrulation.” European Journal of Cell Biology. Elsevier, 2007. https://doi.org/10.1016/j.ejcb.2007.02.002. ieee: M. Krieg, Y. Arboleda, D. Müller, and C.-P. J. Heisenberg, “The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation,” European Journal of Cell Biology, vol. 86, no. Supplement 1. Elsevier, pp. 39–39, 2007. ista: Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. 2007. The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation. European Journal of Cell Biology. 86(Supplement 1), 39–39. mla: Krieg, Michael, et al. “The Role of Cell Adhesion and Contractility for Germ Layer Morphogenesis during Zebrafish Gastrulation.” European Journal of Cell Biology, vol. 86, no. Supplement 1, Elsevier, 2007, pp. 39–39, doi:10.1016/j.ejcb.2007.02.002. short: M. Krieg, Y. Arboleda, D. Müller, C.-P.J. Heisenberg, European Journal of Cell Biology 86 (2007) 39–39. date_created: 2018-12-11T12:07:26Z date_published: 2007-03-22T00:00:00Z date_updated: 2021-01-12T07:55:07Z day: '22' doi: 10.1016/j.ejcb.2007.02.002 extern: '1' intvolume: ' 86' issue: Supplement 1 language: - iso: eng month: '03' oa_version: None page: 39 - 39 publication: European Journal of Cell Biology publication_status: published publisher: Elsevier publist_id: '1937' status: public title: The role of cell adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 86 year: '2007' ... --- _id: '4225' abstract: - lang: eng text: The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show that the specific 64-to-20 mapping found in the genetic code may have been optimized for permitting protein-coding regions to carry this extra information and suggest that this property may have evolved as a side benefit of selection to minimize the negative effects of frameshift errors. 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: Kalin full_name: Vetsigian, Kalin last_name: Vetsigian - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Bollenbach MT, Vetsigian K, Kishony R. Evolution and multilevel optimization of the genetic code. Genome Research. 2007;17(4):401-404. doi:10.1101/gr.6144007 apa: Bollenbach, M. T., Vetsigian, K., & Kishony, R. (2007). Evolution and multilevel optimization of the genetic code. Genome Research. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.6144007 chicago: Bollenbach, Mark Tobias, Kalin Vetsigian, and Roy Kishony. “Evolution and Multilevel Optimization of the Genetic Code.” Genome Research. Cold Spring Harbor Laboratory Press, 2007. https://doi.org/10.1101/gr.6144007. ieee: M. T. Bollenbach, K. Vetsigian, and R. Kishony, “Evolution and multilevel optimization of the genetic code,” Genome Research, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, pp. 401–404, 2007. ista: Bollenbach MT, Vetsigian K, Kishony R. 2007. Evolution and multilevel optimization of the genetic code. Genome Research. 17(4), 401–404. mla: Bollenbach, Mark Tobias, et al. “Evolution and Multilevel Optimization of the Genetic Code.” Genome Research, vol. 17, no. 4, Cold Spring Harbor Laboratory Press, 2007, pp. 401–04, doi:10.1101/gr.6144007. short: M.T. Bollenbach, K. Vetsigian, R. Kishony, Genome Research 17 (2007) 401–404. date_created: 2018-12-11T12:07:42Z date_published: 2007-03-09T00:00:00Z date_updated: 2021-01-12T07:55:26Z day: '09' doi: 10.1101/gr.6144007 extern: '1' intvolume: ' 17' issue: '4' language: - iso: eng month: '03' oa_version: None page: 401 - 404 publication: Genome Research publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '1891' status: public title: Evolution and multilevel optimization of the genetic code type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2007' ... --- _id: '4226' abstract: - lang: eng text: 'In the developing fly wing, secreted morphogens such as Decapentaplegic (Dpp) and Wingless (Wg) form gradients of concentration providing positional information. Dpp forms a longer-range gradient than Wg. To understand how the range is controlled, we measured the four key kinetic parameters governing morphogen spreading: the production rate, the effective diffusion coefficient, the degradation rate, and the immobile fraction. The four parameters had different values for Dpp versus Wg. In addition, Dynamin-dependent endocytosis was required for spreading of Dpp, but not Wg. Thus, the cellular mechanisms of Dpp and Wingless spreading are different: Dpp spreading requires endocytic, intracellular trafficking.' author: - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Periklis full_name: Pantazis, Periklis last_name: Pantazis - first_name: Tobias full_name: Bollenbach, Tobias last_name: Bollenbach - first_name: Yannis full_name: Kalaidzidis, Yannis last_name: Kalaidzidis - first_name: Thomas full_name: Bittig, Thomas last_name: Bittig - first_name: Frank full_name: Julicher, Frank last_name: Julicher - first_name: Marcos full_name: Gonzalez-Gaitan, Marcos last_name: Gonzalez Gaitan citation: ama: Kicheva A, Pantazis P, Bollenbach T, et al. Kinetics of morphogen gradient formation. Science. 2007;315(5811):521-525. doi:10.1126/science.1135774 apa: Kicheva, A., Pantazis, P., Bollenbach, T., Kalaidzidis, Y., Bittig, T., Julicher, F., & Gonzalez Gaitan, M. (2007). Kinetics of morphogen gradient formation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1135774 chicago: Kicheva, Anna, Periklis Pantazis, Tobias Bollenbach, Yannis Kalaidzidis, Thomas Bittig, Frank Julicher, and Marcos Gonzalez Gaitan. “Kinetics of Morphogen Gradient Formation.” Science. American Association for the Advancement of Science, 2007. https://doi.org/10.1126/science.1135774. ieee: A. Kicheva et al., “Kinetics of morphogen gradient formation,” Science, vol. 315, no. 5811. American Association for the Advancement of Science, pp. 521–525, 2007. ista: Kicheva A, Pantazis P, Bollenbach T, Kalaidzidis Y, Bittig T, Julicher F, Gonzalez Gaitan M. 2007. Kinetics of morphogen gradient formation. Science. 315(5811), 521–525. mla: Kicheva, Anna, et al. “Kinetics of Morphogen Gradient Formation.” Science, vol. 315, no. 5811, American Association for the Advancement of Science, 2007, pp. 521–25, doi:10.1126/science.1135774. short: A. Kicheva, P. Pantazis, T. Bollenbach, Y. Kalaidzidis, T. Bittig, F. Julicher, M. Gonzalez Gaitan, Science 315 (2007) 521–525. date_created: 2018-12-11T12:07:42Z date_published: 2007-01-26T00:00:00Z date_updated: 2021-01-12T07:55:26Z day: '26' doi: 10.1126/science.1135774 extern: 1 intvolume: ' 315' issue: '5811' month: '01' page: 521 - 525 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '1892' quality_controlled: 0 status: public title: Kinetics of morphogen gradient formation type: journal_article volume: 315 year: '2007' ... --- _id: '4342' abstract: - lang: eng text: "Library 2.0 and user-generated content are two terms, which are closely connected. In the\r\n\r\npresentation, I will briefly define both terms. Two example projects where user- generated content and libraries interact will be presented. The cooperation of Wikipedia and the Personennamendatei, the German cooperative name authority files is the first. The second will be Wikisource where users provide transcribed source material. Another important area of user-generated content is social tagging where users index different resources. And if the users will do so much in the future, is there still a place for librarians? But in the future user\r\n\r\nand librarians become partners and the library will provide the platform: the library 2.0." author: - first_name: Patrick full_name: Danowski, Patrick id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 citation: ama: 'Danowski P. Library 2.0 and User-Generated Content - What can the users do for us? In: IFLA; 2007. doi:601' apa: 'Danowski, P. (2007). Library 2.0 and User-Generated Content - What can the users do for us? Presented at the WLIC: World Library and Information Congress, Durban, South Africa: IFLA. https://doi.org/601' chicago: Danowski, Patrick. “Library 2.0 and User-Generated Content - What Can the Users Do for Us?” IFLA, 2007. https://doi.org/601. ieee: 'P. Danowski, “Library 2.0 and User-Generated Content - What can the users do for us?,” presented at the WLIC: World Library and Information Congress, Durban, South Africa, 2007.' ista: 'Danowski P. 2007. Library 2.0 and User-Generated Content - What can the users do for us? WLIC: World Library and Information Congress.' mla: Danowski, Patrick. Library 2.0 and User-Generated Content - What Can the Users Do for Us? IFLA, 2007, doi:601. short: P. Danowski, in:, IFLA, 2007. conference: end_date: 2007-08-23 location: Durban, South Africa name: 'WLIC: World Library and Information Congress' start_date: 2007-08-19 date_created: 2018-12-11T12:08:22Z date_published: 2007-05-25T00:00:00Z date_updated: 2021-01-12T07:56:16Z day: '25' doi: '601' extern: '1' language: - iso: eng main_file_link: - url: http://www.ifla.org/IV/ifla73/papers/113-Danowski-en.pdf month: '05' oa_version: None publication_status: published publisher: IFLA publist_id: '1232' status: public title: Library 2.0 and User-Generated Content - What can the users do for us? type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2007' ... --- _id: '4343' author: - first_name: Patrick full_name: Patrick Danowski id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 - first_name: Barbara full_name: Pfeifer,Barbara last_name: Pfeifer citation: ama: 'Danowski P, Pfeifer B. Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei. Bibliothek - Forschung Und Praxis. 2007;31(2):149-155. doi:485' apa: 'Danowski, P., & Pfeifer, B. (2007). Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei. Bibliothek - Forschung Und Praxis. De Gruyter. https://doi.org/485' chicago: 'Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege Der Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” Bibliothek - Forschung Und Praxis. De Gruyter, 2007. https://doi.org/485.' ieee: 'P. Danowski and B. Pfeifer, “Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei,” Bibliothek - Forschung Und Praxis, vol. 31, no. 2. De Gruyter, pp. 149–155, 2007.' ista: 'Danowski P, Pfeifer B. 2007. Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei. Bibliothek - Forschung Und Praxis. 31(2), 149–155.' mla: 'Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege Der Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” Bibliothek - Forschung Und Praxis, vol. 31, no. 2, De Gruyter, 2007, pp. 149–55, doi:485.' short: P. Danowski, B. Pfeifer, Bibliothek - Forschung Und Praxis 31 (2007) 149–155. date_created: 2018-12-11T12:08:22Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:56:17Z day: '01' doi: '485' extern: 1 intvolume: ' 31' issue: '2' month: '01' page: 149 - 155 publication: Bibliothek - Forschung Und Praxis publication_status: published publisher: De Gruyter publist_id: '1231' quality_controlled: 0 status: public title: 'Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation mit der Personennamendatei' type: journal_article volume: 31 year: '2007' ... --- _id: '4344' author: - first_name: Patrick full_name: Patrick Danowski id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 - first_name: Lambert full_name: Heller,Lambert last_name: Heller citation: ama: Danowski P, Heller L. Bibliothek 2.0 ? Wird alles anders? Bibliothek - Forschung Und Praxis. 2007;31(2007):130-136. doi:45 apa: Danowski, P., & Heller, L. (2007). Bibliothek 2.0 ? Wird alles anders? Bibliothek - Forschung Und Praxis. De Gruyter. https://doi.org/45 chicago: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?” Bibliothek - Forschung Und Praxis. De Gruyter, 2007. https://doi.org/45. ieee: P. Danowski and L. Heller, “Bibliothek 2.0 ? Wird alles anders?,” Bibliothek - Forschung Und Praxis, vol. 31, no. 2007. De Gruyter, pp. 130–136, 2007. ista: Danowski P, Heller L. 2007. Bibliothek 2.0 ? Wird alles anders? Bibliothek - Forschung Und Praxis. 31(2007), 130–136. mla: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?” Bibliothek - Forschung Und Praxis, vol. 31, no. 2007, De Gruyter, 2007, pp. 130–36, doi:45. short: P. Danowski, L. Heller, Bibliothek - Forschung Und Praxis 31 (2007) 130–136. date_created: 2018-12-11T12:08:22Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:56:17Z day: '01' doi: '45' extern: 1 intvolume: ' 31' issue: '2007' main_file_link: - open_access: '0' url: http://www.bibliothek-saur.de/2007_2/130-136.pdf month: '01' page: 130 - 136 publication: Bibliothek - Forschung Und Praxis publication_status: published publisher: De Gruyter publist_id: '1230' quality_controlled: 0 status: public title: Bibliothek 2.0 ? Wird alles anders? type: journal_article volume: 31 year: '2007' ... --- _id: '4353' abstract: - lang: eng text: 'BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources. METHODOLOGY: We use conventional PCR with 5''-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences). Each DNA sequence is subsequently traced back to its individual source through 5''tag-analysis. CONCLUSIONS: We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate&lt;0.4%). Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5'' nucleotide of the tag. In particular, primers 5'' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5'' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5''primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial analyses, population genetics, and phylogenetics.' acknowledgement: JB and EW were supported by the Wellcome Trust, UK, the Carlsberg Foundation, DK, and the National Science Foundation, DK. MTPG acknowledges the Marie Curie Actions FP6-MEIF-CT-2005-025002 ‘FORMAPLEX’ grant for funding his research. JPB and RN were funded by the Danish FSS and the National Science Foundation, DK. None of the sponsors or funders have had any influence on the data or manuscript presented here. author: - first_name: Jonas full_name: Binladen, Jonas last_name: Binladen - first_name: M Thomas full_name: Gilbert, M Thomas last_name: Gilbert - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Frank full_name: Panitz, Frank last_name: Panitz - first_name: Christian full_name: Bendixen, Christian last_name: Bendixen - first_name: Rasmus full_name: Nielsen, Rasmus last_name: Nielsen - first_name: Eske full_name: Willerslev, Eske last_name: Willerslev citation: ama: Binladen J, Gilbert MT, Bollback JP, et al. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One. 2007;2(2). doi:10.1371/journal.pone.0000197 apa: Binladen, J., Gilbert, M. T., Bollback, J. P., Panitz, F., Bendixen, C., Nielsen, R., & Willerslev, E. (2007). The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0000197 chicago: Binladen, Jonas, M Thomas Gilbert, Jonathan P Bollback, Frank Panitz, Christian Bendixen, Rasmus Nielsen, and Eske Willerslev. “The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.” PLoS One. Public Library of Science, 2007. https://doi.org/10.1371/journal.pone.0000197. ieee: J. Binladen et al., “The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing,” PLoS One, vol. 2, no. 2. Public Library of Science, 2007. ista: Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One. 2(2). mla: Binladen, Jonas, et al. “The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.” PLoS One, vol. 2, no. 2, Public Library of Science, 2007, doi:10.1371/journal.pone.0000197. short: J. Binladen, M.T. Gilbert, J.P. Bollback, F. Panitz, C. Bendixen, R. Nielsen, E. Willerslev, PLoS One 2 (2007). date_created: 2018-12-11T12:08:25Z date_published: 2007-02-14T00:00:00Z date_updated: 2021-01-12T07:56:21Z day: '14' doi: 10.1371/journal.pone.0000197 extern: 1 intvolume: ' 2' issue: '2' month: '02' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '1105' quality_controlled: 0 status: public title: The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing 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: 2 year: '2007' ... --- _id: '4356' abstract: - lang: eng text: We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence for positive selection, such as the enigmatic rhs elements and transposases. Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome. author: - first_name: Lise full_name: Petersen, Lise last_name: Petersen - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Matt full_name: Dimmic, Matt last_name: Dimmic - first_name: Melissa full_name: Hubisz, Melissa last_name: Hubisz - first_name: Rasmus full_name: Nielsen, Rasmus last_name: Nielsen citation: ama: Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive selection in Escherichia coli. Genome Research. 2007;17(9):1336-1343. doi:10.1101/gr.6254707 apa: Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M., & Nielsen, R. (2007). Genes under positive selection in Escherichia coli. Genome Research. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.6254707 chicago: Petersen, Lise, Jonathan P Bollback, Matt Dimmic, Melissa Hubisz, and Rasmus Nielsen. “Genes under Positive Selection in Escherichia Coli.” Genome Research. Cold Spring Harbor Laboratory Press, 2007. https://doi.org/10.1101/gr.6254707. ieee: L. Petersen, J. P. Bollback, M. Dimmic, M. Hubisz, and R. Nielsen, “Genes under positive selection in Escherichia coli,” Genome Research, vol. 17, no. 9. Cold Spring Harbor Laboratory Press, pp. 1336–1343, 2007. ista: Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. 2007. Genes under positive selection in Escherichia coli. Genome Research. 17(9), 1336–1343. mla: Petersen, Lise, et al. “Genes under Positive Selection in Escherichia Coli.” Genome Research, vol. 17, no. 9, Cold Spring Harbor Laboratory Press, 2007, pp. 1336–43, doi:10.1101/gr.6254707. short: L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen, Genome Research 17 (2007) 1336–1343. date_created: 2018-12-11T12:08:26Z date_published: 2007-08-03T00:00:00Z date_updated: 2021-01-12T07:56:22Z day: '03' doi: 10.1101/gr.6254707 extern: 1 intvolume: ' 17' issue: '9' month: '08' page: 1336 - 1343 publication: Genome Research publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '1103' quality_controlled: 0 status: public title: Genes under positive selection in Escherichia coli type: journal_article volume: 17 year: '2007' ... --- _id: '4355' abstract: - lang: eng text: When a beneficial mutation is fixed in a population that lacks recombination, the genetic background linked to that mutation is fixed. As a result, beneficial mutations on different backgrounds experience competition, or "clonal interference," that can cause asexual populations to evolve more slowly than their sexual counterparts. Factors such as a large population size (N) and high mutation rates (mu) increase the number of competing beneficial mutations, and hence are expected to increase the intensity of clonal interference. However, recent theory suggests that, with very large values of Nmu, the severity of clonal interference may instead decline. The reason is that, with large Nmu, genomes including both beneficial mutations are rapidly created by recurrent mutation, obviating the need for recombination. Here, we analyze data from experimentally evolved asexual populations of a bacteriophage and find that, in these nonrecombining populations with very large Nmu, recurrent mutation does appear to ameliorate this cost of asexuality. acknowledgement: R01 GM069801-08/GM/NIGMS NIH HHS/United States author: - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: John full_name: Huelsenbeck, John P last_name: Huelsenbeck citation: ama: Bollback JP, Huelsenbeck J. Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution. 2007;24(6):1397-1406. doi:10.1093/molbev/msm056 apa: Bollback, J. P., & Huelsenbeck, J. (2007). Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msm056 chicago: Bollback, Jonathan P, and John Huelsenbeck. “Clonal Interference Is Alleviated by High Mutation Rates in Large Populations.” Molecular Biology and Evolution. Oxford University Press, 2007. https://doi.org/10.1093/molbev/msm056. ieee: J. P. Bollback and J. Huelsenbeck, “Clonal interference is alleviated by high mutation rates in large populations,” Molecular Biology and Evolution, vol. 24, no. 6. Oxford University Press, pp. 1397–1406, 2007. ista: Bollback JP, Huelsenbeck J. 2007. Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution. 24(6), 1397–1406. mla: Bollback, Jonathan P., and John Huelsenbeck. “Clonal Interference Is Alleviated by High Mutation Rates in Large Populations.” Molecular Biology and Evolution, vol. 24, no. 6, Oxford University Press, 2007, pp. 1397–406, doi:10.1093/molbev/msm056. short: J.P. Bollback, J. Huelsenbeck, Molecular Biology and Evolution 24 (2007) 1397–1406. date_created: 2018-12-11T12:08:26Z date_published: 2007-03-22T00:00:00Z date_updated: 2021-01-12T07:56:22Z day: '22' doi: 10.1093/molbev/msm056 extern: 1 intvolume: ' 24' issue: '6' month: '03' page: 1397 - 1406 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '1104' quality_controlled: 0 status: public title: Clonal interference is alleviated by high mutation rates in large populations type: journal_article volume: 24 year: '2007' ... --- _id: '4354' abstract: - lang: eng text: Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness of methods such as BLAST, FASTA, HMMer, and Infernal. Surprisingly, the most popular homology search methods are often the least accurate. As a result, many studies have used inappropriate tools for their analyses. On the basis of our results, we suggest homology search strategies using the currently available tools and some directions for future development. author: - first_name: Eva full_name: Freyhult, Eva K last_name: Freyhult - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Paul full_name: Gardner, Paul P last_name: Gardner citation: ama: 'Freyhult E, Bollback JP, Gardner P. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. 2007;17(1):117-125. doi:10.1101/gr.5890907' apa: 'Freyhult, E., Bollback, J. P., & Gardner, P. (2007). Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.5890907' chicago: 'Freyhult, Eva, Jonathan P Bollback, and Paul Gardner. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” Genome Research. Cold Spring Harbor Laboratory Press, 2007. https://doi.org/10.1101/gr.5890907.' ieee: 'E. Freyhult, J. P. Bollback, and P. Gardner, “Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA,” Genome Research, vol. 17, no. 1. Cold Spring Harbor Laboratory Press, pp. 117–25, 2007.' ista: 'Freyhult E, Bollback JP, Gardner P. 2007. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. 17(1), 117–25.' mla: 'Freyhult, Eva, et al. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” Genome Research, vol. 17, no. 1, Cold Spring Harbor Laboratory Press, 2007, pp. 117–25, doi:10.1101/gr.5890907.' short: E. Freyhult, J.P. Bollback, P. Gardner, Genome Research 17 (2007) 117–25. date_created: 2018-12-11T12:08:25Z date_published: 2007-01-01T00:00:00Z date_updated: 2021-01-12T07:56:21Z day: '01' doi: 10.1101/gr.5890907 extern: 1 intvolume: ' 17' issue: '1' main_file_link: - open_access: '0' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716261 month: '01' page: 117 - 25 publication: Genome Research publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '1106' quality_controlled: 0 status: public title: 'Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA' type: journal_article volume: 17 year: '2007' ...