--- _id: '3880' abstract: - lang: eng text: We consider imperfect-information parity games in which strategies rely on observations that provide imperfect information about the history of a play. To solve such games, i.e., to determine the winning regions of players and corresponding winning strategies, one can use the subset construction to build an equivalent perfect-information game. Recently, an algorithm that avoids the inefficient subset construction has been proposed. The algorithm performs a fixed-point computation in a lattice of antichains, thus maintaining a succinct representation of state sets. However, this representation does not allow to recover winning strategies. In this paper, we build on the antichain approach to develop an algorithm for constructing the winning strategies in parity games of imperfect information. We have implemented this algorithm as a prototype. To our knowledge, this is the first implementation of a procedure for solving imperfect-information parity games on graphs. alternative_title: - LNCS author: - first_name: Dietmar full_name: Berwanger, Dietmar last_name: Berwanger - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Sangram full_name: Raje, Sangram last_name: Raje citation: ama: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. Strategy construction for parity games with imperfect information. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:325-339. doi:10.1007/978-3-540-85361-9' apa: 'Berwanger, D., Chatterjee, K., Doyen, L., Henzinger, T. A., & Raje, S. (2008). Strategy construction for parity games with imperfect information (Vol. 5201, pp. 325–339). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9' chicago: Berwanger, Dietmar, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger, and Sangram Raje. “Strategy Construction for Parity Games with Imperfect Information,” 5201:325–39. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9. ieee: 'D. Berwanger, K. Chatterjee, L. Doyen, T. A. Henzinger, and S. Raje, “Strategy construction for parity games with imperfect information,” presented at the CONCUR: Concurrency Theory, 2008, vol. 5201, pp. 325–339.' ista: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. 2008. Strategy construction for parity games with imperfect information. CONCUR: Concurrency Theory, LNCS, vol. 5201, 325–339.' mla: Berwanger, Dietmar, et al. Strategy Construction for Parity Games with Imperfect Information. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 325–39, doi:10.1007/978-3-540-85361-9. short: D. Berwanger, K. Chatterjee, L. Doyen, T.A. Henzinger, S. Raje, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 325–339. conference: name: 'CONCUR: Concurrency Theory' date_created: 2018-12-11T12:05:40Z date_published: 2008-07-30T00:00:00Z date_updated: 2023-02-23T11:46:01Z day: '30' doi: 10.1007/978-3-540-85361-9 extern: 1 intvolume: ' 5201' month: '07' page: 325 - 339 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '2291' quality_controlled: 0 related_material: record: - id: '3863' relation: later_version status: public status: public title: Strategy construction for parity games with imperfect information type: conference volume: 5201 year: '2008' ... --- _id: '3903' abstract: - lang: eng text: "Background\r\n\r\nThe invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We evaluate the relative informative power of the three methodological approaches and estimate both the number of independent introduction events from a yet unknown native range somewhere in the Black Sea area, and the invasive potential of the existing introduced populations.\r\n\r\nResults\r\n\r\nThree clusters of genetically similar populations were detected, and all but one population had a similar chemical profile. Aggression between populations could be predicted from their genetic and chemical distance, and two major clusters of non-aggressive groups of populations were found. However, populations of L. neglectus did not separate into clear supercolonial associations, as is typical for other invasive ants.\r\n\r\nConclusion\r\n\r\nThe three methodological approaches gave consistent and complementary results. All joint evidence supports the inference that the 14 introduced populations of L. neglectus in Europe likely arose from only very few independent introductions from the native range, and that new infestations were typically started through introductions from other invasive populations. This indicates that existing introduced populations have a very high invasive potential when the ants are inadvertently spread by human transport. " 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: Falko full_name: Drijfhout, Falko last_name: Drijfhout - first_name: Daniel full_name: Kronauer, Daniel last_name: Kronauer - first_name: Jacobus full_name: Boomsma, Jacobus last_name: Boomsma - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen - 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, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches. BMC Biology. 2008;6(11). doi:10.1186/1741-7007-6-11' apa: 'Ugelvig, L. V., Drijfhout, F., Kronauer, D., Boomsma, J., Pedersen, J., & Cremer, S. (2008). The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches. BMC Biology. BioMed Central. https://doi.org/10.1186/1741-7007-6-11' chicago: 'Ugelvig, Line V, Falko Drijfhout, Daniel Kronauer, Jacobus Boomsma, Jes Pedersen, and Sylvia Cremer. “The Introduction History of Invasive Garden Ants in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology. BioMed Central, 2008. https://doi.org/10.1186/1741-7007-6-11.' ieee: 'L. V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, and S. Cremer, “The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches,” BMC Biology, vol. 6, no. 11. BioMed Central, 2008.' ista: 'Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. 2008. The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches. BMC Biology. 6(11).' mla: 'Ugelvig, Line V., et al. “The Introduction History of Invasive Garden Ants in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology, vol. 6, no. 11, BioMed Central, 2008, doi:10.1186/1741-7007-6-11.' short: L.V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, S. Cremer, BMC Biology 6 (2008). date_created: 2018-12-11T12:05:48Z date_published: 2008-02-26T00:00:00Z date_updated: 2021-01-12T07:53:05Z day: '26' doi: 10.1186/1741-7007-6-11 extern: '1' intvolume: ' 6' issue: '11' language: - iso: eng month: '02' oa_version: None publication: BMC Biology publication_status: published publisher: BioMed Central publist_id: '2249' status: public title: 'The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches' 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 user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2008' ... --- _id: '3905' abstract: - lang: eng text: Winged and wingless males coexist in the ant Cardiocondyla obscurior. Wingless (“ergatoid”) males never leave their maternal colony and fight remorselessly among each other for the access to emerging females. The peaceful winged males disperse after about 10 days, but beforehand also mate in the nest. In the first 5 days of their life, winged males perform a chemical female mimicry that protects them against attack and even makes them sexually attractive to ergatoid males. When older, the chemical profile of winged males no longer matches that of virgin females; nevertheless, they are still tolerated, which so far has been puzzling. Contrasting this general pattern, we have identified a single aberrant colony in which all winged males were attacked and killed by the ergatoid males. A comparative analysis of the morphology and chemical profile of these untypical attacked winged males and the tolerated males from several normal colonies revealed that normal old males are still performing some chemical mimicry to the virgin queens, though less perfect than in their young ages. The anomalous attacked winged males, on the other hand, had a very different odour to the females. Our study thus exemplifies that the analysis of rare malfunctioning can add valuable insight on functioning under normal conditions and allows the conclusion that older winged males from normal colonies of the ant C. obscurior are guarded through an imperfect chemical female mimicry, still close enough to protect against attacks by the wingless fighters yet dissimilar enough not to elicit their sexual interest. author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Patrizia full_name: D'Ettorre, Patrizia last_name: D'Ettorre - first_name: Falko full_name: Drijfhout, Falko last_name: Drijfhout - first_name: Matthew full_name: Sledge, Matthew last_name: Sledge - first_name: Stefano full_name: Turillazzi, Stefano last_name: Turillazzi - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften. 2008;95(11):1101-1105. doi:10.1007/s00114-008-0430-8 apa: Cremer, S., D’Ettorre, P., Drijfhout, F., Sledge, M., Turillazzi, S., & Heinze, J. (2008). Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-008-0430-8 chicago: Cremer, Sylvia, Patrizia D’Ettorre, Falko Drijfhout, Matthew Sledge, Stefano Turillazzi, and Jürgen Heinze. “Imperfect Chemical Female Mimicry in Males of the Ant Cardiocondyla Obscurior.” Naturwissenschaften. Springer, 2008. https://doi.org/10.1007/s00114-008-0430-8. ieee: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, and J. Heinze, “Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior,” Naturwissenschaften, vol. 95, no. 11. Springer, pp. 1101–1105, 2008. ista: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. 2008. Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften. 95(11), 1101–1105. mla: Cremer, Sylvia, et al. “Imperfect Chemical Female Mimicry in Males of the Ant Cardiocondyla Obscurior.” Naturwissenschaften, vol. 95, no. 11, Springer, 2008, pp. 1101–05, doi:10.1007/s00114-008-0430-8. short: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, J. Heinze, Naturwissenschaften 95 (2008) 1101–1105. date_created: 2018-12-11T12:05:48Z date_published: 2008-08-05T00:00:00Z date_updated: 2021-01-12T07:53:06Z day: '05' doi: 10.1007/s00114-008-0430-8 extern: '1' intvolume: ' 95' issue: '11' language: - iso: eng month: '08' oa_version: None page: 1101 - 1105 publication: Naturwissenschaften publication_status: published publisher: Springer publist_id: '2246' status: public title: Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 95 year: '2008' ... --- _id: '3907' abstract: - lang: eng text: 'Wingless males of the ant genus Cardiocondyla engage in fatal fighting for access to female sexual nestmates. Older, heavily sclerotized males are usually capable of eliminating all younger rivals, whose cuticle is still soft. In Cardiocondyla sp. A, this type of local mate competition (LMC) has turned the standard pattern of brood production of social insects upside down, in that mother queens in multi-queen colonies produce extremely long-lived sons very early in the life cycle of the colony. Here, we investigated the emergence pattern of sexuals in two species with LMC, in which males are much less long-lived. Queens of Cardiocondyla obscurior and Cardiocondyla minutior reared their first sons significantly earlier in multi-queen than in single-queen societies. In addition, first female sexuals also emerged earlier in multi-queen colonies, so that early males had mating opportunities. Hence, the timing of sexual production appears to be well predicted by evolutionary theory, in particular by local mate and queen–queen competition. ' author: - first_name: Masaki full_name: Suefuji, Masaki last_name: Suefuji - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jan full_name: Oettler, Jan last_name: Oettler - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: Suefuji M, Cremer S, Oettler J, Heinze J. Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters. 2008;4(6):670-673. doi:10.1098/rsbl.2008.0355 apa: Suefuji, M., Cremer, S., Oettler, J., & Heinze, J. (2008). Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters. Royal Society, The. https://doi.org/10.1098/rsbl.2008.0355 chicago: Suefuji, Masaki, Sylvia Cremer, Jan Oettler, and Jürgen Heinze. “Queen Number Influences the Timing of the Sexual Production in Colonies of Cardiocondyla Ants.” Biology Letters. Royal Society, The, 2008. https://doi.org/10.1098/rsbl.2008.0355. ieee: M. Suefuji, S. Cremer, J. Oettler, and J. Heinze, “Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants,” Biology Letters, vol. 4, no. 6. Royal Society, The, pp. 670–673, 2008. ista: Suefuji M, Cremer S, Oettler J, Heinze J. 2008. Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters. 4(6), 670–673. mla: Suefuji, Masaki, et al. “Queen Number Influences the Timing of the Sexual Production in Colonies of Cardiocondyla Ants.” Biology Letters, vol. 4, no. 6, Royal Society, The, 2008, pp. 670–73, doi:10.1098/rsbl.2008.0355. short: M. Suefuji, S. Cremer, J. Oettler, J. Heinze, Biology Letters 4 (2008) 670–673. date_created: 2018-12-11T12:05:49Z date_published: 2008-12-23T00:00:00Z date_updated: 2021-01-12T07:53:07Z day: '23' doi: 10.1098/rsbl.2008.0355 extern: '1' intvolume: ' 4' issue: '6' language: - iso: eng month: '12' oa_version: None page: 670 - 673 publication: Biology Letters publication_status: published publisher: Royal Society, The publist_id: '2248' status: public title: Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2008' ... --- _id: '3906' acknowledgement: 'Funding was obtained from the European Community: FP5 EU research-training network ‘INSECTS’ (JJB SC PD FPD DPH) and FP6 Individual Marie Curie EIF grant (SC), the Alexander-von-Humboldt Foundation (Feodor-Lynen postdoctoral stipend to SC), the Danish Natural Science Research Council (JSP), the Danish National Research Foundation (JJB DRN JSP), and the Austrian Science Fund (BCS FMS CS HK).' author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - 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: Falko full_name: Drijfhout, Falko last_name: Drijfhout - first_name: Birgit full_name: Schlick Steiner, Birgit last_name: Schlick Steiner - first_name: Florian full_name: Steiner, Florian last_name: Steiner - first_name: Bernhard full_name: Seifert, Bernhard last_name: Seifert - first_name: David full_name: Hughes, David last_name: Hughes - first_name: Andreas full_name: Schulz, Andreas last_name: Schulz - first_name: Klaus full_name: Petersen, Klaus last_name: Petersen - first_name: Heino full_name: Konrad, Heino last_name: Konrad - first_name: Christian full_name: Stauffer, Christian last_name: Stauffer - first_name: Kadri full_name: Kiran, Kadri last_name: Kiran - first_name: Xavier full_name: Espadaler, Xavier last_name: Espadaler - first_name: Patrizia full_name: D'Ettorre, Patrizia last_name: D'Ettorre - first_name: Nihat full_name: Aktaç, Nihat last_name: Aktaç - first_name: Jørgen full_name: Eilenberg, Jørgen last_name: Eilenberg - first_name: Graeme full_name: Jones, Graeme last_name: Jones - first_name: David full_name: Nash, David last_name: Nash - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen - first_name: Jacobus full_name: Boomsma, Jacobus last_name: Boomsma citation: ama: Cremer S, Ugelvig LV, Drijfhout F, et al. The evolution of invasiveness in garden ants. PLoS One. 2008;3(12). doi:10.1371/journal.pone.0003838 apa: Cremer, S., Ugelvig, L. V., Drijfhout, F., Schlick Steiner, B., Steiner, F., Seifert, B., … Boomsma, J. (2008). The evolution of invasiveness in garden ants. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0003838 chicago: Cremer, Sylvia, Line V Ugelvig, Falko Drijfhout, Birgit Schlick Steiner, Florian Steiner, Bernhard Seifert, David Hughes, et al. “The Evolution of Invasiveness in Garden Ants.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0003838. ieee: S. Cremer et al., “The evolution of invasiveness in garden ants,” PLoS One, vol. 3, no. 12. Public Library of Science, 2008. ista: Cremer S, Ugelvig LV, Drijfhout F, Schlick Steiner B, Steiner F, Seifert B, Hughes D, Schulz A, Petersen K, Konrad H, Stauffer C, Kiran K, Espadaler X, D’Ettorre P, Aktaç N, Eilenberg J, Jones G, Nash D, Pedersen J, Boomsma J. 2008. The evolution of invasiveness in garden ants. PLoS One. 3(12). mla: Cremer, Sylvia, et al. “The Evolution of Invasiveness in Garden Ants.” PLoS One, vol. 3, no. 12, Public Library of Science, 2008, doi:10.1371/journal.pone.0003838. short: S. Cremer, L.V. Ugelvig, F. Drijfhout, B. Schlick Steiner, F. Steiner, B. Seifert, D. Hughes, A. Schulz, K. Petersen, H. Konrad, C. Stauffer, K. Kiran, X. Espadaler, P. D’Ettorre, N. Aktaç, J. Eilenberg, G. Jones, D. Nash, J. Pedersen, J. Boomsma, PLoS One 3 (2008). date_created: 2018-12-11T12:05:49Z date_published: 2008-12-03T00:00:00Z date_updated: 2021-01-12T07:53:06Z day: '03' doi: 10.1371/journal.pone.0003838 extern: '1' intvolume: ' 3' issue: '12' language: - iso: eng month: '12' oa_version: None publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '2247' status: public title: The evolution of invasiveness in garden ants 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 user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2008' ... --- _id: '3939' abstract: - lang: eng text: The priming of a T cell results from its physical interaction with a dendritic cell (DC) that presents the cognate antigenic peptide. The success rate of such interactions is extremely low, because the precursor frequency of a naive T cell recognizing a specific antigen is in the range of 1:10(5)-10(6). To make this principle practicable, encounter frequencies between DCs and T cells are maximized within lymph nodes (LNs) that are compact immunological projections of the peripheral tissue they drain. But LNs are more than passive meeting places for DCs that immigrated from the tissue and lymphocytes that recirculated via the blood. The microanatomy of the LN stroma actively organizes the cellular encounters by providing preformed migration tracks that create dynamic but highly ordered movement patterns. LN architecture further acts as a sophisticated filtration system that sieves the incoming interstitial fluid at different levels and guarantees that immunologically relevant antigens are loaded on DCs or B cells while inert substances are channeled back into the blood circulation. This review focuses on the non-hematopoietic infrastructure of the lymph node. We describe the association between fibroblastic reticular cell, conduit, DC, and T cell as the essential functional unit of the T-cell cortex. author: - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Lämmermann T, Sixt MK. The microanatomy of T-cell responses. Immunological Reviews. 2008;221(1):26-43. doi:10.1111/j.1600-065X.2008.00592.x apa: Lämmermann, T., & Sixt, M. K. (2008). The microanatomy of T-cell responses. Immunological Reviews. Wiley-Blackwell. https://doi.org/10.1111/j.1600-065X.2008.00592.x chicago: Lämmermann, Tim, and Michael K Sixt. “The Microanatomy of T-Cell Responses.” Immunological Reviews. Wiley-Blackwell, 2008. https://doi.org/10.1111/j.1600-065X.2008.00592.x. ieee: T. Lämmermann and M. K. Sixt, “The microanatomy of T-cell responses,” Immunological Reviews, vol. 221, no. 1. Wiley-Blackwell, pp. 26–43, 2008. ista: Lämmermann T, Sixt MK. 2008. The microanatomy of T-cell responses. Immunological Reviews. 221(1), 26–43. mla: Lämmermann, Tim, and Michael K. Sixt. “The Microanatomy of T-Cell Responses.” Immunological Reviews, vol. 221, no. 1, Wiley-Blackwell, 2008, pp. 26–43, doi:10.1111/j.1600-065X.2008.00592.x. short: T. Lämmermann, M.K. Sixt, Immunological Reviews 221 (2008) 26–43. date_created: 2018-12-11T12:06:00Z date_published: 2008-02-07T00:00:00Z date_updated: 2021-01-12T07:53:20Z day: '07' doi: 10.1111/j.1600-065X.2008.00592.x extern: '1' intvolume: ' 221' issue: '1' language: - iso: eng month: '02' oa_version: None page: 26 - 43 publication: Immunological Reviews publication_status: published publisher: Wiley-Blackwell publist_id: '2187' status: public title: The microanatomy of T-cell responses type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 221 year: '2008' ... --- _id: '3940' abstract: - lang: eng text: Until recently little information was available on the molecular details of the extracellular matrix (ECM) of secondary lymphoid tissues. There is now growing evidence that these ECMs are unique structures, combining characteristics of basement membranes and interstitial or fibrillar matrices, resulting in scaffolds that are strong and highly flexible and, in certain secondary lymphoid compartments, also forming conduit networks for rapid fluid transport. This review will address the structural characteristics of the ECM of the murine spleen and its potential role as an organizer of immune cell compartments, with reference to the lymph node where relevant. author: - first_name: Zerina full_name: Lokmic, Zerina last_name: Lokmic - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Susanna full_name: Cardell, Susanna last_name: Cardell - first_name: Rupert full_name: Hallmann, Rupert last_name: Hallmann - first_name: Lydia full_name: Sorokin, Lydia last_name: Sorokin citation: ama: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. The extracellular matrix of the spleen as a potential organizer of immune cell compartments. Seminars in Immunology. 2008;20(1):4-13. doi:10.1016/j.smim.2007.12.009 apa: Lokmic, Z., Lämmermann, T., Sixt, M. K., Cardell, S., Hallmann, R., & Sorokin, L. (2008). The extracellular matrix of the spleen as a potential organizer of immune cell compartments. Seminars in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2007.12.009 chicago: Lokmic, Zerina, Tim Lämmermann, Michael K Sixt, Susanna Cardell, Rupert Hallmann, and Lydia Sorokin. “The Extracellular Matrix of the Spleen as a Potential Organizer of Immune Cell Compartments.” Seminars in Immunology. Academic Press, 2008. https://doi.org/10.1016/j.smim.2007.12.009. ieee: Z. Lokmic, T. Lämmermann, M. K. Sixt, S. Cardell, R. Hallmann, and L. Sorokin, “The extracellular matrix of the spleen as a potential organizer of immune cell compartments,” Seminars in Immunology, vol. 20, no. 1. Academic Press, pp. 4–13, 2008. ista: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. 2008. The extracellular matrix of the spleen as a potential organizer of immune cell compartments. Seminars in Immunology. 20(1), 4–13. mla: Lokmic, Zerina, et al. “The Extracellular Matrix of the Spleen as a Potential Organizer of Immune Cell Compartments.” Seminars in Immunology, vol. 20, no. 1, Academic Press, 2008, pp. 4–13, doi:10.1016/j.smim.2007.12.009. short: Z. Lokmic, T. Lämmermann, M.K. Sixt, S. Cardell, R. Hallmann, L. Sorokin, Seminars in Immunology 20 (2008) 4–13. date_created: 2018-12-11T12:06:00Z date_published: 2008-02-01T00:00:00Z date_updated: 2021-01-12T07:53:20Z day: '01' doi: 10.1016/j.smim.2007.12.009 extern: 1 intvolume: ' 20' issue: '1' month: '02' page: 4 - 13 publication: Seminars in Immunology publication_status: published publisher: Academic Press publist_id: '2188' quality_controlled: 0 status: public title: The extracellular matrix of the spleen as a potential organizer of immune cell compartments type: journal_article volume: 20 year: '2008' ... --- _id: '3970' abstract: - lang: eng text: 'While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently generated to study the transcriptional program of the mouse segmentation clock, a biological oscillator associated with the periodic formation of the segments of the body axis. A method related to Fourier analysis, the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset, leading to the identification of a novel set of cyclic genes associated with the segmentation clock. Here, we applied to the same microarray time series dataset four distinct mathematical methods to identify significant patterns in gene expression profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron test and Stable persistence, and are based on different conceptual frameworks that are either hypothesis- or data-driven. Some of the methods, unlike Fourier transforms, are not dependent on the assumption of periodicity of the pattern of interest. Remarkably, these methods identified blindly the expression profiles of known cyclic genes as the most significant patterns in the dataset. Many candidate genes predicted by more than one approach appeared to be true positive cyclic genes and will be of particular interest for future research. In addition, these methods predicted novel candidate cyclic genes that were consistent with previous biological knowledge and experimental validation in mouse embryos. Our results demonstrate the utility of these novel pattern detection strategies, notably for detection of periodic profiles, and suggest that combining several distinct mathematical approaches to analyze microarray datasets is a valuable strategy for identifying genes that exhibit novel, interesting transcriptional patterns.' acknowledgement: This research was partially supported by DARPA grant HR 0011-05-1-0057. HE and YM mathematical work was supported by DARPA grant HR0011-05-1-0007. AS research was supported by a Lucent Technologies Bell Labs Graduate Research. Fellowship; AK and MR research was supported by NIH grant GM U54 GM74942; and SA research was supported by Association pour la Recherche sur le Cancer (ARC), France. OP, AM, MLD, EG and GH research was supported by the Stowers Institute for Medical Research. OP is a Howard Hughes Medical Institute Investigator. author: - first_name: Mary full_name: Dequéant, Mary-Lee last_name: Dequéant - first_name: Sebastian full_name: Ahnert, Sebastian last_name: Ahnert - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Thomas full_name: Fink, Thomas M last_name: Fink - first_name: Earl full_name: Glynn, Earl F last_name: Glynn - first_name: Gaye full_name: Hattem, Gaye last_name: Hattem - first_name: Andrzej full_name: Kudlicki, Andrzej last_name: Kudlicki - first_name: Yuriy full_name: Mileyko, Yuriy last_name: Mileyko - first_name: Jason full_name: Morton, Jason last_name: Morton - first_name: Arcady full_name: Mushegian, Arcady R last_name: Mushegian - first_name: Lior full_name: Pachter, Lior last_name: Pachter - first_name: Maga full_name: Rowicka, Maga last_name: Rowicka - first_name: Anne full_name: Shiu, Anne last_name: Shiu - first_name: Bernd full_name: Sturmfels, Bernd last_name: Sturmfels - first_name: Olivier full_name: Pourquie, Olivier last_name: Pourquie citation: ama: Dequéant M, Ahnert S, Edelsbrunner H, et al. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. 2008;3(8). doi:10.1371/journal.pone.0002856 apa: Dequéant, M., Ahnert, S., Edelsbrunner, H., Fink, T., Glynn, E., Hattem, G., … Pourquie, O. (2008). Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0002856 chicago: Dequéant, Mary, Sebastian Ahnert, Herbert Edelsbrunner, Thomas Fink, Earl Glynn, Gaye Hattem, Andrzej Kudlicki, et al. “Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002856. ieee: M. Dequéant et al., “Comparison of pattern detection methods in microarray time series of the segmentation clock,” PLoS One, vol. 3, no. 8. Public Library of Science, 2008. ista: Dequéant M, Ahnert S, Edelsbrunner H, Fink T, Glynn E, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian A, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquie O. 2008. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. 3(8). mla: Dequéant, Mary, et al. “Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock.” PLoS One, vol. 3, no. 8, Public Library of Science, 2008, doi:10.1371/journal.pone.0002856. short: M. Dequéant, S. Ahnert, H. Edelsbrunner, T. Fink, E. Glynn, G. Hattem, A. Kudlicki, Y. Mileyko, J. Morton, A. Mushegian, L. Pachter, M. Rowicka, A. Shiu, B. Sturmfels, O. Pourquie, PLoS One 3 (2008). date_created: 2018-12-11T12:06:11Z date_published: 2008-08-06T00:00:00Z date_updated: 2021-01-12T07:53:33Z day: '06' doi: 10.1371/journal.pone.0002856 extern: 1 intvolume: ' 3' issue: '8' month: '08' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '2157' quality_controlled: 0 status: public title: Comparison of pattern detection methods in microarray time series of the segmentation clock 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: 3 year: '2008' ... --- _id: '3971' abstract: - lang: eng text: The Reeb graph is a useful tool in visualizing real-valued data obtained from computational simulations of physical processes. We characterize the evolution of the Reeb graph of a time-varying continuous function defined in three-dimensional space. We show how to maintain the Reeb graph over time and compress the entire sequence of Reeb graphs into a single, partially persistent data structure, and augment this data structure with Betti numbers to describe the topology of level sets and with path seeds to assist in the fast extraction of level sets for visualization. author: - 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: Ajith full_name: Mascarenhas, Ajith last_name: Mascarenhas - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci - first_name: Jack full_name: Snoeyink, Jack last_name: Snoeyink citation: ama: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. 2008;41(3):149-166. doi:10.1016/j.comgeo.2007.11.001' apa: 'Edelsbrunner, H., Harer, J., Mascarenhas, A., Pascucci, V., & Snoeyink, J. (2008). Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2007.11.001' chicago: 'Edelsbrunner, Herbert, John Harer, Ajith Mascarenhas, Valerio Pascucci, and Jack Snoeyink. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” Computational Geometry: Theory and Applications. Elsevier, 2008. https://doi.org/10.1016/j.comgeo.2007.11.001.' ieee: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, and J. Snoeyink, “Time-varying Reeb graphs for continuous space-time data,” Computational Geometry: Theory and Applications, vol. 41, no. 3. Elsevier, pp. 149–166, 2008.' ista: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. 2008. Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. 41(3), 149–166.' mla: 'Edelsbrunner, Herbert, et al. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” Computational Geometry: Theory and Applications, vol. 41, no. 3, Elsevier, 2008, pp. 149–66, doi:10.1016/j.comgeo.2007.11.001.' short: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational Geometry: Theory and Applications 41 (2008) 149–166.' date_created: 2018-12-11T12:06:12Z date_published: 2008-11-01T00:00:00Z date_updated: 2021-01-12T07:53:34Z day: '01' doi: 10.1016/j.comgeo.2007.11.001 extern: 1 intvolume: ' 41' issue: '3' month: '11' page: 149 - 166 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '2158' quality_controlled: 0 status: public title: Time-varying Reeb graphs for continuous space-time data type: journal_article volume: 41 year: '2008' ... --- _id: '3969' abstract: - lang: eng text: Persistent homology is an algebraic tool for measuring topological features of shapes and functions. It casts the multi-scale organization we frequently observe in nature into a mathematical formalism. Here we give a record of the short history of persistent homology and present its basic concepts. Besides the mathematics we focus on algorithms and mention the various connections to applications, including to biomolecules, biological networks, data analysis, and geometric modeling. acknowledgement: Supported in part by DARPA under grants HR0011-05-1-0007 and HR0011-05-0057 and by the NSF under grant DBI-06-06873. alternative_title: - Contemporary Mathematics author: - 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 citation: ama: 'Edelsbrunner H, Harer J. Persistent homology - a survey. In: Surveys on Discrete and Computational Geometry: Twenty Years Later. American Mathematical Society; 2008:257-282.' apa: 'Edelsbrunner, H., & Harer, J. (2008). Persistent homology - a survey. In Surveys on Discrete and Computational Geometry: Twenty Years Later (pp. 257–282). American Mathematical Society.' chicago: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” In Surveys on Discrete and Computational Geometry: Twenty Years Later, 257–82. American Mathematical Society, 2008.' ieee: 'H. Edelsbrunner and J. Harer, “Persistent homology - a survey,” in Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.' ista: 'Edelsbrunner H, Harer J. 2008.Persistent homology - a survey. In: Surveys on Discrete and Computational Geometry: Twenty Years Later. Contemporary Mathematics, , 257–282.' mla: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–82.' short: 'H. Edelsbrunner, J. Harer, in:, Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.' date_created: 2018-12-11T12:06:11Z date_published: 2008-03-28T00:00:00Z date_updated: 2021-01-12T07:53:33Z day: '28' extern: 1 month: '03' page: 257 - 282 publication: 'Surveys on Discrete and Computational Geometry: Twenty Years Later' publication_status: published publisher: American Mathematical Society publist_id: '2156' quality_controlled: 0 status: public title: Persistent homology - a survey type: book_chapter year: '2008' ... --- _id: '4141' abstract: - lang: eng text: The zyxin-related LPP protein is localized at focal adhesions and cell-cell contacts and is involved in the regulation of smooth muscle cell migration. A known interaction partner of LPP in human is the tumor suppressor protein SCRIB. Knocking down scrib expression c uring zebrafish embryonic development results in defects of convergence and extension (C&amp;E) movements, which occur during gastrulation and mediate elongation of the anterior-posterior body axis. Mediolateral cell polarization underlying C&amp;E is regulated by a noncanonical Writ signaling pathway constituting the vertebrate planar cell polarity (PCP) pathway. Here, we investigated the role of Lpp during early zebrafish development. We show that morpholino knockdown of Ipp results in defects of C&amp;E, phenocopying noncanonical Wnt signaling mutants. Time-lapse analysis associates the defective dorsal convergence movements with a reduced ability to migrate along straight paths. In addition, expression of Lpp is significantly reduced in Wnt11 morphants and in embryos overexpressing Wnt11 or a dominant-negative form of Rho kinase 2, which is a downstream effector of Wnt11, Suggesting that Lpp expression is dependent on noncanonical Wnt signaling. Finally, we demonstrate that Lpp interacts with the PCP protein Scrib in zebrafish, and that Lpp and Scrib cooperate for the mediation of C&amp;E. (C) 2008 Elsevier Inc. All rights reserved. article_processing_charge: No author: - first_name: Hilke full_name: Vervenne, Hilke last_name: Vervenne - first_name: Koen full_name: Crombez, Koen last_name: Crombez - first_name: Kathleen full_name: Lambaerts, Kathleen last_name: Lambaerts - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: Mathias full_name: Köppen, Mathias last_name: Köppen - 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 - first_name: Wim full_name: Van De Ven, Wim last_name: Van De Ven - first_name: Marleen full_name: Petit, Marleen last_name: Petit citation: ama: Vervenne H, Crombez K, Lambaerts K, et al. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. 2008;320(1):267-277. doi:10.1016/j.ydbio.2008.05.529 apa: Vervenne, H., Crombez, K., Lambaerts, K., Carvalho, L., Köppen, M., Heisenberg, C.-P. J., … Petit, M. (2008). Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2008.05.529 chicago: Vervenne, Hilke, Koen Crombez, Kathleen Lambaerts, Lara Carvalho, Mathias Köppen, Carl-Philipp J Heisenberg, Wim Van De Ven, and Marleen Petit. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” Developmental Biology. Elsevier, 2008. https://doi.org/10.1016/j.ydbio.2008.05.529. ieee: H. Vervenne et al., “Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation,” Developmental Biology, vol. 320, no. 1. Elsevier, pp. 267–277, 2008. ista: Vervenne H, Crombez K, Lambaerts K, Carvalho L, Köppen M, Heisenberg C-PJ, Van De Ven W, Petit M. 2008. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. 320(1), 267–277. mla: Vervenne, Hilke, et al. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” Developmental Biology, vol. 320, no. 1, Elsevier, 2008, pp. 267–77, doi:10.1016/j.ydbio.2008.05.529. short: H. Vervenne, K. Crombez, K. Lambaerts, L. Carvalho, M. Köppen, C.-P.J. Heisenberg, W. Van De Ven, M. Petit, Developmental Biology 320 (2008) 267–277. date_created: 2018-12-11T12:07:11Z date_published: 2008-08-01T00:00:00Z date_updated: 2021-01-12T07:54:48Z day: '01' doi: 10.1016/j.ydbio.2008.05.529 extern: '1' intvolume: ' 320' issue: '1' language: - iso: eng month: '08' oa_version: None page: 267 - 277 publication: Developmental Biology publication_status: published publisher: Elsevier publist_id: '1978' status: public title: Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 320 year: '2008' ... --- _id: '4161' abstract: - lang: eng text: Handedness of the vertebrate body plan critically depends on transient embryonic structures/ organs that generate cilia-dependent leftward fluid flow within constrained extracellular environments. Although the function of ciliated organs in laterality determination has been extensively studied, how they are formed during embryogenesis is still poorly understood. Here we show that Kupffer's vesicle (KV), the zebrafish organ of laterality, arises from a surface epithelium previously thought to adopt exclusively extra-embryonic fates. Live multi-photon confocal imaging reveals that surface epithelial cells undergo Nodal/TGF beta signalling-dependent ingression at the dorsal germ ring margin prior to gastrulation, to give rise to dorsal forerunner cells (DFCs), the precursors of KV. DFCs then migrate attached to the overlying surface epithelium and rearrange into rosette-like epithelial structures at the end of gastrulation. During early somitogenesis, these epithelial rosettes coalesce into a single rosette that differentiates into the KV with a ciliated lumen at its apical centre. Our results provide novel insights into the morphogenetic transformations that shape the laterality organ in zebrafish and suggest a conserved progenitor role of the surface epithelium during laterality organ formation in vertebrates. article_processing_charge: No author: - first_name: Pablo full_name: Oteíza, Pablo last_name: Oteíza - first_name: Mathias full_name: Köppen, Mathias last_name: Köppen - first_name: Miguel full_name: Concha, Miguel last_name: Concha - 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: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. Origin and shaping of the laterality organ in zebrafish. Development. 2008;135(16):2807-2813. doi:10.1242/dev.022228 apa: Oteíza, P., Köppen, M., Concha, M., & Heisenberg, C.-P. J. (2008). Origin and shaping of the laterality organ in zebrafish. Development. Company of Biologists. https://doi.org/10.1242/dev.022228 chicago: Oteíza, Pablo, Mathias Köppen, Miguel Concha, and Carl-Philipp J Heisenberg. “Origin and Shaping of the Laterality Organ in Zebrafish.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.022228. ieee: P. Oteíza, M. Köppen, M. Concha, and C.-P. J. Heisenberg, “Origin and shaping of the laterality organ in zebrafish,” Development, vol. 135, no. 16. Company of Biologists, pp. 2807–2813, 2008. ista: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. 2008. Origin and shaping of the laterality organ in zebrafish. Development. 135(16), 2807–2813. mla: Oteíza, Pablo, et al. “Origin and Shaping of the Laterality Organ in Zebrafish.” Development, vol. 135, no. 16, Company of Biologists, 2008, pp. 2807–13, doi:10.1242/dev.022228. short: P. Oteíza, M. Köppen, M. Concha, C.-P.J. Heisenberg, Development 135 (2008) 2807–2813. date_created: 2018-12-11T12:07:19Z date_published: 2008-08-15T00:00:00Z date_updated: 2021-01-12T07:54:57Z day: '15' doi: 10.1242/dev.022228 extern: '1' intvolume: ' 135' issue: '16' language: - iso: eng month: '08' oa_version: None page: 2807 - 2813 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1956' status: public title: Origin and shaping of the laterality organ in zebrafish type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2008' ... --- _id: '4190' abstract: - lang: eng text: During vertebrate gastrulation, cells forming the prechordal plate undergo directed migration as a cohesive cluster. Recent studies revealed that E-cadherin-mediated coherence between these cells plays an important role in effective anterior migration, and that platelet-derived growth factor (Pdgf) appears to act as a guidance cue in this process. However, the mechanisms underlying this process at the individual cell level remain poorly understood. We have identified miles apart (mil) as a suppressor of defective anterior migration of the prospective prechordal plate in silberblick (slb)/wnt11 mutant embryos, in which E-cadherin-mediated coherence of cell movement is reduced. mil encodes Edg5, a sphingosine-1-phosphate (S1P) receptor belonging to a family of five G-protein-coupled receptors (S1PRs). S1P is a lipid signalling molecule that has been implicated in regulating cytoskeletal rearrangements, cell motility and cell adhesion in a variety of cell types. We examined the roles of Mil in anterior migration of prechordal plate progenitor cells and found that, in slb embryos injected with mil-MO, cells migrate with increased motility but decreased directionality, without restoring the coherence of cell migration. This indicates that prechordal plate progenitor cells can migrate effectively as individuals, as well as in a coherent cluster of cells. Moreover, we demonstrate that Mil regulates cell motility and polarisation through Pdgf and its intracellular effecter PI3K, but modulates cell coherence independently of the Pdgf/PI3K pathway, thus co-ordinating cell motility and coherence. These results suggest that the net migration of prechordal plate progenitors is determined by different parameters, including motility, persistence and coherence. article_processing_charge: No author: - first_name: Masatake full_name: Kai, Masatake last_name: Kai - 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 - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada citation: ama: Kai M, Heisenberg C-PJ, Tada M. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. 2008;135(18):3043-3051. doi:10.1242/dev.020396 apa: Kai, M., Heisenberg, C.-P. J., & Tada, M. (2008). Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.020396 chicago: Kai, Masatake, Carl-Philipp J Heisenberg, and Masazumi Tada. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.020396. ieee: M. Kai, C.-P. J. Heisenberg, and M. Tada, “Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation,” Development, vol. 135, no. 18. Company of Biologists, pp. 3043–3051, 2008. ista: Kai M, Heisenberg C-PJ, Tada M. 2008. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. 135(18), 3043–3051. mla: Kai, Masatake, et al. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development, vol. 135, no. 18, Company of Biologists, 2008, pp. 3043–51, doi:10.1242/dev.020396. short: M. Kai, C.-P.J. Heisenberg, M. Tada, Development 135 (2008) 3043–3051. date_created: 2018-12-11T12:07:29Z date_published: 2008-09-15T00:00:00Z date_updated: 2021-01-12T07:55:11Z day: '15' doi: 10.1242/dev.020396 extern: '1' intvolume: ' 135' issue: '18' language: - iso: eng month: '09' oa_version: None page: 3043 - 3051 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1928' status: public title: Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2008' ... --- _id: '4384' abstract: - lang: eng text: |- Model checking software transactional memories (STMs) is difficult because of the unbounded number, length, and delay of concurrent transactions and the unbounded size of the memory. We show that, under certain conditions, the verification problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several STMs, including two-phase locking, DSTM, TL2, and optimistic concurrency control. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom. Our main contribution lies in the structure of the proofs, which are largely automated and not restricted to the STMs mentioned above. In a first step we show that every STM that enjoys certain structural properties either violates a safety or liveness requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step we use a model checker to prove the requirement for the STM applied to a most general program with two threads and two variables. In the safety case, the model checker constructs a simulation relation between two carefully constructed finite-state transition systems, one representing the given STM applied to a most general program, and the other representing a most liberal safe STM applied to the same program. In the liveness case, the model checker analyzes fairness conditions on the given STM transition system. author: - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Vasu full_name: Vasu Singh id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh citation: ama: 'Guerraoui R, Henzinger TA, Jobstmann B, Singh V. Model checking transactional memories. In: ACM; 2008:372-382. doi:10.1145/1375581.1375626' apa: 'Guerraoui, R., Henzinger, T. A., Jobstmann, B., & Singh, V. (2008). Model checking transactional memories (pp. 372–382). Presented at the PLDI: Programming Languages Design and Implementation, ACM. https://doi.org/10.1145/1375581.1375626' chicago: Guerraoui, Rachid, Thomas A Henzinger, Barbara Jobstmann, and Vasu Singh. “Model Checking Transactional Memories,” 372–82. ACM, 2008. https://doi.org/10.1145/1375581.1375626. ieee: 'R. Guerraoui, T. A. Henzinger, B. Jobstmann, and V. Singh, “Model checking transactional memories,” presented at the PLDI: Programming Languages Design and Implementation, 2008, pp. 372–382.' ista: 'Guerraoui R, Henzinger TA, Jobstmann B, Singh V. 2008. Model checking transactional memories. PLDI: Programming Languages Design and Implementation, 372–382.' mla: Guerraoui, Rachid, et al. Model Checking Transactional Memories. ACM, 2008, pp. 372–82, doi:10.1145/1375581.1375626. short: R. Guerraoui, T.A. Henzinger, B. Jobstmann, V. Singh, in:, ACM, 2008, pp. 372–382. conference: name: 'PLDI: Programming Languages Design and Implementation' date_created: 2018-12-11T12:08:34Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:56:34Z day: '01' doi: 10.1145/1375581.1375626 extern: 1 file: - access_level: open_access checksum: 1238258a27f212fc1a2050a9a246da20 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:05Z date_updated: 2020-07-14T12:46:28Z file_id: '5054' file_name: IST-2012-74-v1+1_Model_checking_transactional_memories.pdf file_size: 201583 relation: main_file file_date_updated: 2020-07-14T12:46:28Z main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/model_checking_transactional_memories.pdf month: '01' oa: 1 page: 372 - 382 publication_status: published publisher: ACM publist_id: '1073' quality_controlled: 0 status: public title: Model checking transactional memories type: conference year: '2008' ... --- _id: '4386' abstract: - lang: eng text: We introduce the notion of permissiveness in transactional memories (TM). Intuitively, a TM is permissive if it never aborts a transaction when it need not. More specifically, a TM is permissive with respect to a safety property p if the TM accepts every history that satisfies p. Permissiveness, like safety and liveness, can be used as a metric to compare TMs. We illustrate that it is impractical to achieve permissiveness deterministically, and then show how randomization can be used to achieve permissiveness efficiently. We introduce Adaptive Validation STM (AVSTM), which is probabilistically permissive with respect to opacity; that is, every opaque history is accepted by AVSTM with positive probability. Moreover, AVSTM guarantees lock freedom. Owing to its permissiveness, AVSTM outperforms other STMs by up to 40% in read dominated workloads in high contention scenarios. But, in low contention scenarios, the book-keeping done by AVSTM to achieve permissiveness makes AVSTM, on average, 20-30% worse than existing STMs. acknowledgement: This research was supported by the Swiss National Science Foundation. alternative_title: - LNCS author: - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Vasu full_name: Vasu Singh id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh citation: ama: 'Guerraoui R, Henzinger TA, Singh V. Permissiveness in transactional memories. In: Vol 5218. Springer; 2008:305-319. doi:10.1007/978-3-540-87779-0_21' apa: 'Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Permissiveness in transactional memories (Vol. 5218, pp. 305–319). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-540-87779-0_21' chicago: Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Permissiveness in Transactional Memories,” 5218:305–19. Springer, 2008. https://doi.org/10.1007/978-3-540-87779-0_21. ieee: 'R. Guerraoui, T. A. Henzinger, and V. Singh, “Permissiveness in transactional memories,” presented at the DISC: Distributed Computing, 2008, vol. 5218, pp. 305–319.' ista: 'Guerraoui R, Henzinger TA, Singh V. 2008. Permissiveness in transactional memories. DISC: Distributed Computing, LNCS, vol. 5218, 305–319.' mla: Guerraoui, Rachid, et al. Permissiveness in Transactional Memories. Vol. 5218, Springer, 2008, pp. 305–19, doi:10.1007/978-3-540-87779-0_21. short: R. Guerraoui, T.A. Henzinger, V. Singh, in:, Springer, 2008, pp. 305–319. conference: name: 'DISC: Distributed Computing' date_created: 2018-12-11T12:08:35Z date_published: 2008-09-10T00:00:00Z date_updated: 2021-01-12T07:56:35Z day: '10' doi: 10.1007/978-3-540-87779-0_21 extern: 1 intvolume: ' 5218' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/permissiveness_in_transactional_memories.pdf month: '09' page: 305 - 319 publication_status: published publisher: Springer publist_id: '1072' quality_controlled: 0 status: public title: Permissiveness in transactional memories type: conference volume: 5218 year: '2008' ... --- _id: '4387' abstract: - lang: eng text: Software transactional memory (STM) offers a disciplined concurrent programming model for exploiting the parallelism of modern processor architectures. This paper presents the first deterministic specification automata for strict serializability and opacity in STMs. Using an antichain-based tool, we show our deterministic specifications to be equivalent to more intuitive, nondeterministic specification automata (which are too large to be determinized automatically). Using deterministic specification automata, we obtain a complete verification tool for STMs. We also show how to model and verify contention management within STMs. We automatically check the opacity of popular STM algorithms, such as TL2 and DSTM, with a universal contention manager. The universal contention manager is nondeterministic and establishes correctness for all possible contention management schemes. acknowledgement: This research was supported by the Swiss National Science Foundation. alternative_title: - LNCS author: - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Vasu full_name: Vasu Singh id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh citation: ama: 'Guerraoui R, Henzinger TA, Singh V. Completeness and nondeterminism in model checking transactional memories. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:21-35. doi:10.1007/978-3-540-85361-9_6' apa: 'Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Completeness and nondeterminism in model checking transactional memories (Vol. 5201, pp. 21–35). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9_6' chicago: Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Completeness and Nondeterminism in Model Checking Transactional Memories,” 5201:21–35. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9_6. ieee: 'R. Guerraoui, T. A. Henzinger, and V. Singh, “Completeness and nondeterminism in model checking transactional memories,” presented at the CONCUR: Concurrency Theory, 2008, vol. 5201, pp. 21–35.' ista: 'Guerraoui R, Henzinger TA, Singh V. 2008. Completeness and nondeterminism in model checking transactional memories. CONCUR: Concurrency Theory, LNCS, vol. 5201, 21–35.' mla: Guerraoui, Rachid, et al. Completeness and Nondeterminism in Model Checking Transactional Memories. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 21–35, doi:10.1007/978-3-540-85361-9_6. short: R. Guerraoui, T.A. Henzinger, V. Singh, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 21–35. conference: name: 'CONCUR: Concurrency Theory' date_created: 2018-12-11T12:08:35Z date_published: 2008-07-30T00:00:00Z date_updated: 2021-01-12T07:56:35Z day: '30' doi: 10.1007/978-3-540-85361-9_6 extern: 1 intvolume: ' 5201' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/completeness_and_nondeterminism_in_model_checking_transactional_memories.pdf month: '07' page: 21 - 35 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '1071' quality_controlled: 0 status: public title: Completeness and nondeterminism in model checking transactional memories type: conference volume: 5201 year: '2008' ... --- _id: '4397' alternative_title: - LNCS 5123 author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Damien full_name: Damien Zufferey id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: 'Beyer D, Zufferey D, Majumdar R. CSIsat: Interpolation for LA+EUF. In: Springer; 2008:304-308.' apa: 'Beyer, D., Zufferey, D., & Majumdar, R. (2008). CSIsat: Interpolation for LA+EUF (pp. 304–308). Presented at the CAV: Computer Aided Verification, Springer.' chicago: 'Beyer, Dirk, Damien Zufferey, and Ritankar Majumdar. “CSIsat: Interpolation for LA+EUF,” 304–8. Springer, 2008.' ieee: 'D. Beyer, D. Zufferey, and R. Majumdar, “CSIsat: Interpolation for LA+EUF,” presented at the CAV: Computer Aided Verification, 2008, pp. 304–308.' ista: 'Beyer D, Zufferey D, Majumdar R. 2008. CSIsat: Interpolation for LA+EUF. CAV: Computer Aided Verification, LNCS 5123, , 304–308.' mla: 'Beyer, Dirk, et al. CSIsat: Interpolation for LA+EUF. Springer, 2008, pp. 304–08.' short: D. Beyer, D. Zufferey, R. Majumdar, in:, Springer, 2008, pp. 304–308. conference: name: 'CAV: Computer Aided Verification' date_created: 2018-12-11T12:08:38Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:56:40Z day: '01' extern: 1 month: '01' page: 304 - 308 publication_status: published publisher: Springer publist_id: '1060' quality_controlled: 0 status: public title: 'CSIsat: Interpolation for LA+EUF' type: conference year: '2008' ... --- _id: '4400' author: - first_name: Adam full_name: Aviv,Adam J. last_name: Aviv - first_name: Pavol full_name: Pavol Cerny id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Sandy full_name: Clark,Sandy last_name: Clark - first_name: Eric full_name: Cronin,Eric last_name: Cronin - first_name: Gaurav full_name: Shah,Gaurav last_name: Shah - first_name: Micah full_name: Sherr,Micah last_name: Sherr - first_name: Matt full_name: Blaze,Matt last_name: Blaze citation: ama: 'Aviv A, Cerny P, Clark S, et al. Security Evaluation of ES&amp;S Voting Machines and Election Management System. In: USENIX; 2008. doi:1545' apa: Aviv, A., Cerny, P., Clark, S., Cronin, E., Shah, G., Sherr, M., & Blaze, M. (2008). Security Evaluation of ES&amp;S Voting Machines and Election Management System. Presented at the Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08, USENIX. https://doi.org/1545 chicago: Aviv, Adam, Pavol Cerny, Sandy Clark, Eric Cronin, Gaurav Shah, Micah Sherr, and Matt Blaze. “Security Evaluation of ES&amp;S Voting Machines and Election Management System.” USENIX, 2008. https://doi.org/1545. ieee: A. Aviv et al., “Security Evaluation of ES&amp;S Voting Machines and Election Management System,” presented at the Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08, 2008. ista: Aviv A, Cerny P, Clark S, Cronin E, Shah G, Sherr M, Blaze M. 2008. Security Evaluation of ES&amp;S Voting Machines and Election Management System. Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08. mla: Aviv, Adam, et al. Security Evaluation of ES&amp;S Voting Machines and Election Management System. USENIX, 2008, doi:1545. short: A. Aviv, P. Cerny, S. Clark, E. Cronin, G. Shah, M. Sherr, M. Blaze, in:, USENIX, 2008. conference: name: Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08 date_created: 2018-12-11T12:08:39Z date_published: 2008-07-29T00:00:00Z date_updated: 2021-01-12T07:56:42Z day: '29' doi: '1545' extern: 1 main_file_link: - open_access: '0' url: http://www.usenix.org/event/evt08/tech/full_papers/aviv/aviv.pdf month: '07' publication_status: published publisher: USENIX publist_id: '1057' quality_controlled: 0 status: public title: Security Evaluation of ES&S Voting Machines and Election Management System type: conference year: '2008' ... --- _id: '4409' abstract: - lang: eng text: "Models of timed systems must incorporate not only the sequence of system events, but the timings of these events as well to capture the real-time aspects of physical systems. Timed automata are models of real-time systems in which states consist of discrete locations and values for real-time clocks. The presence of real-time clocks leads to an uncountable state space. This thesis studies verification problems on timed automata in a game theoretic framework.\r\n\r\nFor untimed systems, two systems are close if every sequence of events of one system is also observable in the second system. For timed systems, the difference in timings of the two corresponding sequences is also of importance. We propose the notion of bisimulation distance which quantifies timing differences; if the bisimulation distance between two systems is epsilon, then (a) every sequence of events of one system has a corresponding matching sequence in the other, and (b) the timings of matching events in between the two corresponding traces do not differ by more than epsilon. We show that we can compute the bisimulation distance between two timed automata to within any desired degree of accuracy. We also show that the timed verification logic TCTL is robust with respect to our notion of quantitative bisimilarity, in particular, if a system satisfies a formula, then every close system satisfies a close formula.\r\n\r\nTimed games are used for distinguishing between the actions of several agents, typically a controller and an environment. The controller must achieve its objective against all possible choices of the environment. The modeling of the passage of time leads to the presence of zeno executions, and corresponding unrealizable strategies of the controller which may achieve objectives by blocking time. We disallow such unreasonable strategies by restricting all agents to use only receptive strategies --strategies which while not being required to ensure time divergence by any agent, are such that no agent is responsible for blocking time. Time divergence is guaranteed when all players use receptive strategies. We show that timed automaton games with receptive strategies can be solved by a reduction to finite state turn based game graphs. We define the logic timed alternating-time temporal logic for verification of timed automaton games and show that the logic can be model checked in EXPTIME. We also show that the minimum time required by an agent to reach a desired location, and the maximum time an agent can stay safe within a set of locations, against all possible actions of its adversaries are both computable.\r\n\r\nWe next study the memory requirements of winning strategies for timed automaton games. We prove that finite memory strategies suffice for safety objectives, and that winning strategies for reachability objectives may require infinite memory in general. We introduce randomized strategies in which an agent can propose a probabilistic distribution of moves and show that finite memory randomized strategies suffice for all omega-regular objectives. We also show that while randomization helps in simplifying winning strategies, and thus allows the construction of simpler controllers, it does not help a player in winning at more states, and thus does not allow the construction of more powerful controllers.\r\n\r\nFinally we study robust winning strategies in timed games. In a physical system, a controller may propose an action together with a time delay, but the action cannot be assumed to be executed at the exact proposed time delay. We present robust strategies which incorporate such jitters and show that the set of states from which an agent can win robustly is computable." article_processing_charge: No author: - first_name: Vinayak full_name: Prabhu, Vinayak last_name: Prabhu citation: ama: Prabhu V. Games for the verification of timed systems. 2008:1-137. apa: Prabhu, V. (2008). Games for the verification of timed systems. University of California, Berkeley. chicago: Prabhu, Vinayak. “Games for the Verification of Timed Systems.” University of California, Berkeley, 2008. ieee: V. Prabhu, “Games for the verification of timed systems,” University of California, Berkeley, 2008. ista: Prabhu V. 2008. Games for the verification of timed systems. University of California, Berkeley. mla: Prabhu, Vinayak. Games for the Verification of Timed Systems. University of California, Berkeley, 2008, pp. 1–137. short: V. Prabhu, Games for the Verification of Timed Systems, University of California, Berkeley, 2008. date_created: 2018-12-11T12:08:42Z date_published: 2008-09-01T00:00:00Z date_updated: 2022-02-14T14:35:11Z day: '01' degree_awarded: PhD extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www2.eecs.berkeley.edu/Pubs/TechRpts/2008/EECS-2008-97.html month: '09' oa: 1 oa_version: None page: 1 - 137 publication_status: published publisher: University of California, Berkeley publist_id: '319' status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: John full_name: Steel, John last_name: Steel - first_name: Pravin full_name: Varaiya, Pravin last_name: Varaiya title: Games for the verification of timed systems type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2008' ... --- _id: '4415' abstract: - lang: eng text: 'Many computing applications, especially those in safety critical embedded systems, require highly predictable timing properties. However, time is often not present in the prevailing computing and networking abstractions. In fact, most advances in computer architecture, software, and networking favor average-case performance over timing predictability. This thesis studies several methods for the design of concurrent and/or distributed embedded systems with precise timing guarantees. The focus is on flexible and compositional methods for programming and verification of the timing properties. The presented methods together with related formalisms cover two levels of design: (1) Programming language/model level. We propose the distributed variant of Giotto, a coordination programming language with an explicit temporal semantics—the logical execution time (LET) semantics. The LET of a task is an interval of time that specifies the time instants at which task inputs and outputs become available (task release and termination instants). The LET of a task is always non-zero. This allows us to communicate values across the network without changing the timing information of the task, and without introducing nondeterminism. We show how this methodology supports distributed code generation for distributed real-time systems. The method gives up some performance in favor of composability and predictability. We characterize the tradeoff by comparing the LET semantics with the semantics used in Simulink. (2) Abstract task graph level. We study interface-based design and verification of applications represented with task graphs. We consider task sequence graphs with general event models, and cyclic graphs with periodic event models with jitter and phase. Here an interface of a component exposes time and resource constraints of the component. Together with interfaces we formally define interface composition operations and the refinement relation. For efficient and flexible composability checking two properties are important: incremental design and independent refinement. According to the incremental design property the composition of interfaces can be performed in any order, even if interfaces for some components are not known. The refinement relation is defined such that in a design we can always substitute a refined interface for an abstract one. We show that the framework supports independent refinement, i.e., the refinement relation is preserved under composition operations.' acknowledgement: 978-0-549-83480-9 article_processing_charge: No author: - first_name: Slobodan full_name: Matic, Slobodan last_name: Matic citation: ama: Matic S. Compositionality in deterministic real-time embedded systems. 2008:1-148. apa: Matic, S. (2008). Compositionality in deterministic real-time embedded systems. University of California, Berkeley. chicago: Matic, Slobodan. “Compositionality in Deterministic Real-Time Embedded Systems.” University of California, Berkeley, 2008. ieee: S. Matic, “Compositionality in deterministic real-time embedded systems,” University of California, Berkeley, 2008. ista: Matic S. 2008. Compositionality in deterministic real-time embedded systems. University of California, Berkeley. mla: Matic, Slobodan. Compositionality in Deterministic Real-Time Embedded Systems. University of California, Berkeley, 2008, pp. 1–148. short: S. Matic, Compositionality in Deterministic Real-Time Embedded Systems, University of California, Berkeley, 2008. date_created: 2018-12-11T12:08:44Z date_published: 2008-01-01T00:00:00Z date_updated: 2022-02-14T14:08:50Z day: '01' degree_awarded: PhD extern: '1' language: - iso: eng month: '01' oa_version: None page: 1 - 148 publication_status: published publisher: University of California, Berkeley publist_id: '316' status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Edward full_name: Lee, Edward last_name: Lee - first_name: Raja full_name: Sengupta, Raja last_name: Sengupta title: Compositionality in deterministic real-time embedded systems type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2008' ... --- _id: '4452' abstract: - lang: eng text: We describe Valigator, a software tool for imperative program verification that efficiently combines symbolic computation and automated reasoning in a uniform framework. The system offers support for automatically generating and proving verification conditions and, most importantly, for automatically inferring loop invariants and bound assertions by means of symbolic summation, Gröbner basis computation, and quantifier elimination. We present general principles of the implementation and illustrate them on examples. acknowledgement: This research was supported by the Swiss NSF. alternative_title: - LNCS author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Thibaud full_name: Hottelier, Thibaud last_name: Hottelier - first_name: Laura full_name: Kovács, Laura last_name: Kovács citation: ama: 'Henzinger TA, Hottelier T, Kovács L. Valigator: A verification tool with bound and invariant generation. In: Vol 5330. Springer; 2008:333-342. doi:10.1007/978-3-540-89439-1_24' apa: 'Henzinger, T. A., Hottelier, T., & Kovács, L. (2008). Valigator: A verification tool with bound and invariant generation (Vol. 5330, pp. 333–342). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Springer. https://doi.org/10.1007/978-3-540-89439-1_24' chicago: 'Henzinger, Thomas A, Thibaud Hottelier, and Laura Kovács. “Valigator: A Verification Tool with Bound and Invariant Generation,” 5330:333–42. Springer, 2008. https://doi.org/10.1007/978-3-540-89439-1_24.' ieee: 'T. A. Henzinger, T. Hottelier, and L. Kovács, “Valigator: A verification tool with bound and invariant generation,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, 2008, vol. 5330, pp. 333–342.' ista: 'Henzinger TA, Hottelier T, Kovács L. 2008. Valigator: A verification tool with bound and invariant generation. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 5330, 333–342.' mla: 'Henzinger, Thomas A., et al. Valigator: A Verification Tool with Bound and Invariant Generation. Vol. 5330, Springer, 2008, pp. 333–42, doi:10.1007/978-3-540-89439-1_24.' short: T.A. Henzinger, T. Hottelier, L. Kovács, in:, Springer, 2008, pp. 333–342. conference: name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning' date_created: 2018-12-11T12:08:55Z date_published: 2008-11-13T00:00:00Z date_updated: 2021-01-12T07:57:04Z day: '13' doi: 10.1007/978-3-540-89439-1_24 extern: 1 intvolume: ' 5330' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/valigator.pdf month: '11' page: 333 - 342 publication_status: published publisher: Springer publist_id: '277' quality_controlled: 0 status: public title: 'Valigator: A verification tool with bound and invariant generation' type: conference volume: 5330 year: '2008' ... --- _id: '4509' abstract: - lang: eng text: 'I discuss two main challenges in embedded systems design: the challenge to build predictable systems, and that to build robust systems. I suggest how predictability can be formalized as a form of determinism, and robustness as a form of continuity.' author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Henzinger TA. Two challenges in embedded systems design: Predictability and robustness. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. 2008;366(1881):3727-3736. doi:10.1098/rsta.2008.0141' apa: 'Henzinger, T. A. (2008). Two challenges in embedded systems design: Predictability and robustness. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rsta.2008.0141' chicago: 'Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability and Robustness.” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. Royal Society of London, 2008. https://doi.org/10.1098/rsta.2008.0141.' ieee: 'T. A. Henzinger, “Two challenges in embedded systems design: Predictability and robustness,” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, vol. 366, no. 1881. Royal Society of London, pp. 3727–3736, 2008.' ista: 'Henzinger TA. 2008. Two challenges in embedded systems design: Predictability and robustness. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. 366(1881), 3727–3736.' mla: 'Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability and Robustness.” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, vol. 366, no. 1881, Royal Society of London, 2008, pp. 3727–36, doi:10.1098/rsta.2008.0141.' short: T.A. Henzinger, Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences 366 (2008) 3727–3736. date_created: 2018-12-11T12:09:13Z date_published: 2008-07-31T00:00:00Z date_updated: 2021-01-12T07:59:19Z day: '31' doi: 10.1098/rsta.2008.0141 extern: 1 intvolume: ' 366' issue: '1881' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/two_challenges_in_embedded_systems_design.pdf month: '07' page: 3727 - 3736 publication: Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences publication_status: published publisher: Royal Society of London publist_id: '219' quality_controlled: 0 status: public title: 'Two challenges in embedded systems design: Predictability and robustness' type: journal_article volume: 366 year: '2008' ... --- _id: '4524' abstract: - lang: eng text: "Complex requirements, time-to-market pressure and regulatory constraints have made the designing of embedded systems extremely challenging. This is evident by the increase in effort and expenditure for design of safety-driven real-time control-dominated applications like automotive and avionic controllers. Design processes are often challenged by lack of proper programming tools for specifying and verifying critical requirements (e.g. timing and reliability) of such applications. Platform based design, an approach for designing embedded systems, addresses the above concerns by separating requirement from architecture. The requirement specifies the intended behavior of an application while the architecture specifies the guarantees (e.g. execution speed, failure rate etc). An implementation, a mapping of the requirement on the architecture, is then analyzed for correctness. The orthogonalization of concerns makes the specification and analyses simpler. An effective use of such design methodology has been proposed in Logical Execution Time (LET) model of real-time tasks. The model separates the timing requirements (specified by release and termination instances of a task) from the architecture guarantees (specified by worst-case execution time of the task).\r\n\r\nThis dissertation proposes a coordination language, Hierarchical Timing Language (HTL), that captures the timing and reliability requirements of real-time applications. An implementation of the program on an architecture is then analyzed to check whether desired timing and reliability requirements are met or not. The core framework extends the LET model by accounting for reliability and refinement. The reliability model separates the reliability requirements of tasks from the reliability guarantees of the architecture. The requirement expresses the desired long-term reliability while the architecture provides a short-term reliability guarantee (e.g. failure rate for each iteration). The analysis checks if the short-term guarantee ensures the desired long-term reliability. The refinement model allows replacing a task by another task during program execution. Refinement preserves schedulability and reliability, i.e., if a refined task is schedulable and reliable for an implementation, then the refining task is also schedulable and reliable for the implementation. Refinement helps in concise specification without overloading analysis.\r\n\r\nThe work presents the formal model, the analyses (both with and without refinement), and a compiler for HTL programs. The compiler checks composition and refinement constraints, performs schedulability and reliability analyses, and generates code for implementation of an HTL program on a virtual machine. Three real-time controllers, one each from automatic control, automotive control and avionic control, are used to illustrate the steps in modeling and analyzing HTL programs." acknowledgement: 978-0-549-83679-7 article_processing_charge: No author: - first_name: Arkadeb full_name: Ghosal, Arkadeb last_name: Ghosal citation: ama: Ghosal A. A hierarchical coordination language for reliable real-time tasks. 2008:1-210. apa: Ghosal, A. (2008). A hierarchical coordination language for reliable real-time tasks. University of California, Berkeley. chicago: Ghosal, Arkadeb. “A Hierarchical Coordination Language for Reliable Real-Time Tasks.” University of California, Berkeley, 2008. ieee: A. Ghosal, “A hierarchical coordination language for reliable real-time tasks,” University of California, Berkeley, 2008. ista: Ghosal A. 2008. A hierarchical coordination language for reliable real-time tasks. University of California, Berkeley. mla: Ghosal, Arkadeb. A Hierarchical Coordination Language for Reliable Real-Time Tasks. University of California, Berkeley, 2008, pp. 1–210. short: A. Ghosal, A Hierarchical Coordination Language for Reliable Real-Time Tasks, University of California, Berkeley, 2008. date_created: 2018-12-11T12:09:18Z date_published: 2008-01-31T00:00:00Z date_updated: 2021-01-12T07:59:26Z day: '31' extern: '1' language: - iso: eng month: '01' oa_version: None page: 1 - 210 publication_status: published publisher: University of California, Berkeley publist_id: '199' status: public supervisor: - first_name: Alberto full_name: Sangiovanni-Vincentelli, Alberto last_name: Sangiovanni-Vincentelli - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Edward full_name: Lee, Edward last_name: Lee - first_name: Karl full_name: Hedrick, Karl last_name: Hedrick title: A hierarchical coordination language for reliable real-time tasks type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2008' ... --- _id: '4521' abstract: - lang: eng text: The search for proof and the search for counterexamples (bugs) are complementary activities that need to be pursued concurrently in order to maximize the practical success rate of verification tools.While this is well-understood in safety verification, the current focus of liveness verification has been almost exclusively on the search for termination proofs. A counterexample to termination is an infinite programexecution. In this paper, we propose a method to search for such counterexamples. The search proceeds in two phases. We first dynamically enumerate lasso-shaped candidate paths for counterexamples, and then statically prove their feasibility. We illustrate the utility of our nontermination prover, called TNT, on several nontrivial examples, some of which require bit-level reasoning about integer representations. author: - first_name: Ashutosh full_name: Ashutosh Gupta id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Andrey full_name: Rybalchenko, Andrey last_name: Rybalchenko - first_name: Ru full_name: Xu, Ru-Gang last_name: Xu citation: ama: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. Proving non-termination. In: ACM; 2008:147-158. doi:10.1145/1328438.1328459' apa: 'Gupta, A., Henzinger, T. A., Majumdar, R., Rybalchenko, A., & Xu, R. (2008). Proving non-termination (pp. 147–158). Presented at the POPL: Principles of Programming Languages, ACM. https://doi.org/10.1145/1328438.1328459' chicago: Gupta, Ashutosh, Thomas A Henzinger, Ritankar Majumdar, Andrey Rybalchenko, and Ru Xu. “Proving Non-Termination,” 147–58. ACM, 2008. https://doi.org/10.1145/1328438.1328459. ieee: 'A. Gupta, T. A. Henzinger, R. Majumdar, A. Rybalchenko, and R. Xu, “Proving non-termination,” presented at the POPL: Principles of Programming Languages, 2008, pp. 147–158.' ista: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. 2008. Proving non-termination. POPL: Principles of Programming Languages, 147–158.' mla: Gupta, Ashutosh, et al. Proving Non-Termination. ACM, 2008, pp. 147–58, doi:10.1145/1328438.1328459. short: A. Gupta, T.A. Henzinger, R. Majumdar, A. Rybalchenko, R. Xu, in:, ACM, 2008, pp. 147–158. conference: name: 'POPL: Principles of Programming Languages' date_created: 2018-12-11T12:09:17Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:59:25Z day: '01' doi: 10.1145/1328438.1328459 extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/proving_non-termination.pdf month: '01' page: 147 - 158 publication_status: published publisher: ACM publist_id: '208' quality_controlled: 0 status: public title: Proving non-termination type: conference year: '2008' ... --- _id: '4527' abstract: - lang: eng text: |- We introduce bounded asynchrony, a notion of concurrency tailored to the modeling of biological cell-cell interactions. Bounded asynchrony is the result of a scheduler that bounds the number of steps that one process gets ahead of other processes; this allows the components of a system to move independently while keeping them coupled. Bounded asynchrony accurately reproduces the experimental observations made about certain cell-cell interactions: its constrained nondeterminism captures the variability observed in cells that, although equally potent, assume distinct fates. Real-life cells are not “scheduled”, but we show that distributed real-time behavior can lead to component interactions that are observationally equivalent to bounded asynchrony; this provides a possible mechanistic explanation for the phenomena observed during cell fate specification. We use model checking to determine cell fates. The nondeterminism of bounded asynchrony causes state explosion during model checking, but partial-order methods are not directly applicable. We present a new algorithm that reduces the number of states that need to be explored: our optimization takes advantage of the bounded-asynchronous progress and the spatially local interactions of components that model cells. We compare our own communication-based reduction with partial-order reduction (on a restricted form of bounded asynchrony) and experiments illustrate that our algorithm leads to significant savings. acknowledgement: Supported in part by the Swiss National Science Foundation (grant 205321-111840). alternative_title: - LNCS author: - first_name: Jasmin full_name: Fisher, Jasmin last_name: Fisher - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Maria full_name: Maria Mateescu id: 3B43276C-F248-11E8-B48F-1D18A9856A87 last_name: Mateescu - first_name: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: 'Fisher J, Henzinger TA, Mateescu M, Piterman N. Bounded asynchrony: Concurrency for modeling cell-cell interactions. In: Vol 5054. Springer; 2008:17-32. doi:10.1007/978-3-540-68413-8_2' apa: 'Fisher, J., Henzinger, T. A., Mateescu, M., & Piterman, N. (2008). Bounded asynchrony: Concurrency for modeling cell-cell interactions (Vol. 5054, pp. 17–32). Presented at the FMSB: Formal Methods in Systems Biology, Springer. https://doi.org/10.1007/978-3-540-68413-8_2' chicago: 'Fisher, Jasmin, Thomas A Henzinger, Maria Mateescu, and Nir Piterman. “Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions,” 5054:17–32. Springer, 2008. https://doi.org/10.1007/978-3-540-68413-8_2.' ieee: 'J. Fisher, T. A. Henzinger, M. Mateescu, and N. Piterman, “Bounded asynchrony: Concurrency for modeling cell-cell interactions,” presented at the FMSB: Formal Methods in Systems Biology, 2008, vol. 5054, pp. 17–32.' ista: 'Fisher J, Henzinger TA, Mateescu M, Piterman N. 2008. Bounded asynchrony: Concurrency for modeling cell-cell interactions. FMSB: Formal Methods in Systems Biology, LNCS, vol. 5054, 17–32.' mla: 'Fisher, Jasmin, et al. Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions. Vol. 5054, Springer, 2008, pp. 17–32, doi:10.1007/978-3-540-68413-8_2.' short: J. Fisher, T.A. Henzinger, M. Mateescu, N. Piterman, in:, Springer, 2008, pp. 17–32. conference: name: 'FMSB: Formal Methods in Systems Biology' date_created: 2018-12-11T12:09:19Z date_published: 2008-05-26T00:00:00Z date_updated: 2021-01-12T07:59:27Z day: '26' doi: 10.1007/978-3-540-68413-8_2 extern: 1 intvolume: ' 5054' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/bounded_asynchrony.pdf month: '05' page: 17 - 32 publication_status: published publisher: Springer publist_id: '196' quality_controlled: 0 status: public title: 'Bounded asynchrony: Concurrency for modeling cell-cell interactions' type: conference volume: 5054 year: '2008' ... --- _id: '4532' abstract: - lang: eng text: We consider the equivalence problem for labeled Markov chains (LMCs), where each state is labeled with an observation. Two LMCs are equivalent if every finite sequence of observations has the same probability of occurrence in the two LMCs. We show that equivalence can be decided in polynomial time, using a reduction to the equivalence problem for probabilistic automata, which is known to be solvable in polynomial time. We provide an alternative algorithm to solve the equivalence problem, which is based on a new definition of bisimulation for probabilistic automata. We also extend the technique to decide the equivalence of weighted probabilistic automata. author: - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jean full_name: Raskin, Jean-François last_name: Raskin citation: ama: Doyen L, Henzinger TA, Raskin J. Equivalence of labeled Markov chains. International Journal of Foundations of Computer Science. 2008;19(3):549-563. doi:10.1142/S0129054108005814 apa: Doyen, L., Henzinger, T. A., & Raskin, J. (2008). Equivalence of labeled Markov chains. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054108005814 chicago: Doyen, Laurent, Thomas A Henzinger, and Jean Raskin. “Equivalence of Labeled Markov Chains.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2008. https://doi.org/10.1142/S0129054108005814 . ieee: L. Doyen, T. A. Henzinger, and J. Raskin, “Equivalence of labeled Markov chains,” International Journal of Foundations of Computer Science, vol. 19, no. 3. World Scientific Publishing, pp. 549–563, 2008. ista: Doyen L, Henzinger TA, Raskin J. 2008. Equivalence of labeled Markov chains. International Journal of Foundations of Computer Science. 19(3), 549–563. mla: Doyen, Laurent, et al. “Equivalence of Labeled Markov Chains.” International Journal of Foundations of Computer Science, vol. 19, no. 3, World Scientific Publishing, 2008, pp. 549–63, doi:10.1142/S0129054108005814 . short: L. Doyen, T.A. Henzinger, J. Raskin, International Journal of Foundations of Computer Science 19 (2008) 549–563. date_created: 2018-12-11T12:09:20Z date_published: 2008-06-01T00:00:00Z date_updated: 2021-01-12T07:59:30Z day: '01' doi: '10.1142/S0129054108005814 ' extern: 1 intvolume: ' 19' issue: '3' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/equivalence_of_labeled_markov_chains.pdf month: '06' page: 549 - 563 publication: International Journal of Foundations of Computer Science publication_status: published publisher: World Scientific Publishing publist_id: '192' quality_controlled: 0 status: public title: Equivalence of labeled Markov chains type: journal_article volume: 19 year: '2008' ... --- _id: '4533' abstract: - lang: eng text: Interface theories have been proposed to support incremental design and independent implementability. Incremental design means that the compatibility checking of interfaces can proceed for partial system descriptions, without knowing the interfaces of all components. Independent implementability means that compatible interfaces can be refined separately, maintaining compatibility. We show that these interface theories provide no formal support for component reuse, meaning that the same component cannot be used to implement several different interfaces in a design. We add a new operation to interface theories in order to support such reuse. For example, different interfaces for the same component may refer to different aspects such as functionality, timing, and power consumption. We give both stateless and stateful examples for interface theories with component reuse. To illustrate component reuse in interface-based design, we show how the stateful theory provides a natural framework for specifying and refining PCI bus clients. author: - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Tatjana full_name: Tatjana Petrov id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 citation: ama: 'Doyen L, Henzinger TA, Jobstmann B, Petrov T. Interface theories with component reuse. In: ACM; 2008:79-88. doi:10.1145/1450058.1450070' apa: 'Doyen, L., Henzinger, T. A., Jobstmann, B., & Petrov, T. (2008). Interface theories with component reuse (pp. 79–88). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1450058.1450070' chicago: Doyen, Laurent, Thomas A Henzinger, Barbara Jobstmann, and Tatjana Petrov. “Interface Theories with Component Reuse,” 79–88. ACM, 2008. https://doi.org/10.1145/1450058.1450070. ieee: 'L. Doyen, T. A. Henzinger, B. Jobstmann, and T. Petrov, “Interface theories with component reuse,” presented at the EMSOFT: Embedded Software , 2008, pp. 79–88.' ista: 'Doyen L, Henzinger TA, Jobstmann B, Petrov T. 2008. Interface theories with component reuse. EMSOFT: Embedded Software , 79–88.' mla: Doyen, Laurent, et al. Interface Theories with Component Reuse. ACM, 2008, pp. 79–88, doi:10.1145/1450058.1450070. short: L. Doyen, T.A. Henzinger, B. Jobstmann, T. Petrov, in:, ACM, 2008, pp. 79–88. conference: name: 'EMSOFT: Embedded Software ' date_created: 2018-12-11T12:09:21Z date_published: 2008-10-01T00:00:00Z date_updated: 2021-01-12T07:59:30Z day: '01' doi: 10.1145/1450058.1450070 extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/interface_theories_with_component_reuse.pdf month: '10' page: 79 - 88 publication_status: published publisher: ACM publist_id: '193' quality_controlled: 0 status: public title: Interface theories with component reuse type: conference year: '2008' ... --- _id: '4534' abstract: - lang: eng text: A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with ω-regular winning conditions specified as parity objectives, and mean-payoff (or limit-average) objectives. These games lie in NP ∩ coNP. We present a polynomial-time Turing reduction of stochastic parity games to stochastic mean-payoff games. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, Henzinger TA. Reduction of stochastic parity to stochastic mean-payoff games. Information Processing Letters. 2008;106(1):1-7. doi:10.1016/j.ipl.2007.08.035 apa: Chatterjee, K., & Henzinger, T. A. (2008). Reduction of stochastic parity to stochastic mean-payoff games. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2007.08.035 chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Reduction of Stochastic Parity to Stochastic Mean-Payoff Games.” Information Processing Letters. Elsevier, 2008. https://doi.org/10.1016/j.ipl.2007.08.035. ieee: K. Chatterjee and T. A. Henzinger, “Reduction of stochastic parity to stochastic mean-payoff games,” Information Processing Letters, vol. 106, no. 1. Elsevier, pp. 1–7, 2008. ista: Chatterjee K, Henzinger TA. 2008. Reduction of stochastic parity to stochastic mean-payoff games. Information Processing Letters. 106(1), 1–7. mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “Reduction of Stochastic Parity to Stochastic Mean-Payoff Games.” Information Processing Letters, vol. 106, no. 1, Elsevier, 2008, pp. 1–7, doi:10.1016/j.ipl.2007.08.035. short: K. Chatterjee, T.A. Henzinger, Information Processing Letters 106 (2008) 1–7. date_created: 2018-12-11T12:09:21Z date_published: 2008-03-31T00:00:00Z date_updated: 2021-01-12T07:59:30Z day: '31' doi: 10.1016/j.ipl.2007.08.035 extern: 1 intvolume: ' 106' issue: '1' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/reduction_of_stochastic_parity_to_stochastic_mean-payoff_games.pdf month: '03' page: 1 - 7 publication: Information Processing Letters publication_status: published publisher: Elsevier publist_id: '188' quality_controlled: 0 status: public title: Reduction of stochastic parity to stochastic mean-payoff games type: journal_article volume: 106 year: '2008' ... --- _id: '4546' abstract: - lang: eng text: We propose the notion of logical reliability for real-time program tasks that interact through periodically updated program variables. We describe a reliability analysis that checks if the given short-term (e.g., single-period) reliability of a program variable update in an implementation is sufficient to meet the logical reliability requirement (of the program variable) in the long run. We then present a notion of design by refinement where a task can be refined by another task that writes to program variables with less logical reliability. The resulting analysis can be combined with an incremental schedulability analysis for interacting real-time tasks proposed earlier for the Hierarchical Timing Language (HTL), a coordination language for distributed real-time systems. We implemented a logical-reliability-enhanced prototype of the compiler and runtime infrastructure for HTL. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Arkadeb full_name: Ghosal, Arkadeb last_name: Ghosal - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Daniel full_name: Iercan, Daniel last_name: Iercan - first_name: Christoph full_name: Kirsch, Christoph M last_name: Kirsch - first_name: Claudio full_name: Pinello, Claudio last_name: Pinello - first_name: Alberto full_name: Sangiovanni-Vincentelli, Alberto last_name: Sangiovanni Vincentelli citation: ama: 'Chatterjee K, Ghosal A, Henzinger TA, et al. Logical reliability of interacting real-time tasks. In: IEEE; 2008:909-914. doi:10.1145/1403375.1403595' apa: 'Chatterjee, K., Ghosal, A., Henzinger, T. A., Iercan, D., Kirsch, C., Pinello, C., & Sangiovanni Vincentelli, A. (2008). Logical reliability of interacting real-time tasks (pp. 909–914). Presented at the DATE: Design, Automation and Test in Europe, IEEE. https://doi.org/10.1145/1403375.1403595' chicago: Chatterjee, Krishnendu, Arkadeb Ghosal, Thomas A Henzinger, Daniel Iercan, Christoph Kirsch, Claudio Pinello, and Alberto Sangiovanni Vincentelli. “Logical Reliability of Interacting Real-Time Tasks,” 909–14. IEEE, 2008. https://doi.org/10.1145/1403375.1403595. ieee: 'K. Chatterjee et al., “Logical reliability of interacting real-time tasks,” presented at the DATE: Design, Automation and Test in Europe, 2008, pp. 909–914.' ista: 'Chatterjee K, Ghosal A, Henzinger TA, Iercan D, Kirsch C, Pinello C, Sangiovanni Vincentelli A. 2008. Logical reliability of interacting real-time tasks. DATE: Design, Automation and Test in Europe, 909–914.' mla: Chatterjee, Krishnendu, et al. Logical Reliability of Interacting Real-Time Tasks. IEEE, 2008, pp. 909–14, doi:10.1145/1403375.1403595. short: K. Chatterjee, A. Ghosal, T.A. Henzinger, D. Iercan, C. Kirsch, C. Pinello, A. Sangiovanni Vincentelli, in:, IEEE, 2008, pp. 909–914. conference: name: 'DATE: Design, Automation and Test in Europe' date_created: 2018-12-11T12:09:25Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:59:36Z day: '01' doi: 10.1145/1403375.1403595 extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/logical_reliability_of_interacting_real-time_tasks.pdf month: '01' page: 909 - 914 publication_status: published publisher: IEEE publist_id: '171' quality_controlled: 0 status: public title: Logical reliability of interacting real-time tasks type: conference year: '2008' ... --- _id: '4548' abstract: - lang: eng text: The value of a finite-state two-player zero-sum stochastic game with limit-average payoff can be approximated to within ε in time exponential in a polynomial in the size of the game times polynomial in logarithmic in 1/ε, for all ε > 0. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, Majumdar R, Henzinger TA. Stochastic limit-average games are in EXPTIME. International Journal of Game Theory. 2008;37(2):219-234. doi:10.1007/s00182-007-0110-5 apa: Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2008). Stochastic limit-average games are in EXPTIME. International Journal of Game Theory. Springer. https://doi.org/10.1007/s00182-007-0110-5 chicago: Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Stochastic Limit-Average Games Are in EXPTIME.” International Journal of Game Theory. Springer, 2008. https://doi.org/10.1007/s00182-007-0110-5. ieee: K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Stochastic limit-average games are in EXPTIME,” International Journal of Game Theory, vol. 37, no. 2. Springer, pp. 219–234, 2008. ista: Chatterjee K, Majumdar R, Henzinger TA. 2008. Stochastic limit-average games are in EXPTIME. International Journal of Game Theory. 37(2), 219–234. mla: Chatterjee, Krishnendu, et al. “Stochastic Limit-Average Games Are in EXPTIME.” International Journal of Game Theory, vol. 37, no. 2, Springer, 2008, pp. 219–34, doi:10.1007/s00182-007-0110-5. short: K. Chatterjee, R. Majumdar, T.A. Henzinger, International Journal of Game Theory 37 (2008) 219–234. date_created: 2018-12-11T12:09:25Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:59:37Z day: '01' doi: 10.1007/s00182-007-0110-5 extern: 1 intvolume: ' 37' issue: '2' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/stochastic_limit-average_games_are_in_exptime.pdf month: '01' page: 219 - 234 publication: International Journal of Game Theory publication_status: published publisher: Springer publist_id: '168' quality_controlled: 0 status: public title: Stochastic limit-average games are in EXPTIME type: journal_article volume: 37 year: '2008' ... --- _id: '4568' abstract: - lang: eng text: We present and evaluate a framework and tool for combining multiple program analyses which allows the dynamic (on-line) adjustment of the precision of each analysis depending on the accumulated results. For example, the explicit tracking of the values of a variable may be switched off in favor of a predicate abstraction when and where the number of different variable values that have been encountered has exceeded a specified threshold. The method is evaluated on verifying the SSH client/server software and shows significant gains compared with predicate abstraction-based model checking. author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Grégory full_name: Théoduloz, Grégory last_name: Théoduloz citation: ama: 'Beyer D, Henzinger TA, Théoduloz G. Program analysis with dynamic change of precision. In: ACM; 2008:29-38. doi:10.1109/ASE.2008.13' apa: 'Beyer, D., Henzinger, T. A., & Théoduloz, G. (2008). Program analysis with dynamic change of precision (pp. 29–38). Presented at the ASE: Automated Software Engineering, ACM. https://doi.org/10.1109/ASE.2008.13' chicago: Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Program Analysis with Dynamic Change of Precision,” 29–38. ACM, 2008. https://doi.org/10.1109/ASE.2008.13. ieee: 'D. Beyer, T. A. Henzinger, and G. Théoduloz, “Program analysis with dynamic change of precision,” presented at the ASE: Automated Software Engineering, 2008, pp. 29–38.' ista: 'Beyer D, Henzinger TA, Théoduloz G. 2008. Program analysis with dynamic change of precision. ASE: Automated Software Engineering, 29–38.' mla: Beyer, Dirk, et al. Program Analysis with Dynamic Change of Precision. ACM, 2008, pp. 29–38, doi:10.1109/ASE.2008.13. short: D. Beyer, T.A. Henzinger, G. Théoduloz, in:, ACM, 2008, pp. 29–38. conference: name: 'ASE: Automated Software Engineering' date_created: 2018-12-11T12:09:31Z date_published: 2008-10-07T00:00:00Z date_updated: 2021-01-12T07:59:46Z day: '07' doi: 10.1109/ASE.2008.13 extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/program_analysis_with_dynamic_change_of_precision.pdf month: '10' page: 29 - 38 publication_status: published publisher: ACM publist_id: '140' quality_controlled: 0 status: public title: Program analysis with dynamic change of precision type: conference year: '2008' ... --- _id: '581' abstract: - lang: eng text: We have detected a spin-dependent displacement perpendicular to the refractive index gradient for photons passing through an air-glass interface. The effect is the photonic version of the spin Hall effect in electronic systems, indicating the universality of the effect for particles of different nature. Treating the effect as a weak measurement of the spin projection of the photons, we used a preselection and postselection technique on the spin state to enhance the original displacement by nearly four orders of magnitude, attaining sensitivity to displacements of ∼1 angstrom. The spin Hall effect can be used for manipulating photonic angular momentum states, and the measurement technique holds promise for precision metrology. author: - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Paul full_name: Kwiat, Paul last_name: Kwiat citation: ama: Hosten O, Kwiat P. Observation of the spin hall effect of light via weak measurements. Science. 2008;319(5864):787-790. doi:10.1126/science.1152697 apa: Hosten, O., & Kwiat, P. (2008). Observation of the spin hall effect of light via weak measurements. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1152697 chicago: Hosten, Onur, and Paul Kwiat. “Observation of the Spin Hall Effect of Light via Weak Measurements.” Science. American Association for the Advancement of Science, 2008. https://doi.org/10.1126/science.1152697. ieee: O. Hosten and P. Kwiat, “Observation of the spin hall effect of light via weak measurements,” Science, vol. 319, no. 5864. American Association for the Advancement of Science, pp. 787–790, 2008. ista: Hosten O, Kwiat P. 2008. Observation of the spin hall effect of light via weak measurements. Science. 319(5864), 787–790. mla: Hosten, Onur, and Paul Kwiat. “Observation of the Spin Hall Effect of Light via Weak Measurements.” Science, vol. 319, no. 5864, American Association for the Advancement of Science, 2008, pp. 787–90, doi:10.1126/science.1152697. short: O. Hosten, P. Kwiat, Science 319 (2008) 787–790. date_created: 2018-12-11T11:47:19Z date_published: 2008-02-08T00:00:00Z date_updated: 2021-01-12T08:03:38Z day: '08' doi: 10.1126/science.1152697 extern: 1 intvolume: ' 319' issue: '5864' month: '02' page: 787 - 790 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '7226' quality_controlled: 0 status: public title: Observation of the spin hall effect of light via weak measurements type: journal_article volume: 319 year: '2008' ... --- _id: '584' abstract: - lang: eng text: Using “quantum weak-measurements” as a coherent enhancement technique for small signals, we have measured the recently proposed “spin Hall effect” of light at an air-glass interface, and are working on the smoothly varying refractive-index case. alternative_title: - Optics InfoBase Conference Papers article_processing_charge: No author: - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Paul full_name: Kwiat, Paul last_name: Kwiat citation: ama: 'Hosten O, Kwiat P. Spin hall effect of light via weak measurements: Sharp and smooth index variations. In: Optica Publishing Group; 2008.' apa: 'Hosten, O., & Kwiat, P. (2008). Spin hall effect of light via weak measurements: Sharp and smooth index variations. Presented at the QELS: Quantum Electronics and Laser Science Conference, San Jose, CA, United States: Optica Publishing Group.' chicago: 'Hosten, Onur, and Paul Kwiat. “Spin Hall Effect of Light via Weak Measurements: Sharp and Smooth Index Variations.” Optica Publishing Group, 2008.' ieee: 'O. Hosten and P. Kwiat, “Spin hall effect of light via weak measurements: Sharp and smooth index variations,” presented at the QELS: Quantum Electronics and Laser Science Conference, San Jose, CA, United States, 2008.' ista: 'Hosten O, Kwiat P. 2008. Spin hall effect of light via weak measurements: Sharp and smooth index variations. QELS: Quantum Electronics and Laser Science Conference, Optics InfoBase Conference Papers, .' mla: 'Hosten, Onur, and Paul Kwiat. Spin Hall Effect of Light via Weak Measurements: Sharp and Smooth Index Variations. Optica Publishing Group, 2008.' short: O. Hosten, P. Kwiat, in:, Optica Publishing Group, 2008. conference: end_date: 2008-05-09 location: San Jose, CA, United States name: 'QELS: Quantum Electronics and Laser Science Conference' start_date: 2008-05-04 date_created: 2018-12-11T11:47:20Z date_published: 2008-01-01T00:00:00Z date_updated: 2022-05-24T09:10:41Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: https://opg.optica.org/abstract.cfm?URI=QELS-2008-QFB7 month: '01' oa_version: None publication_identifier: isbn: - 978-155752859-9 issn: - '21622701' publication_status: published publisher: Optica Publishing Group publist_id: '7227' quality_controlled: '1' scopus_import: '1' status: public title: 'Spin hall effect of light via weak measurements: Sharp and smooth index variations' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2008' ... --- _id: '6146' abstract: - lang: eng text: Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental to all animals. Here we examine the CO2 response of the nematode Caenorhabditis elegans. This species inhabits rotting material, which typically has a broad CO2 concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%. Animals can respond to both absolute CO2 concentrations and changes in CO2 levels within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16, strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1. The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1, besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs so that one response dominates. Food and allelic variation at NPR-1 regulate which response prevails. Our results suggest that multiple sensory inputs are coordinated by C. elegans to generate different coherent foraging strategies. author: - first_name: A. J. full_name: Bretscher, A. J. last_name: Bretscher - first_name: K. E. full_name: Busch, K. E. last_name: Busch - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Bretscher AJ, Busch KE, de Bono M. A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 2008;105(23):8044-8049. doi:10.1073/pnas.0707607105 apa: Bretscher, A. J., Busch, K. E., & de Bono, M. (2008). A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0707607105 chicago: Bretscher, A. J., K. E. Busch, and Mario de Bono. “A Carbon Dioxide Avoidance Behavior Is Integrated with Responses to Ambient Oxygen and Food in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0707607105. ieee: A. J. Bretscher, K. E. Busch, and M. de Bono, “A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans,” Proceedings of the National Academy of Sciences, vol. 105, no. 23. Proceedings of the National Academy of Sciences, pp. 8044–8049, 2008. ista: Bretscher AJ, Busch KE, de Bono M. 2008. A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 105(23), 8044–8049. mla: Bretscher, A. J., et al. “A Carbon Dioxide Avoidance Behavior Is Integrated with Responses to Ambient Oxygen and Food in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences, vol. 105, no. 23, Proceedings of the National Academy of Sciences, 2008, pp. 8044–49, doi:10.1073/pnas.0707607105. short: A.J. Bretscher, K.E. Busch, M. de Bono, Proceedings of the National Academy of Sciences 105 (2008) 8044–8049. date_created: 2019-03-21T08:10:15Z date_published: 2008-06-10T00:00:00Z date_updated: 2021-01-12T08:06:21Z day: '10' ddc: - '570' doi: 10.1073/pnas.0707607105 extern: '1' external_id: pmid: - '18524954' file: - access_level: open_access checksum: eac0413064b022c1489f7b6719e7228c content_type: application/pdf creator: kschuh date_created: 2019-03-21T08:14:54Z date_updated: 2020-07-14T12:47:20Z file_id: '6147' file_name: 2008_PNAS_Bretscher.pdf file_size: 501506 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 105' issue: '23' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 8044-8049 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 105 year: '2008' ... --- _id: '6148' author: - first_name: Jan E. full_name: Kammenga, Jan E. last_name: Kammenga - first_name: Patrick C. full_name: Phillips, Patrick C. last_name: Phillips - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Agnieszka full_name: Doroszuk, Agnieszka last_name: Doroszuk citation: ama: 'Kammenga JE, Phillips PC, de Bono M, Doroszuk A. Beyond induced mutants: using worms to study natural variation in genetic pathways. Trends in Genetics. 2008;24(4):178-185. doi:10.1016/j.tig.2008.01.001' apa: 'Kammenga, J. E., Phillips, P. C., de Bono, M., & Doroszuk, A. (2008). Beyond induced mutants: using worms to study natural variation in genetic pathways. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2008.01.001' chicago: 'Kammenga, Jan E., Patrick C. Phillips, Mario de Bono, and Agnieszka Doroszuk. “Beyond Induced Mutants: Using Worms to Study Natural Variation in Genetic Pathways.” Trends in Genetics. Elsevier, 2008. https://doi.org/10.1016/j.tig.2008.01.001.' ieee: 'J. E. Kammenga, P. C. Phillips, M. de Bono, and A. Doroszuk, “Beyond induced mutants: using worms to study natural variation in genetic pathways,” Trends in Genetics, vol. 24, no. 4. Elsevier, pp. 178–185, 2008.' ista: 'Kammenga JE, Phillips PC, de Bono M, Doroszuk A. 2008. Beyond induced mutants: using worms to study natural variation in genetic pathways. Trends in Genetics. 24(4), 178–185.' mla: 'Kammenga, Jan E., et al. “Beyond Induced Mutants: Using Worms to Study Natural Variation in Genetic Pathways.” Trends in Genetics, vol. 24, no. 4, Elsevier, 2008, pp. 178–85, doi:10.1016/j.tig.2008.01.001.' short: J.E. Kammenga, P.C. Phillips, M. de Bono, A. Doroszuk, Trends in Genetics 24 (2008) 178–185. date_created: 2019-03-21T08:19:45Z date_published: 2008-04-01T00:00:00Z date_updated: 2021-01-12T08:06:21Z day: '01' doi: 10.1016/j.tig.2008.01.001 extern: '1' external_id: pmid: - '18325626' intvolume: ' 24' issue: '4' language: - iso: eng month: '04' oa_version: None page: 178-185 pmid: 1 publication: Trends in Genetics publication_identifier: issn: - 0168-9525 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Beyond induced mutants: using worms to study natural variation in genetic pathways' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2008' ... --- _id: '6149' article_processing_charge: No author: - first_name: Birgitta full_name: Olofsson, Birgitta last_name: Olofsson - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: 'Olofsson B, de Bono M. Sleep: dozy worms and sleepy flies. Current Biology. 2008;18(5):R204-R206. doi:10.1016/j.cub.2008.01.002' apa: 'Olofsson, B., & de Bono, M. (2008). Sleep: dozy worms and sleepy flies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2008.01.002' chicago: 'Olofsson, Birgitta, and Mario de Bono. “Sleep: Dozy Worms and Sleepy Flies.” Current Biology. Elsevier, 2008. https://doi.org/10.1016/j.cub.2008.01.002.' ieee: 'B. Olofsson and M. de Bono, “Sleep: dozy worms and sleepy flies,” Current Biology, vol. 18, no. 5. Elsevier, pp. R204–R206, 2008.' ista: 'Olofsson B, de Bono M. 2008. Sleep: dozy worms and sleepy flies. Current Biology. 18(5), R204–R206.' mla: 'Olofsson, Birgitta, and Mario de Bono. “Sleep: Dozy Worms and Sleepy Flies.” Current Biology, vol. 18, no. 5, Elsevier, 2008, pp. R204–06, doi:10.1016/j.cub.2008.01.002.' short: B. Olofsson, M. de Bono, Current Biology 18 (2008) R204–R206. date_created: 2019-03-21T08:23:24Z date_published: 2008-03-11T00:00:00Z date_updated: 2022-08-25T15:03:41Z day: '11' doi: 10.1016/j.cub.2008.01.002 extern: '1' external_id: pmid: - '18334193' intvolume: ' 18' issue: '5' language: - iso: eng month: '03' oa_version: None page: R204-R206 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Sleep: dozy worms and sleepy flies' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2008' ... --- _id: '7321' abstract: - lang: eng text: Cell interaction phenomena in polymer electrolyte fuel cell stacks that arise from imbalance between adjacent cells are investigated in detail experimentally and theoretically. A specialized two-cell stack with advanced localized diagnostics was developed and used to analyze the mechanism and effect of cell-to-cell coupling as a result of operationally relevant variations in reactant feed flow. Contributions to overall and local voltage changes with respect to uniformly operated cells are scrutinized. Unequal operation of the cells causes in-plane current in the bipolar plate to redistribute current and result in inhomogeneous polarization. Both increasing and decreasing polarization along the air-flow path reduces cell power as compared to isopotential operation. A two-dimensional model based on a commercial computational fluid dynamics code is used to back and extend the experimental results to more general cases. Furthermore, the experimental setup presented allowed for the first time to perform simultaneous localized electrochemical impedance spectroscopy beyond the single-cell level. The mechanism of mutual cell interaction on local and integral spectra is revealed. Results show that virtually identical operation of the cells is essential to obtain meaningful integral spectra. article_number: B704 article_processing_charge: No article_type: original author: - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Ingo A. full_name: Schneider, Ingo A. last_name: Schneider - first_name: Pang-Chieh full_name: Sui, Pang-Chieh last_name: Sui - first_name: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Nedjib full_name: Djilali, Nedjib last_name: Djilali - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. Cell interaction phenomena in polymer electrolyte fuel cell stacks. Journal of The Electrochemical Society. 2008;155(7). doi:10.1149/1.2913095 apa: Freunberger, S. A., Schneider, I. A., Sui, P.-C., Wokaun, A., Djilali, N., & Büchi, F. N. (2008). Cell interaction phenomena in polymer electrolyte fuel cell stacks. Journal of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2913095 chicago: Freunberger, Stefan Alexander, Ingo A. Schneider, Pang-Chieh Sui, Alexander Wokaun, Nedjib Djilali, and Felix N. Büchi. “Cell Interaction Phenomena in Polymer Electrolyte Fuel Cell Stacks.” Journal of The Electrochemical Society. The Electrochemical Society, 2008. https://doi.org/10.1149/1.2913095. ieee: S. A. Freunberger, I. A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, and F. N. Büchi, “Cell interaction phenomena in polymer electrolyte fuel cell stacks,” Journal of The Electrochemical Society, vol. 155, no. 7. The Electrochemical Society, 2008. ista: Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. 2008. Cell interaction phenomena in polymer electrolyte fuel cell stacks. Journal of The Electrochemical Society. 155(7), B704. mla: Freunberger, Stefan Alexander, et al. “Cell Interaction Phenomena in Polymer Electrolyte Fuel Cell Stacks.” Journal of The Electrochemical Society, vol. 155, no. 7, B704, The Electrochemical Society, 2008, doi:10.1149/1.2913095. short: S.A. Freunberger, I.A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, F.N. Büchi, Journal of The Electrochemical Society 155 (2008). date_created: 2020-01-15T12:21:47Z date_published: 2008-05-08T00:00:00Z date_updated: 2021-01-12T08:13:03Z day: '08' doi: 10.1149/1.2913095 extern: '1' intvolume: ' 155' issue: '7' language: - iso: eng month: '05' oa_version: None publication: Journal of The Electrochemical Society publication_identifier: issn: - 0013-4651 publication_status: published publisher: The Electrochemical Society quality_controlled: '1' status: public title: Cell interaction phenomena in polymer electrolyte fuel cell stacks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 155 year: '2008' ... --- _id: '7320' abstract: - lang: eng text: A comparative, experimental diffusivity study of gas diffusion layer (GDL) materials for polymer electrolyte fuel cells (PEFC) is presented for the first time. The GDL plays an important role for electrochemical losses due to gas transport limitations at high current densities. Characterization and optimization of these layers is therefore essential to improve power density. A recently developed method which allows for fast diffusimetry is applied and data compared to the literature values. Measurements are made as a function of direction and compression and the effect of different binder structures and hydrophobic treatments on effective diffusivities are discussed. A better understanding of the results is gained by including novel GDL cross-section images and a meaningful unit cell model for the interpretation of the data. The diffusivity data is valuable for GDL manufacturers and future PEFC models. The study reveals that a binder–fiber ratio larger than 50% has a negative impact on the effective diffusion properties. The hydrophobic treatment which is necessary to improve the water management can impede diffusion and thus reduce the power density. Furthermore binder has an isotropic effect while compression pronounces the in-plane orientation of the fibers. article_processing_charge: No article_type: original author: - first_name: Reto full_name: Flückiger, Reto last_name: Flückiger - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Denis full_name: Kramer, Denis last_name: Kramer - first_name: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Günther G. full_name: Scherer, Günther G. last_name: Scherer - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. Electrochimica Acta. 2008;54(2):551-559. doi:10.1016/j.electacta.2008.07.034 apa: Flückiger, R., Freunberger, S. A., Kramer, D., Wokaun, A., Scherer, G. G., & Büchi, F. N. (2008). Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2008.07.034 chicago: Flückiger, Reto, Stefan Alexander Freunberger, Denis Kramer, Alexander Wokaun, Günther G. Scherer, and Felix N. Büchi. “Anisotropic, Effective Diffusivity of Porous Gas Diffusion Layer Materials for PEFC.” Electrochimica Acta. Elsevier, 2008. https://doi.org/10.1016/j.electacta.2008.07.034. ieee: R. Flückiger, S. A. Freunberger, D. Kramer, A. Wokaun, G. G. Scherer, and F. N. Büchi, “Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC,” Electrochimica Acta, vol. 54, no. 2. Elsevier, pp. 551–559, 2008. ista: Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. 2008. Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. Electrochimica Acta. 54(2), 551–559. mla: Flückiger, Reto, et al. “Anisotropic, Effective Diffusivity of Porous Gas Diffusion Layer Materials for PEFC.” Electrochimica Acta, vol. 54, no. 2, Elsevier, 2008, pp. 551–59, doi:10.1016/j.electacta.2008.07.034. short: R. Flückiger, S.A. Freunberger, D. Kramer, A. Wokaun, G.G. Scherer, F.N. Büchi, Electrochimica Acta 54 (2008) 551–559. date_created: 2020-01-15T12:21:36Z date_published: 2008-12-30T00:00:00Z date_updated: 2021-01-12T08:13:02Z day: '30' doi: 10.1016/j.electacta.2008.07.034 extern: '1' intvolume: ' 54' issue: '2' language: - iso: eng month: '12' oa_version: None page: 551-559 publication: Electrochimica Acta publication_identifier: issn: - 0013-4686 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2008' ... --- _id: '7322' abstract: - lang: eng text: The gas diffusion layers (GDLs) of a membrane electrode assembly (MEA) serve as link between flow field and porous electrode within a polymer electrolyte fuel cell. Beside ensuring sufficient electrical and thermal contact between the whole electrode area and the flow field, these typically 200–400 μm thick porous structures enable the access of educts to the electrode area which would be occluded by the flow field lands if the flow field is directly attached to the electrode. Hence, the characterisation of properties pertaining to mass transport of educts and products through these structures is indispensable whilst examining the contribution of the GDLs to the overall electrochemical characteristics of a MEA. A fast and cost effective method to measure the effective diffusivity of a GDL is presented. Electrochemical impedance spectroscopy is applied to measure the effective ionic conductivity of an electrolyte-soaked GDL. Taking advantage of the analogy between Ficks and Ohms law, this provides a measure for the effective diffusivity. The method is described in detail, including experimental as well as theoretical aspects, and selected results, highlighting the anisotropy and dependence on the degree of compression, are shown. Moreover, a two-dimensional model consisting of regularly spaced ellipses is developed to represent the porous structure of the GDL, and by using conformal maps, the agreement between this model and experiment with respect to the sensitivity of the effective diffusivity towards compression is shown. article_processing_charge: No article_type: original author: - first_name: Denis full_name: Kramer, Denis last_name: Kramer - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Reto full_name: Flückiger, Reto last_name: Flückiger - first_name: Ingo A. full_name: Schneider, Ingo A. last_name: Schneider - first_name: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi - first_name: Günther G. full_name: Scherer, Günther G. last_name: Scherer citation: ama: Kramer D, Freunberger SA, Flückiger R, et al. Electrochemical diffusimetry of fuel cell gas diffusion layers. Journal of Electroanalytical Chemistry. 2008;612(1):63-77. doi:10.1016/j.jelechem.2007.09.014 apa: Kramer, D., Freunberger, S. A., Flückiger, R., Schneider, I. A., Wokaun, A., Büchi, F. N., & Scherer, G. G. (2008). Electrochemical diffusimetry of fuel cell gas diffusion layers. Journal of Electroanalytical Chemistry. Elsevier. https://doi.org/10.1016/j.jelechem.2007.09.014 chicago: Kramer, Denis, Stefan Alexander Freunberger, Reto Flückiger, Ingo A. Schneider, Alexander Wokaun, Felix N. Büchi, and Günther G. Scherer. “Electrochemical Diffusimetry of Fuel Cell Gas Diffusion Layers.” Journal of Electroanalytical Chemistry. Elsevier, 2008. https://doi.org/10.1016/j.jelechem.2007.09.014. ieee: D. Kramer et al., “Electrochemical diffusimetry of fuel cell gas diffusion layers,” Journal of Electroanalytical Chemistry, vol. 612, no. 1. Elsevier, pp. 63–77, 2008. ista: Kramer D, Freunberger SA, Flückiger R, Schneider IA, Wokaun A, Büchi FN, Scherer GG. 2008. Electrochemical diffusimetry of fuel cell gas diffusion layers. Journal of Electroanalytical Chemistry. 612(1), 63–77. mla: Kramer, Denis, et al. “Electrochemical Diffusimetry of Fuel Cell Gas Diffusion Layers.” Journal of Electroanalytical Chemistry, vol. 612, no. 1, Elsevier, 2008, pp. 63–77, doi:10.1016/j.jelechem.2007.09.014. short: D. Kramer, S.A. Freunberger, R. Flückiger, I.A. Schneider, A. Wokaun, F.N. Büchi, G.G. Scherer, Journal of Electroanalytical Chemistry 612 (2008) 63–77. date_created: 2020-01-15T12:21:57Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T08:13:03Z day: '01' doi: 10.1016/j.jelechem.2007.09.014 extern: '1' intvolume: ' 612' issue: '1' language: - iso: eng month: '01' oa_version: None page: 63-77 publication: Journal of Electroanalytical Chemistry publication_identifier: issn: - 1572-6657 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Electrochemical diffusimetry of fuel cell gas diffusion layers type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 612 year: '2008' ... --- _id: '7425' abstract: - lang: eng text: The propagation of single cell performance losses to adjacent cells in a polymer electrolyte fuel cell stack is studied by means of local current density measurements in a two cell stack. In this stack, the working conditions of adjacent cells can be controlled independently in order to deliberately change the performance of one cell (inducing cell) and study the coupling effects to the adjacent cell (response cell), while keeping the working conditions of the later one unchanged. The experiments have shown that changes in the current density distribution caused by lowering of the air stoichiometry in the inducing cell cause changes in the current density distribution of the response cell in the order of 60% of the change of the inducing cell, even when the air stoichiometry of the response cell is kept constant. The losses in cell voltage of the inducing cell cause losses in cell voltage of the response cell in a magnitude between 30 and 50%. article_processing_charge: No author: - first_name: Marco full_name: Santis, Marco last_name: Santis - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Matthias full_name: Papra, Matthias last_name: Papra - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: 'Santis M, Freunberger SA, Papra M, Büchi FN. Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. In: 3rd International Conference on Fuel Cell Science, Engineering and Technology. ASMEDC; 2008:763-765. doi:10.1115/fuelcell2005-74116' apa: 'Santis, M., Freunberger, S. A., Papra, M., & Büchi, F. N. (2008). Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. In 3rd International Conference on Fuel Cell Science, Engineering and Technology (pp. 763–765). Ypsilanti, MI, United States: ASMEDC. https://doi.org/10.1115/fuelcell2005-74116' chicago: Santis, Marco, Stefan Alexander Freunberger, Matthias Papra, and Felix N. Büchi. “Experimental Investigation of the Propagation of Local Current Density Variations to Adjacent Cells in PEFC Stacks.” In 3rd International Conference on Fuel Cell Science, Engineering and Technology, 763–65. ASMEDC, 2008. https://doi.org/10.1115/fuelcell2005-74116. ieee: M. Santis, S. A. Freunberger, M. Papra, and F. N. Büchi, “Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks,” in 3rd International Conference on Fuel Cell Science, Engineering and Technology, Ypsilanti, MI, United States, 2008, pp. 763–765. ista: Santis M, Freunberger SA, Papra M, Büchi FN. 2008. Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. 3rd International Conference on Fuel Cell Science, Engineering and Technology. International conference on fuel cell science, engineering and technology, 763–765. mla: Santis, Marco, et al. “Experimental Investigation of the Propagation of Local Current Density Variations to Adjacent Cells in PEFC Stacks.” 3rd International Conference on Fuel Cell Science, Engineering and Technology, ASMEDC, 2008, pp. 763–65, doi:10.1115/fuelcell2005-74116. short: M. Santis, S.A. Freunberger, M. Papra, F.N. Büchi, in:, 3rd International Conference on Fuel Cell Science, Engineering and Technology, ASMEDC, 2008, pp. 763–765. conference: end_date: 2005-05-25 location: Ypsilanti, MI, United States name: International conference on fuel cell science, engineering and technology start_date: 2005-05-23 date_created: 2020-01-31T10:14:45Z date_published: 2008-10-13T00:00:00Z date_updated: 2021-01-12T08:13:33Z day: '13' doi: 10.1115/fuelcell2005-74116 extern: '1' language: - iso: eng month: '10' oa_version: None page: 763-765 publication: 3rd International Conference on Fuel Cell Science, Engineering and Technology publication_identifier: isbn: - '0791837645' - '0791837572' publication_status: published publisher: ASMEDC quality_controlled: '1' status: public title: Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2008' ... --- _id: '753' abstract: - lang: eng text: 'This paper addresses the following question: what is the minimum-sized synchronous window needed to solve consensus in an otherwise asynchronous system? In answer to this question, we present the first optimally-resilient algorithm ASAP that solves consensus as soon as possible in an eventually synchronous system, i.e., a system that from some time GST onwards, delivers messages in a timely fashion. ASAP guarantees that, in an execution with at most f failures, every process decides no later than round GST + f + 2, which is optimal.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. How to solve consensus in the smallest window of synchrony. In: Vol 5218 LNCS. Springer; 2008:32-46. doi:10.1007/978-3-540-87779-0_3' apa: 'Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2008). How to solve consensus in the smallest window of synchrony (Vol. 5218 LNCS, pp. 32–46). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-540-87779-0_3' chicago: Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “How to Solve Consensus in the Smallest Window of Synchrony,” 5218 LNCS:32–46. Springer, 2008. https://doi.org/10.1007/978-3-540-87779-0_3. ieee: 'D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “How to solve consensus in the smallest window of synchrony,” presented at the DISC: Distributed Computing, 2008, vol. 5218 LNCS, pp. 32–46.' ista: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2008. How to solve consensus in the smallest window of synchrony. DISC: Distributed Computing, LNCS, vol. 5218 LNCS, 32–46.' mla: Alistarh, Dan-Adrian, et al. How to Solve Consensus in the Smallest Window of Synchrony. Vol. 5218 LNCS, Springer, 2008, pp. 32–46, doi:10.1007/978-3-540-87779-0_3. short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, in:, Springer, 2008, pp. 32–46. conference: name: 'DISC: Distributed Computing' date_created: 2018-12-11T11:48:19Z date_published: 2008-01-01T00:00:00Z date_updated: 2023-02-23T13:10:13Z day: '01' doi: 10.1007/978-3-540-87779-0_3 extern: '1' language: - iso: eng month: '01' oa_version: None page: 32 - 46 publication_status: published publisher: Springer publist_id: '6904' status: public title: How to solve consensus in the smallest window of synchrony type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5218 LNCS year: '2008' ... --- _id: '7752' article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Jill G. full_name: Pilkington, Jill G. last_name: Pilkington - first_name: Tim H. full_name: Clutton-Brock, Tim H. last_name: Clutton-Brock - first_name: Josephine M. full_name: Pemberton, Josephine M. last_name: Pemberton - first_name: Loeske. E.B. full_name: Kruuk, Loeske. E.B. last_name: Kruuk citation: ama: Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. Environmental heterogeneity generates fluctuating selection on a secondary sexual trait. Current Biology. 2008;18(10):751-757. doi:10.1016/j.cub.2008.04.059 apa: Robinson, M. R., Pilkington, J. G., Clutton-Brock, T. H., Pemberton, J. M., & Kruuk, L. E. B. (2008). Environmental heterogeneity generates fluctuating selection on a secondary sexual trait. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2008.04.059 chicago: Robinson, Matthew Richard, Jill G. Pilkington, Tim H. Clutton-Brock, Josephine M. Pemberton, and Loeske. E.B. Kruuk. “Environmental Heterogeneity Generates Fluctuating Selection on a Secondary Sexual Trait.” Current Biology. Elsevier, 2008. https://doi.org/10.1016/j.cub.2008.04.059. ieee: M. R. Robinson, J. G. Pilkington, T. H. Clutton-Brock, J. M. Pemberton, and L. E. B. Kruuk, “Environmental heterogeneity generates fluctuating selection on a secondary sexual trait,” Current Biology, vol. 18, no. 10. Elsevier, pp. 751–757, 2008. ista: Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. 2008. Environmental heterogeneity generates fluctuating selection on a secondary sexual trait. Current Biology. 18(10), 751–757. mla: Robinson, Matthew Richard, et al. “Environmental Heterogeneity Generates Fluctuating Selection on a Secondary Sexual Trait.” Current Biology, vol. 18, no. 10, Elsevier, 2008, pp. 751–57, doi:10.1016/j.cub.2008.04.059. short: M.R. Robinson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton, L.E.B. Kruuk, Current Biology 18 (2008) 751–757. date_created: 2020-04-30T11:02:13Z date_published: 2008-05-20T00:00:00Z date_updated: 2021-01-12T08:15:17Z day: '20' doi: 10.1016/j.cub.2008.04.059 extern: '1' intvolume: ' 18' issue: '10' language: - iso: eng month: '05' oa_version: None page: 751-757 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Environmental heterogeneity generates fluctuating selection on a secondary sexual trait type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2008' ... --- _id: '844' abstract: - lang: eng text: Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites. acknowledgement: This work was supported in part by NIH grants R01 GM078598 and U54 LM008748. author: - first_name: Steffen full_name: Schmidt, Steffen last_name: Schmidt - first_name: Anna full_name: Gerasimova, Anna last_name: Gerasimova - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Ivan full_name: Adzuhbei, Ivan A last_name: Adzuhbei - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Shamil full_name: Sunyaev, Shamil R last_name: Sunyaev citation: ama: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 2008;4(11). doi:10.1371/journal.pgen.1000281 apa: Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A., & Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000281 chicago: Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics. Public Library of Science, 2008. https://doi.org/10.1371/journal.pgen.1000281. ieee: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,” PLoS Genetics, vol. 4, no. 11. Public Library of Science, 2008. ista: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. 2008. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 4(11). mla: Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics, vol. 4, no. 11, Public Library of Science, 2008, doi:10.1371/journal.pgen.1000281. short: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S. Sunyaev, PLoS Genetics 4 (2008). date_created: 2018-12-11T11:48:48Z date_published: 2008-11-01T00:00:00Z date_updated: 2021-01-12T08:19:16Z day: '01' doi: 10.1371/journal.pgen.1000281 extern: 1 intvolume: ' 4' issue: '11' month: '11' publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '6800' quality_controlled: 0 status: public title: Hypermutable non-synonymous sites are under stronger negative selection tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 4 year: '2008' ... --- _id: '8481' abstract: - lang: eng text: 'The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans CH34 within the complex cop cluster of genes, for which 21 genes have been identified. The expression of the corresponding periplasmic CopK protein is strongly upregulated in the presence of copper, leading to a high periplasmic accumulation. The structure and metal-binding properties of CopK were investigated by NMR and mass spectrometry. The protein is dimeric in the apo state with a dissociation constant in the range of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed that CopK has two high-affinity Cu(I)-binding sites per monomer with different Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific. The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets in perpendicular orientation with an unstructured C-terminal tail. The dimer interface is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion induces a major structural modification involving dissociation of the dimeric apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm the conservation of the N-terminal β-sheet, while the last strand of the C-terminal sheet appears in slow conformational exchange. We hypothesize that the partial disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange data acquired on the apo-protein are consistent with a lower thermodynamic stability of the C-terminal sheet. CopK contains seven methionine residues, five of which appear highly conserved. Chemical shift data suggest implication of two or three methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second Cu(I) ion further increases protein plasticity. Comparison of the structural and metal-binding properties of CopK with other periplasmic copper-binding proteins reveals two conserved features within these functionally related proteins: the all-β fold and the methionine-rich Cu(I)-binding site.' article_processing_charge: No article_type: original author: - first_name: Beate full_name: Bersch, Beate last_name: Bersch - first_name: Adrien full_name: Favier, Adrien last_name: Favier - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Sébastien full_name: van Aelst, Sébastien last_name: van Aelst - first_name: Tatiana full_name: Vallaeys, Tatiana last_name: Vallaeys - first_name: Jacques full_name: Covès, Jacques last_name: Covès - first_name: Max full_name: Mergeay, Max last_name: Mergeay - first_name: Ruddy full_name: Wattiez, Ruddy last_name: Wattiez citation: ama: Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. 2008;380(2):386-403. doi:10.1016/j.jmb.2008.05.017 apa: Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J., … Wattiez, R. (2008). Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.017 chicago: Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” Journal of Molecular Biology. Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.017. ieee: B. Bersch et al., “Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge,” Journal of Molecular Biology, vol. 380, no. 2. Elsevier, pp. 386–403, 2008. ista: Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M, Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. 380(2), 386–403. mla: Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” Journal of Molecular Biology, vol. 380, no. 2, Elsevier, 2008, pp. 386–403, doi:10.1016/j.jmb.2008.05.017. short: B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M. Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403. date_created: 2020-09-18T10:12:37Z date_published: 2008-07-04T00:00:00Z date_updated: 2021-01-12T08:19:34Z day: '04' doi: 10.1016/j.jmb.2008.05.017 extern: '1' intvolume: ' 380' issue: '2' keyword: - Molecular Biology language: - iso: eng month: '07' oa_version: None page: 386-403 publication: Journal of Molecular Biology publication_identifier: issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 380 year: '2008' ... --- _id: '8480' abstract: - lang: eng text: The KIX domain of the transcription co-activator CBP is a three-helix bundle protein that folds via rapid accumulation of an intermediate state, followed by a slower folding phase. Recent NMR relaxation dispersion studies revealed the presence of a low-populated (excited) state of KIX that exists in equilibrium with the natively folded form under non-denaturing conditions, and likely represents the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium exchange measurements using rapid NMR data acquisition techniques with backbone 15N and 13C relaxation dispersion experiments to further investigate the equilibrium folding of the KIX domain. Residual structure within the folding intermediate is detected by both methods, and their combination enables reliable quantification of the amount of persistent residual structure. Three well-defined folding subunits are found, which display variable stability and correspond closely to the individual helices in the native state. While two of the three helices (α2 and α3) are partially formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C), the third helix is disordered. The observed helical content within the excited state exceeds the helical propensities predicted for the corresponding peptide regions, suggesting that the two helices are weakly mutually stabilized, while methyl 13C relaxation dispersion data indicate that a defined packing arrangement is unlikely. Temperature-dependent experiments reveal that the largest enthalpy and entropy changes along the folding reaction occur during the final transition from the intermediate to the native state. Our experimental data are consistent with a folding mechanism where helices α2 and α3 form rapidly, although to different extents, while helix α1 consolidates only as folding proceeds to complete the native state-structure. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher - first_name: Robert full_name: Konrat, Robert last_name: Konrat - first_name: Martin full_name: Tollinger, Martin last_name: Tollinger citation: ama: 'Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. 2008;380(4):726-741. doi:10.1016/j.jmb.2008.05.040' apa: 'Schanda, P., Brutscher, B., Konrat, R., & Tollinger, M. (2008). Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.040' chicago: 'Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” Journal of Molecular Biology. Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.040.' ieee: 'P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,” Journal of Molecular Biology, vol. 380, no. 4. Elsevier, pp. 726–741, 2008.' ista: 'Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. 380(4), 726–741.' mla: 'Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” Journal of Molecular Biology, vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:10.1016/j.jmb.2008.05.040.' short: P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology 380 (2008) 726–741. date_created: 2020-09-18T10:12:29Z date_published: 2008-07-18T00:00:00Z date_updated: 2021-01-12T08:19:34Z day: '18' doi: 10.1016/j.jmb.2008.05.040 extern: '1' intvolume: ' 380' issue: '4' keyword: - Molecular Biology language: - iso: eng month: '07' oa_version: None page: 726-741 publication: Journal of Molecular Biology publication_identifier: issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 380 year: '2008' ... --- _id: '8482' abstract: - lang: eng text: The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants. article_processing_charge: No article_type: letter_note author: - first_name: Thomas full_name: Kern, Thomas last_name: Kern - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Kern T, Schanda P, Brutscher B. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. 2008;190(2):333-338. doi:10.1016/j.jmr.2007.11.015 apa: Kern, T., Schanda, P., & Brutscher, B. (2008). Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2007.11.015 chicago: Kern, Thomas, Paul Schanda, and Bernhard Brutscher. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” Journal of Magnetic Resonance. Elsevier, 2008. https://doi.org/10.1016/j.jmr.2007.11.015. ieee: T. Kern, P. Schanda, and B. Brutscher, “Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load,” Journal of Magnetic Resonance, vol. 190, no. 2. Elsevier, pp. 333–338, 2008. ista: Kern T, Schanda P, Brutscher B. 2008. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. 190(2), 333–338. mla: Kern, Thomas, et al. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” Journal of Magnetic Resonance, vol. 190, no. 2, Elsevier, 2008, pp. 333–38, doi:10.1016/j.jmr.2007.11.015. short: T. Kern, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 190 (2008) 333–338. date_created: 2020-09-18T10:12:46Z date_published: 2008-02-01T00:00:00Z date_updated: 2021-01-12T08:19:35Z day: '01' doi: 10.1016/j.jmr.2007.11.015 extern: '1' intvolume: ' 190' issue: '2' keyword: - Nuclear and High Energy Physics - Biophysics - Biochemistry - Condensed Matter Physics language: - iso: eng month: '02' oa_version: None page: 333-338 publication: Journal of Magnetic Resonance publication_identifier: issn: - 1090-7807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 190 year: '2008' ... --- _id: '9537' abstract: - lang: eng text: DNA methylation is an ancient process found in all domains of life. Although the enzymes that mediate methylation have remained highly conserved, DNA methylation has been adapted for a variety of uses throughout evolution, including defense against transposable elements and control of gene expression. Defects in DNA methylation are linked to human diseases, including cancer. Methylation has been lost several times in the course of animal and fungal evolution, thus limiting the opportunity for study in common model organisms. In the past decade, plants have emerged as a premier model system for genetic dissection of DNA methylation. A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more. article_processing_charge: No article_type: review author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zilberman D. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 2008;11(5):554-559. doi:10.1016/j.pbi.2008.07.004 apa: Zilberman, D. (2008). The evolving functions of DNA methylation. Current Opinion in Plant Biology. Elsevier . https://doi.org/10.1016/j.pbi.2008.07.004 chicago: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current Opinion in Plant Biology. Elsevier , 2008. https://doi.org/10.1016/j.pbi.2008.07.004. ieee: D. Zilberman, “The evolving functions of DNA methylation,” Current Opinion in Plant Biology, vol. 11, no. 5. Elsevier , pp. 554–559, 2008. ista: Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 11(5), 554–559. mla: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current Opinion in Plant Biology, vol. 11, no. 5, Elsevier , 2008, pp. 554–59, doi:10.1016/j.pbi.2008.07.004. short: D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559. date_created: 2021-06-08T13:13:37Z date_published: 2008-10-01T00:00:00Z date_updated: 2021-12-14T08:54:07Z department: - _id: DaZi doi: 10.1016/j.pbi.2008.07.004 extern: '1' external_id: pmid: - '18774331' intvolume: ' 11' issue: '5' language: - iso: eng month: '10' oa_version: None page: 554-559 pmid: 1 publication: Current Opinion in Plant Biology publication_identifier: issn: - 1369-5266 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' scopus_import: '1' status: public title: The evolving functions of DNA methylation type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 11 year: '2008' ... --- _id: '965' abstract: - lang: eng text: We give many examples of applying Bogoliubov's forest formula to iterative solutions of various nonlinear equations. The same formula describes an extremely wide class of objects, from an ordinary quadratic equation to renormalization in quantum field theory. acknowledgement: |- This work is supported in part by the Dynasty Foundation (M. N. S.), the Russian Foundation for Basic Research (Grant No s. 07-02-00878 and 07-02-00645), a joint grant (Grant No. 06-01-92059-CE), the NWO (Project No. 047.011.2004.026), INTAS (Grant No. 05-1000008-7865), the Program for Supporting Leading Scientific School s (Grant No. NSh-8004.2006.2), and also by a project (Project No. ANR-05-BLAN-0029-01, A. Yu. M.). author: - first_name: Alexei full_name: Morozov, Alexei Y last_name: Morozov - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Morozov A, Serbyn M. Nonlinear algebra and Bogoliubov’s recursion. Theoretical and Mathematical Physics. 2008;154(2):270-293. doi:10.1007/s11232-008-0026-7 apa: Morozov, A., & Serbyn, M. (2008). Nonlinear algebra and Bogoliubov’s recursion. Theoretical and Mathematical Physics. Elsevier. https://doi.org/10.1007/s11232-008-0026-7 chicago: Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.” Theoretical and Mathematical Physics. Elsevier, 2008. https://doi.org/10.1007/s11232-008-0026-7. ieee: A. Morozov and M. Serbyn, “Nonlinear algebra and Bogoliubov’s recursion,” Theoretical and Mathematical Physics, vol. 154, no. 2. Elsevier, pp. 270–293, 2008. ista: Morozov A, Serbyn M. 2008. Nonlinear algebra and Bogoliubov’s recursion. Theoretical and Mathematical Physics. 154(2), 270–293. mla: Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.” Theoretical and Mathematical Physics, vol. 154, no. 2, Elsevier, 2008, pp. 270–93, doi:10.1007/s11232-008-0026-7. short: A. Morozov, M. Serbyn, Theoretical and Mathematical Physics 154 (2008) 270–293. date_created: 2018-12-11T11:49:26Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T08:22:17Z day: '01' doi: 10.1007/s11232-008-0026-7 extern: 1 intvolume: ' 154' issue: '2' main_file_link: - open_access: '1' url: https://arxiv.org/abs/hep-th/0703258 month: '01' oa: 1 page: 270 - 293 publication: Theoretical and Mathematical Physics publication_status: published publisher: Elsevier publist_id: '6437' quality_controlled: 0 status: public title: Nonlinear algebra and Bogoliubov's recursion type: journal_article volume: 154 year: '2008' ... --- _id: '8510' abstract: - lang: eng text: In this paper, using the ideas of Bessi and Mather, we present a simple mechanical system exhibiting Arnold diffusion. This system of a particle in a small periodic potential can be also interpreted as ray propagation in a periodic optical medium with a near-constant index of refraction. Arnold diffusion in this context manifests itself as an arbitrary finite change of direction for nearly constant index of refraction. article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Mark full_name: Levi, Mark last_name: Levi citation: ama: Kaloshin V, Levi M. An example of Arnold diffusion for near-integrable Hamiltonians. Bulletin of the American Mathematical Society. 2008;45(3):409-427. doi:10.1090/s0273-0979-08-01211-1 apa: Kaloshin, V., & Levi, M. (2008). An example of Arnold diffusion for near-integrable Hamiltonians. Bulletin of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/s0273-0979-08-01211-1 chicago: Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” Bulletin of the American Mathematical Society. American Mathematical Society, 2008. https://doi.org/10.1090/s0273-0979-08-01211-1. ieee: V. Kaloshin and M. Levi, “An example of Arnold diffusion for near-integrable Hamiltonians,” Bulletin of the American Mathematical Society, vol. 45, no. 3. American Mathematical Society, pp. 409–427, 2008. ista: Kaloshin V, Levi M. 2008. An example of Arnold diffusion for near-integrable Hamiltonians. Bulletin of the American Mathematical Society. 45(3), 409–427. mla: Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” Bulletin of the American Mathematical Society, vol. 45, no. 3, American Mathematical Society, 2008, pp. 409–27, doi:10.1090/s0273-0979-08-01211-1. short: V. Kaloshin, M. Levi, Bulletin of the American Mathematical Society 45 (2008) 409–427. date_created: 2020-09-18T10:48:20Z date_published: 2008-07-01T00:00:00Z date_updated: 2021-01-12T08:19:47Z day: '01' doi: 10.1090/s0273-0979-08-01211-1 extern: '1' intvolume: ' 45' issue: '3' keyword: - Applied Mathematics - General Mathematics language: - iso: eng month: '07' oa_version: None page: 409-427 publication: Bulletin of the American Mathematical Society publication_identifier: issn: - 0273-0979 publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: An example of Arnold diffusion for near-integrable Hamiltonians type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2008' ... --- _id: '8509' abstract: - lang: eng text: The goal of this paper is to present to nonspecialists what is perhaps the simplest possible geometrical picture explaining the mechanism of Arnold diffusion. We choose to speak of a specific model—that of geometric rays in a periodic optical medium. This model is equivalent to that of a particle in a periodic potential in ${\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian metric on ${\mathbb R}^{n} $. article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Mark full_name: Levi, Mark last_name: Levi citation: ama: Kaloshin V, Levi M. Geometry of Arnold diffusion. SIAM Review. 2008;50(4):702-720. doi:10.1137/070703235 apa: Kaloshin, V., & Levi, M. (2008). Geometry of Arnold diffusion. SIAM Review. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/070703235 chicago: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM Review. Society for Industrial & Applied Mathematics, 2008. https://doi.org/10.1137/070703235. ieee: V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” SIAM Review, vol. 50, no. 4. Society for Industrial & Applied Mathematics, pp. 702–720, 2008. ista: Kaloshin V, Levi M. 2008. Geometry of Arnold diffusion. SIAM Review. 50(4), 702–720. mla: Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM Review, vol. 50, no. 4, Society for Industrial & Applied Mathematics, 2008, pp. 702–20, doi:10.1137/070703235. short: V. Kaloshin, M. Levi, SIAM Review 50 (2008) 702–720. date_created: 2020-09-18T10:48:12Z date_published: 2008-11-05T00:00:00Z date_updated: 2021-01-12T08:19:46Z day: '05' doi: 10.1137/070703235 extern: '1' intvolume: ' 50' issue: '4' keyword: - Theoretical Computer Science - Applied Mathematics - Computational Mathematics language: - iso: eng month: '11' oa_version: None page: 702-720 publication: SIAM Review publication_identifier: issn: - 0036-1445 - 1095-7200 publication_status: published publisher: Society for Industrial & Applied Mathematics quality_controlled: '1' status: public title: Geometry of Arnold diffusion type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2008' ... --- _id: '895' abstract: - lang: eng text: Background. The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex (CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results. Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion. There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a unique opportunity to assess the functional role of this duplication in contributing to variation in social behavior in primates. While our initial studies show no signs of directional selection on this locus in chimps, pharmacological and genetic association studies support a potential role for this region in influencing V1aR expression and social behavior. acknowledgement: | We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD). author: - first_name: Zoe full_name: Donaldson, Zoe R last_name: Donaldson - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Andrea full_name: Putnam, Andrea S last_name: Putnam - first_name: Yaohui full_name: Bai, Yaohui last_name: Bai - first_name: Tara full_name: Stoinski, Tara S last_name: Stoinski - first_name: Elizabeth full_name: Hammock, Elizabeth A last_name: Hammock - first_name: Larry full_name: Young, Larry last_name: Young citation: ama: Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 2008;8(1). doi:10.1186/1471-2148-8-180 apa: Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock, E., & Young, L. (2008). Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-8-180 chicago: Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski, Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology. BioMed Central, 2008. https://doi.org/10.1186/1471-2148-8-180. ieee: Z. Donaldson et al., “Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene,” BMC Evolutionary Biology, vol. 8, no. 1. BioMed Central, 2008. ista: Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L. 2008. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1). mla: Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology, vol. 8, no. 1, BioMed Central, 2008, doi:10.1186/1471-2148-8-180. short: Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock, L. Young, BMC Evolutionary Biology 8 (2008). date_created: 2018-12-11T11:49:04Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T08:21:29Z day: '01' doi: 10.1186/1471-2148-8-180 extern: 1 intvolume: ' 8' issue: '1' month: '01' publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '6753' quality_controlled: 0 status: public title: Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene 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: 8 year: '2008' ... --- _id: '907' abstract: - lang: eng text: The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process. author: - first_name: Raquel full_name: Assis, Raquel last_name: Assis - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Assis R, Kondrashov A, Koonin E, Kondrashov F. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 2008;24(10):475-478. doi:10.1016/j.tig.2008.08.003 apa: Assis, R., Kondrashov, A., Koonin, E., & Kondrashov, F. (2008). Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2008.08.003 chicago: Assis, Raquel, Alexey Kondrashov, Eugene Koonin, and Fyodor Kondrashov. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics. Elsevier, 2008. https://doi.org/10.1016/j.tig.2008.08.003. ieee: R. Assis, A. Kondrashov, E. Koonin, and F. Kondrashov, “Nested genes and increasing organizational complexity of metazoan genomes,” Trends in Genetics, vol. 24, no. 10. Elsevier, pp. 475–478, 2008. ista: Assis R, Kondrashov A, Koonin E, Kondrashov F. 2008. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 24(10), 475–478. mla: Assis, Raquel, et al. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics, vol. 24, no. 10, Elsevier, 2008, pp. 475–78, doi:10.1016/j.tig.2008.08.003. short: R. Assis, A. Kondrashov, E. Koonin, F. Kondrashov, Trends in Genetics 24 (2008) 475–478. date_created: 2018-12-11T11:49:08Z date_published: 2008-10-01T00:00:00Z date_updated: 2021-01-12T08:21:49Z day: '01' doi: 10.1016/j.tig.2008.08.003 extern: 1 intvolume: ' 24' issue: '10' month: '10' page: 475 - 478 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6743' quality_controlled: 0 status: public title: Nested genes and increasing organizational complexity of metazoan genomes type: journal_article volume: 24 year: '2008' ... --- _id: '9457' abstract: - lang: eng text: Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation. article_processing_charge: No article_type: letter_note author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Devin full_name: Coleman-Derr, Devin last_name: Coleman-Derr - first_name: Tracy full_name: Ballinger, Tracy last_name: Ballinger - first_name: Steven full_name: Henikoff, Steven last_name: Henikoff citation: ama: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 2008;456(7218):125-129. doi:10.1038/nature07324 apa: Zilberman, D., Coleman-Derr, D., Ballinger, T., & Henikoff, S. (2008). Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. Springer Nature. https://doi.org/10.1038/nature07324 chicago: Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” Nature. Springer Nature, 2008. https://doi.org/10.1038/nature07324. ieee: D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks,” Nature, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008. ista: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218), 125–129. mla: Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” Nature, vol. 456, no. 7218, Springer Nature, 2008, pp. 125–29, doi:10.1038/nature07324. short: D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129. date_created: 2021-06-04T11:49:32Z date_published: 2008-11-06T00:00:00Z date_updated: 2021-12-14T08:54:36Z day: '06' department: - _id: DaZi doi: 10.1038/nature07324 extern: '1' external_id: pmid: - '18815594' intvolume: ' 456' issue: '7218' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/ month: '11' oa: 1 oa_version: Submitted Version page: 125-129 pmid: 1 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 456 year: '2008' ... --- _id: '13423' abstract: - lang: eng text: Supraspheres (SS) composed of hundreds to thousands of metal nanoparticles (NPs) and crosslinked by dithiol linkers are assembled into larger structures, which are subsequently converted into nanoporous metals (NMs). Conversion is achieved by heating which removes organic molecules stabilizing the NPs and allows for NP fusion. Heating of SS solutions leads to NMs of overall macroscopic dimensions; localized radiation using collimated electron beam is used to prepare metallized surface micropatterns. Depending on the composition of supraspherical precursors, nanoporous materials composed of up to three metals can be obtained. Strategies for controlling pore size and nanoscale surface roughness of these materials are discussed. article_processing_charge: No article_type: original author: - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Timothy P. full_name: Gray, Timothy P. last_name: Gray - first_name: Paul J. full_name: Wesson, Paul J. last_name: Wesson - first_name: Benjamin D. full_name: Myers, Benjamin D. last_name: Myers - first_name: Vinayak P. full_name: Dravid, Vinayak P. last_name: Dravid - first_name: Stoyan K. full_name: Smoukov, Stoyan K. last_name: Smoukov - first_name: Bartosz A. full_name: Grzybowski, Bartosz A. last_name: Grzybowski citation: ama: Klajn R, Gray TP, Wesson PJ, et al. Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates. Advanced Functional Materials. 2008;18(18):2763-2769. doi:10.1002/adfm.200800293 apa: Klajn, R., Gray, T. P., Wesson, P. J., Myers, B. D., Dravid, V. P., Smoukov, S. K., & Grzybowski, B. A. (2008). Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates. Advanced Functional Materials. Wiley. https://doi.org/10.1002/adfm.200800293 chicago: Klajn, Rafal, Timothy P. Gray, Paul J. Wesson, Benjamin D. Myers, Vinayak P. Dravid, Stoyan K. Smoukov, and Bartosz A. Grzybowski. “Bulk Synthesis and Surface Patterning of Nanoporous Metals and Alloys from Supraspherical Nanoparticle Aggregates.” Advanced Functional Materials. Wiley, 2008. https://doi.org/10.1002/adfm.200800293. ieee: R. Klajn et al., “Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates,” Advanced Functional Materials, vol. 18, no. 18. Wiley, pp. 2763–2769, 2008. ista: Klajn R, Gray TP, Wesson PJ, Myers BD, Dravid VP, Smoukov SK, Grzybowski BA. 2008. Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates. Advanced Functional Materials. 18(18), 2763–2769. mla: Klajn, Rafal, et al. “Bulk Synthesis and Surface Patterning of Nanoporous Metals and Alloys from Supraspherical Nanoparticle Aggregates.” Advanced Functional Materials, vol. 18, no. 18, Wiley, 2008, pp. 2763–69, doi:10.1002/adfm.200800293. short: R. Klajn, T.P. Gray, P.J. Wesson, B.D. Myers, V.P. Dravid, S.K. Smoukov, B.A. Grzybowski, Advanced Functional Materials 18 (2008) 2763–2769. date_created: 2023-08-01T10:30:57Z date_published: 2008-09-23T00:00:00Z date_updated: 2023-08-08T11:16:28Z day: '23' doi: 10.1002/adfm.200800293 extern: '1' intvolume: ' 18' issue: '18' keyword: - Electrochemistry - Condensed Matter Physics - Biomaterials - Electronic - Optical and Magnetic Materials language: - iso: eng month: '09' oa_version: None page: 2763-2769 publication: Advanced Functional Materials publication_identifier: eissn: - 1616-3028 issn: - 1616-301X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2008' ... --- _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' ...