--- _id: '3914' abstract: - lang: eng text: We compare the performances of established means of character selection for discriminant analysis in species distinction with a combination procedure for finding the optimal character combination (minimum classification error, minimum number of required characters), using morphometric data sets from the ant genera Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character selection as well as forward selection, backward elimination and stepwise selection of discriminant analysis. The combination procedure is clearly superior to the established methods of character selection, and is widely applicable. author: - first_name: Karl full_name: Moder, Karl last_name: Moder - first_name: Birgit full_name: Schlick Steiner, Birgit last_name: Schlick Steiner - first_name: Florian full_name: Steiner, Florian last_name: Steiner - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Erhard full_name: Christian, Erhard last_name: Christian - first_name: Bernhard full_name: Seifert, Bernhard last_name: Seifert citation: ama: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 2006;45(1):82-87. doi:10.1111/j.1439-0469.2006.00372.x' apa: 'Moder, K., Schlick Steiner, B., Steiner, F., Cremer, S., Christian, E., & Seifert, B. (2006). Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0469.2006.00372.x' chicago: 'Moder, Karl, Birgit Schlick Steiner, Florian Steiner, Sylvia Cremer, Erhard Christian, and Bernhard Seifert. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1439-0469.2006.00372.x.' ieee: 'K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, and B. Seifert, “Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study,” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1. Wiley-Blackwell, pp. 82–87, 2006.' ista: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. 2006. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 45(1), 82–87.' mla: 'Moder, Karl, et al. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1, Wiley-Blackwell, 2006, pp. 82–87, doi:10.1111/j.1439-0469.2006.00372.x.' short: K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, B. Seifert, Journal of Zoological Systematics and Evolutionary Research 45 (2006) 82–87. date_created: 2018-12-11T12:05:52Z date_published: 2006-08-29T00:00:00Z date_updated: 2021-01-12T07:53:10Z day: '29' doi: 10.1111/j.1439-0469.2006.00372.x extern: '1' intvolume: ' 45' issue: '1' language: - iso: eng month: '08' oa_version: None page: 82 - 87 publication: Journal of Zoological Systematics and Evolutionary Research publication_status: published publisher: Wiley-Blackwell publist_id: '2241' status: public title: 'Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2006' ... --- _id: '3913' abstract: - lang: eng text: Many invasive ant species, such as the Argentine ant or the red imported fire ant, have huge colonies with thousands of mass-foraging workers, which quickly monopolise resources and therefore represent a considerable threat to the native ant fauna. Cardiocondyla obscurior and several other species of this myrmicine genus have similarly been transferred throughout the tropics by human activities. However, because their colonies are tiny and workers forage solitarily, Cardiocondyla are often not recognized as successful invaders. Here, we document that the life history of Cardiocondyla closely resembles that of the more conspicuous tramp species, with polygyny, intranidal mating, budding, worker sterility, low genetic variability, and possibly also unicoloniality. Given that introduced Cardiocondyla may locally reach a very high population density, the effects of these stealthy invaders on the native arthropod fauna should receive more attention. author: - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Norbert full_name: Eckl, Norbert last_name: Eckl - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf citation: ama: 'Heinze J, Cremer S, Eckl N, Schrempf A. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 2006;53(1):1-7. doi:10.1007/s00040-005-0847-4' apa: 'Heinze, J., Cremer, S., Eckl, N., & Schrempf, A. (2006). Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. Springer. https://doi.org/10.1007/s00040-005-0847-4' chicago: 'Heinze, Jürgen, Sylvia Cremer, Norbert Eckl, and Alexandra Schrempf. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux. Springer, 2006. https://doi.org/10.1007/s00040-005-0847-4.' ieee: 'J. Heinze, S. Cremer, N. Eckl, and A. Schrempf, “Stealthy invaders: the biology of Cardiocondyla tramp ants,” Insectes Sociaux, vol. 53, no. 1. Springer, pp. 1–7, 2006.' ista: 'Heinze J, Cremer S, Eckl N, Schrempf A. 2006. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 53(1), 1–7.' mla: 'Heinze, Jürgen, et al. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux, vol. 53, no. 1, Springer, 2006, pp. 1–7, doi:10.1007/s00040-005-0847-4.' short: J. Heinze, S. Cremer, N. Eckl, A. Schrempf, Insectes Sociaux 53 (2006) 1–7. date_created: 2018-12-11T12:05:51Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T07:53:09Z day: '01' doi: 10.1007/s00040-005-0847-4 extern: '1' intvolume: ' 53' issue: '1' language: - iso: eng month: '02' oa_version: None page: 1 - 7 publication: Insectes Sociaux publication_status: published publisher: Springer publist_id: '2240' status: public title: 'Stealthy invaders: the biology of Cardiocondyla tramp ants' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2006' ... --- _id: '3932' abstract: - lang: eng text: 'OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and tissue content of EGFR has been directly associated with poor prognosis in patients with ovarian cancer. The uPA system plays a role in pericellular proteolysis, cell migration, invasion, and is over-expressed in ovarian cancer. This study explored the effects of EGF on uPAR expression in the ovarian cancer cell line OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration assay, time-lapse video microscopy, real-time PCR, assays for cellular binding of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well as EGF-stimulated cells, is present only in the intact, not the cleaved, form. Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas non-occupied receptor sites were not increased. In addition, EGF treatment resulted in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased internalization of uPAR, since the complex is internalized together with uPAR. Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression of uPAR. In addition, we found an immediate increase of uPAR after exposing the cells to EGF and this was accompanied by a transient increase of cell migration. The increase of cell surface uPAR in response to EGF is accompanied by increased release of the soluble form of uPAR (suPAR) to the medium as well as by increased cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis inhibitor colchicine even though cell migration was inhibited, suggesting that the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased cell surface uPAR in response to EGF stimulation results from mobilization of uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and decreased internalization and degradation of uPAR. Both the anti-uPAR antibody R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa inhibited cell migration in response to uPA as well as to EGF, suggesting that EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.' author: - first_name: Emir full_name: Henic, Emir last_name: Henic - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Stefan full_name: Hansson, Stefan last_name: Hansson - first_name: Gunilla full_name: Høyer-Hansen, Gunilla last_name: Høyer Hansen - first_name: Bertil full_name: Casslén, Bertil last_name: Casslén citation: ama: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038 apa: Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006). EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038 chicago: Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology. Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038. ieee: E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp. 28–39, 2006. ista: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 101(1), 28–39. mla: Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology, vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038. short: E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic Oncology 101 (2006) 28–39. date_created: 2018-12-11T12:05:57Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:53:17Z day: '01' doi: 10.1016/j.ygyno.2005.09.038 extern: 1 intvolume: ' 101' issue: '1' month: '04' page: 28 - 39 publication: Gynecologic Oncology publication_status: published publisher: Elsevier publist_id: '2194' quality_controlled: 0 status: public title: EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor type: journal_article volume: 101 year: '2006' ... --- _id: '3978' abstract: - lang: eng text: Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. author: - first_name: Yih full_name: Ban, Yih-En Andrew last_name: Ban - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph - first_name: Pei full_name: Zhou, Pei last_name: Zhou - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 2006;62(4):852-864. doi:10.1002/prot.20811' apa: 'Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811' chicago: 'Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.' ieee: 'Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality of NMR structures by local density of protons,” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.' ista: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 62(4), 852–864.' mla: 'Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.' short: 'Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function and Bioinformatics 62 (2006) 852–864.' date_created: 2018-12-11T12:06:14Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T07:53:36Z day: '01' doi: 10.1002/prot.20811 extern: 1 intvolume: ' 62' issue: '4' month: '03' page: 852 - 864 publication: 'Proteins: Structure, Function and Bioinformatics' publication_status: published publisher: Wiley-Blackwell publist_id: '2146' quality_controlled: 0 status: public title: Evaluating the quality of NMR structures by local density of protons type: journal_article volume: 62 year: '2006' ... --- _id: '3979' abstract: - lang: eng text: Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion. author: - first_name: Yih full_name: Ban, Yih-En Andrew last_name: Ban - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph citation: ama: Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes. Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957 apa: Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957 chicago: Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957. ieee: Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006. ista: Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein complexes. Journal of the ACM. 53(3), 361–378. mla: Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957. short: Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378. date_created: 2018-12-11T12:06:14Z date_published: 2006-05-01T00:00:00Z date_updated: 2021-01-12T07:53:37Z day: '01' doi: 10.1145/1147954.1147957 extern: 1 intvolume: ' 53' issue: '3' month: '05' page: 361 - 378 publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '2147' quality_controlled: 0 status: public title: Interface surfaces for protein-protein complexes type: journal_article volume: 53 year: '2006' ... --- _id: '3980' abstract: - lang: eng text: Given a smoothly embedded 2-manifold in R-3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking. author: - first_name: Pankaj full_name: Agarwal, Pankaj K last_name: Agarwal - 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: Yusu full_name: Wang, Yusu last_name: Wang citation: ama: Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 2006;36(4):553-572. doi:10.1007/s00454-006-1265-8 apa: Agarwal, P., Edelsbrunner, H., Harer, J., & Wang, Y. (2006). Extreme elevation on a 2-manifold. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1265-8 chicago: Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry. Springer, 2006. https://doi.org/10.1007/s00454-006-1265-8. ieee: P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on a 2-manifold,” Discrete & Computational Geometry, vol. 36, no. 4. Springer, pp. 553–572, 2006. ista: Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 36(4), 553–572. mla: Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry, vol. 36, no. 4, Springer, 2006, pp. 553–72, doi:10.1007/s00454-006-1265-8. short: P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete & Computational Geometry 36 (2006) 553–572. date_created: 2018-12-11T12:06:15Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:53:38Z day: '01' doi: 10.1007/s00454-006-1265-8 extern: 1 intvolume: ' 36' issue: '4' month: '12' page: 553 - 572 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '2148' quality_controlled: 0 status: public title: Extreme elevation on a 2-manifold type: journal_article volume: 36 year: '2006' ... --- _id: '4345' abstract: - lang: eng text: Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library 2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt, wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken. Ferner werden neue Anforderungen an Bibliothekare diskutiert. author: - first_name: Patrick full_name: Patrick Danowski id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 - first_name: Lambert full_name: Heller,Lambert last_name: Heller citation: ama: Danowski P, Heller L. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. 2006;40(11):1250-1271. doi:424 apa: Danowski, P., & Heller, L. (2006). Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. Zentral- und Landesbibliothek Berlin. https://doi.org/424 chicago: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” Bibliotheksdienst. Zentral- und Landesbibliothek Berlin, 2006. https://doi.org/424. ieee: P. Danowski and L. Heller, “Bibliothek 2.0 - Die Bibliothek der Zukunft?,” Bibliotheksdienst, vol. 40, no. 11. Zentral- und Landesbibliothek Berlin, pp. 1250–1271, 2006. ista: Danowski P, Heller L. 2006. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst. 40(11), 1250–1271. mla: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der Zukunft?” Bibliotheksdienst, vol. 40, no. 11, Zentral- und Landesbibliothek Berlin, 2006, pp. 1250–71, doi:424. short: P. Danowski, L. Heller, Bibliotheksdienst 40 (2006) 1250–1271. date_created: 2018-12-11T12:08:23Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:17Z day: '01' doi: '424' extern: 1 intvolume: ' 40' issue: '11' main_file_link: - open_access: '0' url: http://www.zlb.de/aktivitaeten/bd_neu/heftinhalte2006/DigitaleBib011106.pdf month: '01' page: 1250 - 1271 publication: Bibliotheksdienst publication_status: published publisher: Zentral- und Landesbibliothek Berlin publist_id: '1229' quality_controlled: 0 status: public title: Bibliothek 2.0 - Die Bibliothek der Zukunft? type: journal_article volume: 40 year: '2006' ... --- _id: '4352' abstract: - lang: eng text: 'Anopheles darlingi is the primary malaria vector in Latin America, and is especially important in Amazonian Brazil. Historically, control efforts have been focused on indoor house spraying using a variety of insecticides, but since the mid-1990s there has been a shift to patient treatment and focal insecticide fogging. Anopheles darlingi was believed to have been significantly reduced in a gold-mining community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated from some districts of the city of Belem (the capital of Para State) in 1968 to reduce malaria, populations around the water protection area in the eastern district were treated only briefly. To investigate the population structure of An. darlingi including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals from seven locations in Brazil: three in Amapa State, three in Para State, and one in Mato Grosso State. Allelic diversity and mean expected heterozygosity were high for all populations (mean number alleles/locus and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between locations. Significant heterozygote deficits were associated with linkage disequilibrium, most likely due to either the Wahlund effect or selection. We found no evidence for a population bottleneck in Peixoto, possibly because the reduction was not extreme enough to be detected. Overall estimates of long-term N(e) varied from 92.4 individuals under the linkage disequilibrium model to infinity under the heterozygote excess model. Fixation indices and analysis of molecular variance demonstrated significant differentiation between locations north and south of the Amazon River, suggesting a degree of genetic isolation between them, attributed to isolation by distance.' author: - first_name: Jan full_name: Conn, Jan E last_name: Conn - first_name: Joseph full_name: Vineis, Joseph H last_name: Vineis - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: David full_name: Onyabe, David Y last_name: Onyabe - first_name: Richard full_name: Wilkerson, Richard C last_name: Wilkerson - first_name: Marinete full_name: Povoa, Marinete M last_name: Povoa citation: ama: Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. 2006;74(5):798-806. apa: Conn, J., Vineis, J., Bollback, J. P., Onyabe, D., Wilkerson, R., & Povoa, M. (2006). Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene. chicago: Conn, Jan, Joseph Vineis, Jonathan P Bollback, David Onyabe, Richard Wilkerson, and Marinete Povoa. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal of Tropical Medicine and Hygiene. American Society of Tropical Medicine and Hygiene, 2006. ieee: J. Conn, J. Vineis, J. P. Bollback, D. Onyabe, R. Wilkerson, and M. Povoa, “Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil,” The American Journal of Tropical Medicine and Hygiene, vol. 74, no. 5. American Society of Tropical Medicine and Hygiene, pp. 798–806, 2006. ista: Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. 2006. Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene. 74(5), 798–806. mla: Conn, Jan, et al. “Population Structure of the Malaria Vector Anopheles Darlingi in a Malaria-Endemic Region of Eastern Amazonian Brazil.” The American Journal of Tropical Medicine and Hygiene, vol. 74, no. 5, American Society of Tropical Medicine and Hygiene, 2006, pp. 798–806. short: J. Conn, J. Vineis, J.P. Bollback, D. Onyabe, R. Wilkerson, M. Povoa, The American Journal of Tropical Medicine and Hygiene 74 (2006) 798–806. date_created: 2018-12-11T12:08:25Z date_published: 2006-05-01T00:00:00Z date_updated: 2021-01-12T07:56:20Z day: '01' extern: 1 intvolume: ' 74' issue: '5' main_file_link: - open_access: '0' url: http://www.ajtmh.org/content/74/5/798.full month: '05' page: 798 - 806 publication: The American Journal of Tropical Medicine and Hygiene publication_status: published publisher: American Society of Tropical Medicine and Hygiene publist_id: '1108' quality_controlled: 0 status: public title: Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil type: journal_article volume: 74 year: '2006' ... --- _id: '4351' abstract: - lang: eng text: 'BACKGROUND: Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS: SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. CONCLUSION: Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.' author: - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: 'Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 2006;7. doi:10.1186/1471-2105-7-88' apa: 'Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-7-88' chicago: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics. BioMed Central, 2006. https://doi.org/10.1186/1471-2105-7-88.' ieee: 'J. P. Bollback, “SIMMAP: stochastic character mapping of discrete traits on phylogenies,” BMC Bioinformatics, vol. 7. BioMed Central, 2006.' ista: 'Bollback JP. 2006. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 7.' mla: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics, vol. 7, BioMed Central, 2006, doi:10.1186/1471-2105-7-88.' short: J.P. Bollback, BMC Bioinformatics 7 (2006). date_created: 2018-12-11T12:08:25Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:20Z day: '01' doi: 10.1186/1471-2105-7-88 extern: 1 intvolume: ' 7' license: https://creativecommons.org/licenses/by/4.0/ month: '01' publication: BMC Bioinformatics publication_status: published publisher: BioMed Central publist_id: '1109' quality_controlled: 0 status: public title: 'SIMMAP: stochastic character mapping of discrete traits on phylogenies' 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: 7 year: '2006' ... --- _id: '3180' abstract: - lang: eng text: 'One of the most exciting advances in early vision has been the development of efficient energy minimization algorithms. Many early vision tasks require labeling each pixel with some quantity such as depth or texture. While many such problems can be elegantly expressed in the language of Markov Random Fields (MRF''s), the resulting energy minimization problems were widely viewed as intractable. Recently, algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: for example, such methods form the basis for almost all the top-performing stereo methods. Unfortunately, most papers define their own energy function, which is minimized with a specific algorithm of their choice. As a result, the tradeoffs among different energy minimization algorithms are not well understood. In this paper we describe a set of energy minimization benchmarks, which we use to compare the solution quality and running time of several common energy minimization algorithms. We investigate three promising recent methods - graph cuts, LBP, and tree-reweighted message passing - as well as the well-known older iterated conditional modes (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching and interactive segmentation. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods with minimal overhead. We expect that the availability of our benchmarks and interface will make it significantly easier for vision researchers to adopt the best method for their specific problems. Benchmarks, code, results and images are available at http://vision.middlebury.edu/MRF.' author: - first_name: Richard full_name: Szeliski, Richard S last_name: Szeliski - first_name: Ramin full_name: Zabih, Ramin last_name: Zabih - first_name: Daniel full_name: Scharstein, Daniel last_name: Scharstein - first_name: Olga full_name: Veksler, Olga last_name: Veksler - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Aseem full_name: Agarwala, Aseem last_name: Agarwala - first_name: Marshall full_name: Tappen, Marshall F last_name: Tappen - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization methods for Markov random fields. In: Vol 3952. Springer; 2006:16-29. doi:10.1007/11744047_2' apa: 'Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala, A., … Rother, C. (2006). A comparative study of energy minimization methods for Markov random fields (Vol. 3952, pp. 16–29). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_2' chicago: Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative Study of Energy Minimization Methods for Markov Random Fields,” 3952:16–29. Springer, 2006. https://doi.org/10.1007/11744047_2. ieee: 'R. Szeliski et al., “A comparative study of energy minimization methods for Markov random fields,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3952, pp. 16–29.' ista: 'Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen M, Rother C. 2006. A comparative study of energy minimization methods for Markov random fields. ECCV: European Conference on Computer Vision vol. 3952, 16–29.' mla: Szeliski, Richard, et al. A Comparative Study of Energy Minimization Methods for Markov Random Fields. Vol. 3952, Springer, 2006, pp. 16–29, doi:10.1007/11744047_2. short: R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala, M. Tappen, C. Rother, in:, Springer, 2006, pp. 16–29. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:01:51Z date_published: 2006-05-03T00:00:00Z date_updated: 2021-01-12T07:41:37Z day: '03' doi: 10.1007/11744047_2 extern: 1 intvolume: ' 3952' main_file_link: - open_access: '0' url: http://research-srv.microsoft.com/pubs/67896/szsvkatr-eccv06.pdf month: '05' page: 16 - 29 publication_status: published publisher: Springer publist_id: '3499' quality_controlled: 0 status: public title: A comparative study of energy minimization methods for Markov random fields type: conference volume: 3952 year: '2006' ... --- _id: '3184' abstract: - lang: eng text: 'Algorithms for discrete energy minimization play a fundamental role for low-level vision. Known techniques include graph cuts, belief propagation (BP) and recently introduced tree-reweighted message passing (TRW). So far, the standard benchmark for their comparison has been a 4-connected grid-graph arising in pixel-labelling stereo. This minimization problem, however, has been largely solved: recent work shows that for many scenes TRW finds the global optimum. Furthermore, it is known that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions into account. We propose the problem of stereo with occlusions as a new test bed for minimization algorithms. This is a more challenging graph since it has much larger connectivity, and it also serves as a better stereo model. An attractive feature of this problem is that increased connectivity does not result in increased complexity of message passing algorithms. Indeed, one contribution of this paper is to show that sophisticated implementations of BP and TRW have the same time and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion of our experimental study is that for our problem graph cut outperforms both TRW and BP considerably. TRW achieves consistently a lower energy than BP. However, as connectivity increases the speed of convergence of TRW becomes slower. Unlike 4-connected grids, the difference between the energy of the best optimization method and the lower bound of TRW appears significant. This shows the hardness of the problem and motivates future research.' alternative_title: - LNCS author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Kolmogorov V, Rother C. Comparison of energy minimization algorithms for highly connected graphs. In: Vol 3952 LNCS. Springer; 2006:1-15. doi:10.1007/11744047_1' apa: 'Kolmogorov, V., & Rother, C. (2006). Comparison of energy minimization algorithms for highly connected graphs (Vol. 3952 LNCS, pp. 1–15). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_1' chicago: Kolmogorov, Vladimir, and Carsten Rother. “Comparison of Energy Minimization Algorithms for Highly Connected Graphs,” 3952 LNCS:1–15. Springer, 2006. https://doi.org/10.1007/11744047_1. ieee: 'V. Kolmogorov and C. Rother, “Comparison of energy minimization algorithms for highly connected graphs,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3952 LNCS, pp. 1–15.' ista: 'Kolmogorov V, Rother C. 2006. Comparison of energy minimization algorithms for highly connected graphs. ECCV: European Conference on Computer Vision, LNCS, vol. 3952 LNCS, 1–15.' mla: Kolmogorov, Vladimir, and Carsten Rother. Comparison of Energy Minimization Algorithms for Highly Connected Graphs. Vol. 3952 LNCS, Springer, 2006, pp. 1–15, doi:10.1007/11744047_1. short: V. Kolmogorov, C. Rother, in:, Springer, 2006, pp. 1–15. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:01:52Z date_published: 2006-05-03T00:00:00Z date_updated: 2021-01-12T07:41:39Z day: '03' doi: 10.1007/11744047_1 extern: 1 main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf month: '05' page: 1 - 15 publication_status: published publisher: Springer publist_id: '3498' quality_controlled: 0 status: public title: Comparison of energy minimization algorithms for highly connected graphs type: conference volume: 3952 LNCS year: '2006' ... --- _id: '3185' abstract: - lang: eng text: This paper describes models and algorithms for the real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from color/contrast or from stereo alone is known to be error-prone. Here, color, contrast, and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended six-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive color model that is learned on-the-fly and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead, the stereo match likelihood is marginalized over disparities to evaluate foreground and background hypotheses and then fused with a contrast-sensitive color model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than either stereo or color/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2006;28(9):1480-1492. doi:10.1109/TPAMI.2006.193 apa: Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2006). Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.193 chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Probabilistic Fusion of Stereo with Color and Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.193. ieee: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Probabilistic fusion of stereo with color and contrast for bilayer segmentation,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 9. IEEE, pp. 1480–1492, 2006. ista: Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2006. Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. 28(9), 1480–1492. mla: Kolmogorov, Vladimir, et al. “Probabilistic Fusion of Stereo with Color and Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 9, IEEE, 2006, pp. 1480–92, doi:10.1109/TPAMI.2006.193. short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 28 (2006) 1480–1492. date_created: 2018-12-11T12:01:53Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T07:41:39Z day: '01' doi: 10.1109/TPAMI.2006.193 extern: 1 intvolume: ' 28' issue: '9' main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf month: '09' page: 1480 - 1492 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '3496' quality_controlled: 0 status: public title: Probabilistic fusion of stereo with color and contrast for bilayer segmentation type: journal_article volume: 28 year: '2006' ... --- _id: '3186' abstract: - lang: eng text: We introduce a new approach to modelling gradient flows of contours and surfaces. While standard variational methods (e.g. level sets) compute local interface motion in a differential fashion by estimating local contour velocity via energy derivatives, we propose to solve surface evolution PDEs by explicitly estimating integral motion of the whole surface. We formulate an optimization problem directly based on an integral characterization of gradient flow as an infinitesimal move of the (whole) surface giving the largest energy decrease among all moves of equal size. We show that this problem can be efficiently solved using recent advances in algorithms for global hypersurface optimization [4, 2, 11]. In particular, we employ the geo-cuts method [4] that uses ideas from integral geometry to represent continuous surfaces as cuts on discrete graphs. The resulting interface evolution algorithm is validated on some 2D and 3D examples similar to typical demonstrations of level-set methods. Our method can compute gradient flows of hypersurfaces with respect to a fairly general class of continuous functional and it is flexible with respect to distance metrics on the space of contours/surfaces. Preliminary tests for standard L2 distance metric demonstrate numerical stability, topological changes and an absence of any oscillatory motion. alternative_title: - LNCS author: - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Daniel full_name: Cremers, Daniel last_name: Cremers - first_name: Andrew full_name: Delong, Andrew last_name: Delong citation: ama: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. An integral solution to surface evolution PDEs via geo cuts. In: Vol 3953. Springer; 2006:409-422. doi:10.1007/11744078_32' apa: 'Boykov, Y., Kolmogorov, V., Cremers, D., & Delong, A. (2006). An integral solution to surface evolution PDEs via geo cuts (Vol. 3953, pp. 409–422). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744078_32' chicago: Boykov, Yuri, Vladimir Kolmogorov, Daniel Cremers, and Andrew Delong. “An Integral Solution to Surface Evolution PDEs via Geo Cuts,” 3953:409–22. Springer, 2006. https://doi.org/10.1007/11744078_32. ieee: 'Y. Boykov, V. Kolmogorov, D. Cremers, and A. Delong, “An integral solution to surface evolution PDEs via geo cuts,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3953, pp. 409–422.' ista: 'Boykov Y, Kolmogorov V, Cremers D, Delong A. 2006. An integral solution to surface evolution PDEs via geo cuts. ECCV: European Conference on Computer Vision, LNCS, vol. 3953, 409–422.' mla: Boykov, Yuri, et al. An Integral Solution to Surface Evolution PDEs via Geo Cuts. Vol. 3953, Springer, 2006, pp. 409–22, doi:10.1007/11744078_32. short: Y. Boykov, V. Kolmogorov, D. Cremers, A. Delong, in:, Springer, 2006, pp. 409–422. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:01:53Z date_published: 2006-04-28T00:00:00Z date_updated: 2021-01-12T07:41:39Z day: '28' doi: 10.1007/11744078_32 extern: 1 intvolume: ' 3953' month: '04' page: 409 - 422 publication_status: published publisher: Springer publist_id: '3497' quality_controlled: 0 status: public title: An integral solution to surface evolution PDEs via geo cuts type: conference volume: 3953 year: '2006' ... --- _id: '3404' alternative_title: - Manuals in Biomedical Research author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Ravi full_name: Sawhney, Ravi K last_name: Sawhney - first_name: Martin full_name: Stark, Martin last_name: Stark - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: 'Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: Techniques in Microscopy for Biomedical Applications. Vol 2. World Scientific Publishing; 2006:213-284.' apa: Janovjak, H. L., Sawhney, R., Stark, M., & Mueller, D. (2006). Atomic force microscopy. In Techniques in Microscopy for Biomedical Applications (Vol. 2, pp. 213–284). World Scientific Publishing. chicago: Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic Force Microscopy.” In Techniques in Microscopy for Biomedical Applications, 2:213–84. World Scientific Publishing, 2006. ieee: H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,” in Techniques in Microscopy for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp. 213–284. ista: 'Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy. In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical Research, vol. 2, 213–284.' mla: Janovjak, Harald L., et al. “Atomic Force Microscopy.” Techniques in Microscopy for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp. 213–84. short: H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284. date_created: 2018-12-11T12:03:09Z date_published: 2006-09-28T00:00:00Z date_updated: 2021-01-12T07:43:15Z day: '28' extern: 1 intvolume: ' 2' month: '09' page: 213 - 284 publication: Techniques in Microscopy for Biomedical Applications publication_status: published publisher: World Scientific Publishing publist_id: '2998' quality_controlled: 0 status: public title: Atomic force microscopy type: book_chapter volume: 2 year: '2006' ... --- _id: '3413' abstract: - lang: eng text: |- Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids. Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded. We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state. author: - first_name: Max full_name: Kessler, Max last_name: Kessler - first_name: Kay full_name: Gottschalk, Kay E last_name: Gottschalk - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller - first_name: Hermann full_name: Gaub, Hermann last_name: Gaub citation: ama: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. 2006;357(2):644-654. doi:10.1016/j.jmb.2005.12.065 apa: Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., & Gaub, H. (2006). Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.12.065 chicago: Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.12.065. ieee: M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin folds into the membrane against an external force,” Journal of Molecular Biology, vol. 357, no. 2. Elsevier, pp. 644–654, 2006. ista: Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. 357(2), 644–654. mla: Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal of Molecular Biology, vol. 357, no. 2, Elsevier, 2006, pp. 644–54, doi:10.1016/j.jmb.2005.12.065. short: M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of Molecular Biology 357 (2006) 644–654. date_created: 2018-12-11T12:03:12Z date_published: 2006-03-24T00:00:00Z date_updated: 2021-01-12T07:43:18Z day: '24' doi: 10.1016/j.jmb.2005.12.065 extern: 1 intvolume: ' 357' issue: '2' month: '03' page: 644 - 654 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '2988' quality_controlled: 0 status: public title: Bacteriorhodopsin folds into the membrane against an external force type: journal_article volume: 357 year: '2006' ... --- _id: '3414' abstract: - lang: eng text: Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter. author: - first_name: Alexej full_name: Kedrov, Alexej last_name: Kedrov - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Christine full_name: Ziegler, Christine last_name: Ziegler - first_name: Werner full_name: Kühlbrandt, Werner last_name: Kühlbrandt - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 2006;355(1):2-8. doi:10.1016/j.jmb.2005.10.028 apa: Kedrov, A., Janovjak, H. L., Ziegler, C., Kühlbrandt, W., & Mueller, D. (2006). Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.10.028 chicago: Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt, and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.10.028. ieee: A. Kedrov, H. L. Janovjak, C. Ziegler, W. Kühlbrandt, and D. Mueller, “Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli,” Journal of Molecular Biology, vol. 355, no. 1. Elsevier, pp. 2–8, 2006. ista: Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. 2006. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 355(1), 2–8. mla: Kedrov, Alexej, et al. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology, vol. 355, no. 1, Elsevier, 2006, pp. 2–8, doi:10.1016/j.jmb.2005.10.028. short: A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal of Molecular Biology 355 (2006) 2–8. date_created: 2018-12-11T12:03:12Z date_published: 2006-01-06T00:00:00Z date_updated: 2021-01-12T07:43:19Z day: '06' doi: 10.1016/j.jmb.2005.10.028 extern: 1 intvolume: ' 355' issue: '1' month: '01' page: 2 - 8 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '2987' quality_controlled: 0 status: public title: Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli type: journal_article volume: 355 year: '2006' ... --- _id: '3415' author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Alexej full_name: Kedrov, Alexej last_name: Kedrov - first_name: David full_name: Cisneros, David last_name: Cisneros - first_name: Tanuj full_name: Sapra, Tanuj K last_name: Sapra - first_name: Jens full_name: Struckmeier, Jens last_name: Struckmeier - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 2006;27:546-561. doi:10.1016/j.neurobiolaging.2005.03.031 apa: Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., & Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. Elsevier. https://doi.org/10.1016/j.neurobiolaging.2005.03.031 chicago: Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier, and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” Neurobiology of Aging. Elsevier, 2006. https://doi.org/10.1016/j.neurobiolaging.2005.03.031. ieee: H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller, “Imaging and detecting molecular interactions of single membrane proteins,” Neurobiology of Aging, vol. 27. Elsevier, pp. 546–561, 2006. ista: Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. 2006. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 27, 546–561. mla: Janovjak, Harald L., et al. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” Neurobiology of Aging, vol. 27, Elsevier, 2006, pp. 546–61, doi:10.1016/j.neurobiolaging.2005.03.031. short: H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller, Neurobiology of Aging 27 (2006) 546–561. date_created: 2018-12-11T12:03:12Z date_published: 2006-01-01T00:00:00Z date_updated: 2019-04-26T07:22:27Z day: '01' doi: 10.1016/j.neurobiolaging.2005.03.031 extern: 1 intvolume: ' 27' month: '01' page: 546 - 561 publication: Neurobiology of Aging publication_status: published publisher: Elsevier publist_id: '2986' quality_controlled: 0 status: public title: Imaging and detecting molecular interactions of single membrane proteins type: review volume: 27 year: '2006' ... --- _id: '3437' abstract: - lang: eng text: The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models. author: - first_name: Andrea full_name: Betancourt, Andrea J last_name: Betancourt - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: 'Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 2006;16(6):618-623. doi:10.1016/j.gde.2006.10.006' apa: 'Betancourt, A., & Bollback, J. P. (2006). Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2006.10.006' chicago: 'Betancourt, Andrea, and Jonathan P Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development. Elsevier, 2006. https://doi.org/10.1016/j.gde.2006.10.006.' ieee: 'A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution,” Current Opinion in Genetics & Development, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.' ista: 'Betancourt A, Bollback JP. 2006. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 16(6), 618–623.' mla: 'Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development, vol. 16, no. 6, Elsevier, 2006, pp. 618–23, doi:10.1016/j.gde.2006.10.006.' short: A. Betancourt, J.P. Bollback, Current Opinion in Genetics & Development 16 (2006) 618–623. date_created: 2018-12-11T12:03:19Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:43:27Z day: '01' doi: 10.1016/j.gde.2006.10.006 extern: 1 intvolume: ' 16' issue: '6' month: '12' page: 618 - 623 publication: Current Opinion in Genetics & Development publication_status: published publisher: Elsevier publist_id: '2963' quality_controlled: 0 status: public title: 'Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution' type: journal_article volume: 16 year: '2006' ... --- _id: '3431' abstract: - lang: eng text: Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses. author: - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: E. full_name: Schneidman, E. last_name: Schneidman - first_name: M. full_name: Berry, M. J. last_name: Berry - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4. apa: Tkačik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models for networks of real neurons. ArXiv. ArXiv. chicago: Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models for Networks of Real Neurons.” ArXiv. ArXiv, 2006. ieee: G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006. ista: Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks of real neurons. ArXiv, 1–4, . mla: Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4. short: G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4. date_created: 2018-12-11T12:03:18Z date_published: 2006-11-22T00:00:00Z date_updated: 2021-01-12T07:43:25Z day: '22' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/q-bio/0611072 month: '11' oa: 1 page: 1 - 4 publication: ArXiv publication_status: published publisher: ArXiv publist_id: '2969' quality_controlled: 0 status: public title: Ising models for networks of real neurons type: preprint year: '2006' ... --- _id: '3449' abstract: - lang: eng text: We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rhada full_name: Jagadeesan, Rhada last_name: Jagadeesan - first_name: Corin full_name: Pitcher, Corin last_name: Pitcher citation: ama: 'Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82. doi:10.1109/CSFW.2006.14' apa: 'Chatterjee, K., Jagadeesan, R., & Pitcher, C. (2006). Games for controls (pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. https://doi.org/10.1109/CSFW.2006.14' chicago: Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for Controls,” 70–82. IEEE, 2006. https://doi.org/10.1109/CSFW.2006.14. ieee: 'K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented at the CSF: Computer Security Foundations, 2006, pp. 70–82.' ista: 'Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer Security Foundations, 70–82.' mla: Chatterjee, Krishnendu, et al. Games for Controls. IEEE, 2006, pp. 70–82, doi:10.1109/CSFW.2006.14. short: K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82. conference: name: 'CSF: Computer Security Foundations' date_created: 2018-12-11T12:03:23Z date_published: 2006-07-31T00:00:00Z date_updated: 2021-01-12T07:43:32Z day: '31' doi: 10.1109/CSFW.2006.14 extern: 1 month: '07' page: 70 - 82 publication_status: published publisher: IEEE publist_id: '2938' quality_controlled: 0 status: public title: Games for controls type: conference year: '2006' ... --- _id: '3463' abstract: - lang: eng text: It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network. author: - first_name: Joseph full_name: Bischofberger, Joseph last_name: Bischofberger - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2' apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2' chicago: 'Bischofberger, Joseph, Dominique Engel, Michael Frotscher, and Peter M Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network. (Review).” Pflugers Archiv : European Journal of Physiology. Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.' ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review),” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–372, 2006.' ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. 453(3), 361–372.' mla: 'Bischofberger, Joseph, et al. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network. (Review).” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:10.1007/s00424-006-0093-2.' short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv : European Journal of Physiology 453 (2006) 361–372.' date_created: 2018-12-11T12:03:28Z date_published: 2006-12-01T00:00:00Z date_updated: 2019-04-26T07:22:28Z day: '01' doi: 10.1007/s00424-006-0093-2 extern: 1 intvolume: ' 453' issue: '3' month: '12' page: 361 - 372 publication: 'Pflugers Archiv : European Journal of Physiology' publication_status: published publisher: Springer publist_id: '2924' quality_controlled: 0 status: public title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review) type: review volume: 453 year: '2006' ... --- _id: '3499' abstract: - lang: eng text: 'We study infinite stochastic games played by n-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players’ goals are not necessarily conflicting), and undiscounted. We show that if each player has an upward-closed objective, then there exists an ε-Nash equilibrium in memoryless strategies, for every ε>0; and exact Nash equilibria need not exist. Upward-closure of an objective means that if a set Z of infinitely repeating states is winning, then all supersets of Z of infinitely repeating states are also winning. Memoryless strategies are strategies that are independent of history of plays and depend only on the current state. We also study the complexity of finding values (payoff profile) of an ε-Nash equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent games with upward-closed objectives for all players can be computed by computing ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives for all players and a polynomial procedure. As a consequence we establish that values of an ε-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME. ' acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR- 0234690, and by the SNSF under the Indo-Swiss Joint Research Programme. alternative_title: - 'LNCS ' author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Chatterjee K. Nash equilibrium for upward-closed objectives. In: Vol 4207. Springer; 2006:271-286. doi:10.1007/11874683_18' apa: 'Chatterjee, K. (2006). Nash equilibrium for upward-closed objectives (Vol. 4207, pp. 271–286). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_18' chicago: Chatterjee, Krishnendu. “Nash Equilibrium for Upward-Closed Objectives,” 4207:271–86. Springer, 2006. https://doi.org/10.1007/11874683_18. ieee: 'K. Chatterjee, “Nash equilibrium for upward-closed objectives,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 271–286.' ista: 'Chatterjee K. 2006. Nash equilibrium for upward-closed objectives. CSL: Computer Science Logic, LNCS , vol. 4207, 271–286.' mla: Chatterjee, Krishnendu. Nash Equilibrium for Upward-Closed Objectives. Vol. 4207, Springer, 2006, pp. 271–86, doi:10.1007/11874683_18. short: K. Chatterjee, in:, Springer, 2006, pp. 271–286. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:03:39Z date_published: 2006-09-28T00:00:00Z date_updated: 2021-01-12T07:43:52Z day: '28' doi: 10.1007/11874683_18 extern: 1 intvolume: ' 4207' month: '09' page: 271 - 286 publication_status: published publisher: Springer publist_id: '2888' quality_controlled: 0 status: public title: Nash equilibrium for upward-closed objectives type: conference volume: 4207 year: '2006' ... --- _id: '3500' abstract: - lang: eng text: The classical algorithm for solving Bu ̈chi games requires time O(n · m) for game graphs with n states and m edges. For game graphs with constant outdegree, the best known algorithm has running time O(n2/logn). We present two new algorithms for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more work than the classical algorithm, but runs in time O(n) on infinitely many graphs of constant outdegree on which the classical algorithm requires time O(n2). Second, we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n) ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically better than the classical algorithm if δ(n) = O(log n). acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610 and the SNSF under the Indo-Swiss Joint Research Programme. 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 - first_name: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: 'Chatterjee K, Henzinger TA, Piterman N. Algorithms for Büchi Games. In: ACM; 2006.' apa: 'Chatterjee, K., Henzinger, T. A., & Piterman, N. (2006). Algorithms for Büchi Games. Presented at the GDV: Games in Design and Verification, ACM.' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Algorithms for Büchi Games.” ACM, 2006. ieee: 'K. Chatterjee, T. A. Henzinger, and N. Piterman, “Algorithms for Büchi Games,” presented at the GDV: Games in Design and Verification, 2006.' ista: 'Chatterjee K, Henzinger TA, Piterman N. 2006. Algorithms for Büchi Games. GDV: Games in Design and Verification.' mla: Chatterjee, Krishnendu, et al. Algorithms for Büchi Games. ACM, 2006. short: K. Chatterjee, T.A. Henzinger, N. Piterman, in:, ACM, 2006. conference: name: 'GDV: Games in Design and Verification' date_created: 2018-12-11T12:03:39Z date_published: 2006-08-21T00:00:00Z date_updated: 2021-01-12T07:43:53Z day: '21' extern: 1 main_file_link: - open_access: '0' url: http://www.cs.le.ac.uk/people/np183/publications/2006/CHP06.pdf month: '08' publication_status: published publisher: ACM publist_id: '2887' quality_controlled: 0 status: public title: Algorithms for Büchi Games type: conference year: '2006' ... --- _id: '3510' abstract: - lang: eng text: Embodiments automatically generate an accurate network of watertight NURBS patches from polygonal models of objects while automatically detecting and preserving character lines thereon. These embodiments generate from an initial triangulation of the surface, a hierarchy of progressively coarser triangulations of the surface by performing a sequence of edge contractions using a greedy algorithm that selects edge contractions by their numerical properties. Operations are also performed to connect the triangulations in the hierarchy using homeomorphisms that preserve the topology of the initial triangulation in the coarsest triangulation. A desired quadrangulation of the surface can then be generated by homeomorphically mapping edges of a coarsest triangulation in the hierarchy back to the initial triangulation. This quadrangulation is topologically consistent with the initial triangulation and is defined by a plurality of quadrangular patches. These quadrangular patches are linked together by a (U, V) mesh that is guaranteed to be continuous at patch boundaries. A grid is then preferably fit to each of the quadrangles in the resulting quadrangulation by decomposing each of the quadrangles into k.sup.2 smaller quadrangles. A watertight NURBS model may be generated from the resulting quadrangulation. applicant: - Raindrop Geomagic, Inc. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ping full_name: Fu, Ping last_name: Fu - first_name: Dmitry full_name: Nekhayev, Dmitry last_name: Nekhayev - first_name: Michael full_name: Facello, Michael last_name: Facello - first_name: Steven full_name: Williams, Steven last_name: Williams citation: ama: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. 2006. apa: Edelsbrunner, H., Fu, P., Nekhayev, D., Facello, M., & Williams, S. (2006). Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. chicago: Edelsbrunner, Herbert, Ping Fu, Dmitry Nekhayev, Michael Facello, and Steven Williams. “Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism,” 2006. ieee: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, and S. Williams, “Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism.” 2006. ista: Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. 2006. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. mla: Edelsbrunner, Herbert, et al. Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism. 2006. short: H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, S. Williams, (2006). date_created: 2018-12-11T12:03:42Z date_published: 2006-02-07T00:00:00Z date_updated: 2022-01-05T12:58:26Z day: '07' extern: '1' ipc: G06F 7/60 ; G06F 17/10 ; G06F 101/00 ipn: US6996505B1 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US6996505 month: '02' oa: 1 oa_version: Published Version publication_date: 2006-02-07 publist_id: '2877' status: public title: Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2006' ... --- _id: '3511' abstract: - lang: eng text: 'Methods, apparatus and computer program products provide efficient techniques for designing and printing shells of hearing-aid devices with a high degree of quality assurance and reliability and with a reduced number of manual and time consuming production steps and operations. These techniques also preferably provide hearing-aid shells having internal volumes that can approach a maximum allowable ratio of internal volume relative to external volume. These high internal volumes facilitate the inclusion of hearing-aid electrical components having higher degrees of functionality and/or the use of smaller and less conspicuous hearing-aid shells. A preferred method includes operations to generate a watertight digital model of a hearing-aid shell by thickening a three-dimensional digital model of a shell surface in a manner that eliminates self-intersections and results in a thickened model having an internal volume that is a high percentage of an external volume of the model. ' acknowledgement: sold to Siemens and Phonak applicant: - Phonak AG article_processing_charge: No author: - first_name: Ping full_name: Fu, Ping last_name: Fu - first_name: Dmitry full_name: Nekhayev, Dmitry last_name: Nekhayev - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Fu P, Nekhayev D, Edelsbrunner H. Manufacturing methods and systems for rapid production of hearing-aid shells. 2006. apa: Fu, P., Nekhayev, D., & Edelsbrunner, H. (2006). Manufacturing methods and systems for rapid production of hearing-aid shells. chicago: Fu, Ping, Dmitry Nekhayev, and Herbert Edelsbrunner. “Manufacturing Methods and Systems for Rapid Production of Hearing-Aid Shells,” 2006. ieee: P. Fu, D. Nekhayev, and H. Edelsbrunner, “Manufacturing methods and systems for rapid production of hearing-aid shells.” 2006. ista: Fu P, Nekhayev D, Edelsbrunner H. 2006. Manufacturing methods and systems for rapid production of hearing-aid shells. mla: Fu, Ping, et al. Manufacturing Methods and Systems for Rapid Production of Hearing-Aid Shells. 2006. short: P. Fu, D. Nekhayev, H. Edelsbrunner, (2006). date_created: 2018-12-11T12:03:43Z date_published: 2006-05-23T00:00:00Z date_updated: 2022-01-05T13:03:56Z day: '23' extern: '1' ipc: G06F 9/00 ipn: US7050876B1 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US7050876B1 month: '05' oa: 1 oa_version: Published Version publication_date: 2006-05-23 publist_id: '2876' status: public title: Manufacturing methods and systems for rapid production of hearing-aid shells type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2006' ... --- _id: '3512' abstract: - lang: eng text: Methods, apparatus and computer program products provide efficient techniques for reconstructing surfaces from data point sets. These techniques include reconstructing surfaces from sets of scanned data points that have preferably undergone preprocessing operations to improve their quality by, for example, reducing noise and removing outliers. These techniques include reconstructing a dense and locally two-dimensionally distributed 3D point set (e.g., point cloud) by merging stars in two-dimensional weighted Delaunay triangulations within estimated tangent planes. The techniques include determining a plurality of stars from a plurality of points p.sub.i in a 3D point set S that at least partially describes the 3D surface, by projecting the plurality of points p.sub.i onto planes T.sub.i that are each estimated to be tangent about a respective one of the plurality of points p.sub.i. The plurality of stars are then merged into a digital model of the 3D surface. applicant: - Geomagic Inc. article_processing_charge: No author: - first_name: Yates full_name: Fletcher, Yates last_name: Fletcher - first_name: Tobias full_name: Gloth, Tobias last_name: Gloth - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ping full_name: Fu, Ping last_name: Fu citation: ama: Fletcher Y, Gloth T, Edelsbrunner H, Fu P. Method, apparatus and computer products that reconstruct surfaces from data points. 2006. apa: Fletcher, Y., Gloth, T., Edelsbrunner, H., & Fu, P. (2006). Method, apparatus and computer products that reconstruct surfaces from data points. chicago: Fletcher, Yates, Tobias Gloth, Herbert Edelsbrunner, and Ping Fu. “Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points,” 2006. ieee: Y. Fletcher, T. Gloth, H. Edelsbrunner, and P. Fu, “Method, apparatus and computer products that reconstruct surfaces from data points.” 2006. ista: Fletcher Y, Gloth T, Edelsbrunner H, Fu P. 2006. Method, apparatus and computer products that reconstruct surfaces from data points. mla: Fletcher, Yates, et al. Method, Apparatus and Computer Products That Reconstruct Surfaces from Data Points. 2006. short: Y. Fletcher, T. Gloth, H. Edelsbrunner, P. Fu, (2006). date_created: 2018-12-11T12:03:43Z date_published: 2006-04-04T00:00:00Z date_updated: 2022-01-05T14:00:00Z day: '04' extern: '1' ipc: ' G06T17/20 ; B33Y50/00' ipn: US7023432B2 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US7023432B2 month: '04' oa: 1 oa_version: Published Version publication_date: 2006-04-04 publist_id: '2875' status: public title: Method, apparatus and computer products that reconstruct surfaces from data points type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2006' ... --- _id: '3545' abstract: - lang: eng text: The functional organization of the basal ganglia ( BG) is often defined according to one of two opposing schemes. The first proposes multiple, essentially independent channels of information processing. The second posits convergence and lateral integration of striatal channels at the level of the globus pallidus ( GP). We tested the hypothesis that these proposed aspects of functional connectivity within the striatopallidal axis are dynamic and related to brain state. Local field potentials ( LFPs) were simultaneously recorded from multiple sites in striatum and GP in anesthetized rats during slow-wave activity( SWA) and during global activation evoked by sensory stimulation. Functional connectivity was inferred from comparative analyses of the internuclear and intranuclear coherence between bipolar derivations of LFPs. During prominent SWA, as shown in the electrocorticogram and local field potentials in the basal ganglia, intranuclear coherence, and, thus, lateral functional connectivity within striatum or globus pallidus was relatively weak. Furthermore, the temporal coupling of LFPs recorded across these two nuclei involved functional convergence at the level of GP. Global activation, indicated by a loss of SWA, was accompanied by a rapid functional reorganization of the striatopallidal axis. Prominent lateral functional connectivity developed within GP and, to a significantly more constrained spatial extent, striatum. Additionally, functional convergence on GP was no longer apparent, despite increased internuclear coherence. These data demonstrate that functional connectivity within the BG is highly dynamic and suggest that the relative expression of organizational principles, such as parallel, independent processing channels, striatopallidal convergence, and lateral integration within BG nuclei, is dependent on brain state. author: - first_name: Peter full_name: Magill,Peter J last_name: Magill - first_name: Alek full_name: Pogosyan,Alek last_name: Pogosyan - first_name: Andrew full_name: Sharott,Andrew last_name: Sharott - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: John full_name: Bolam, John Paul last_name: Bolam - first_name: Peter full_name: Brown,Peter last_name: Brown citation: ama: Magill P, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P. Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo. Journal of Neuroscience. 2006;26(23):6318-6329. doi:10.1523/​JNEUROSCI.0620-06.2006 apa: Magill, P., Pogosyan, A., Sharott, A., Csicsvari, J. L., Bolam, J., & Brown, P. (2006). Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/​JNEUROSCI.0620-06.2006 chicago: Magill, Peter, Alek Pogosyan, Andrew Sharott, Jozsef L Csicsvari, John Bolam, and Peter Brown. “Changes in Functional Connectivity within the Rat Striatopallidal Axis during Global Brain Activation in Vivo.” Journal of Neuroscience. Society for Neuroscience, 2006. https://doi.org/10.1523/​JNEUROSCI.0620-06.2006. ieee: P. Magill, A. Pogosyan, A. Sharott, J. L. Csicsvari, J. Bolam, and P. Brown, “Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo,” Journal of Neuroscience, vol. 26, no. 23. Society for Neuroscience, pp. 6318–6329, 2006. ista: Magill P, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P. 2006. Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo. Journal of Neuroscience. 26(23), 6318–6329. mla: Magill, Peter, et al. “Changes in Functional Connectivity within the Rat Striatopallidal Axis during Global Brain Activation in Vivo.” Journal of Neuroscience, vol. 26, no. 23, Society for Neuroscience, 2006, pp. 6318–29, doi:10.1523/​JNEUROSCI.0620-06.2006. short: P. Magill, A. Pogosyan, A. Sharott, J.L. Csicsvari, J. Bolam, P. Brown, Journal of Neuroscience 26 (2006) 6318–6329. date_created: 2018-12-11T12:03:53Z date_published: 2006-06-07T00:00:00Z date_updated: 2021-01-12T07:44:13Z day: '07' doi: 10.1523/​JNEUROSCI.0620-06.2006 extern: 1 intvolume: ' 26' issue: '23' month: '06' page: 6318 - 6329 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '2840' quality_controlled: 0 status: public title: Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo type: journal_article volume: 26 year: '2006' ... --- _id: '3559' abstract: - lang: eng text: Persistent homology is the mathematical core of recent work on shape, including reconstruction, recognition, and matching. Its per- tinent information is encapsulated by a pairing of the critical values of a function, visualized by points forming a diagram in the plane. The original algorithm in [10] computes the pairs from an ordering of the simplices in a triangulation and takes worst-case time cubic in the number of simplices. The main result of this paper is an algorithm that maintains the pairing in worst-case linear time per transposition in the ordering. A side-effect of the algorithm’s anal- ysis is an elementary proof of the stability of persistence diagrams [7] in the special case of piecewise-linear functions. We use the algorithm to compute 1-parameter families of diagrams which we apply to the study of protein folding trajectories. acknowledgement: Partially supported by NSF under grant CCR- 00-86013, by DARPA under grant HR0011-05-1-0007, and by the Lawrence Livermore National Laboratory under grant B543154. author: - first_name: David full_name: Cohen-Steiner, David last_name: Cohen Steiner - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov citation: ama: 'Cohen Steiner D, Edelsbrunner H, Morozov D. Vines and vineyards by updating persistence in linear time. In: ACM; 2006:119-126. doi:10.1145/1137856.1137877' apa: 'Cohen Steiner, D., Edelsbrunner, H., & Morozov, D. (2006). Vines and vineyards by updating persistence in linear time (pp. 119–126). Presented at the SCG: Symposium on Computational Geometry, ACM. https://doi.org/10.1145/1137856.1137877' chicago: Cohen Steiner, David, Herbert Edelsbrunner, and Dmitriy Morozov. “Vines and Vineyards by Updating Persistence in Linear Time,” 119–26. ACM, 2006. https://doi.org/10.1145/1137856.1137877. ieee: 'D. Cohen Steiner, H. Edelsbrunner, and D. Morozov, “Vines and vineyards by updating persistence in linear time,” presented at the SCG: Symposium on Computational Geometry, 2006, pp. 119–126.' ista: 'Cohen Steiner D, Edelsbrunner H, Morozov D. 2006. Vines and vineyards by updating persistence in linear time. SCG: Symposium on Computational Geometry, 119–126.' mla: Cohen Steiner, David, et al. Vines and Vineyards by Updating Persistence in Linear Time. ACM, 2006, pp. 119–26, doi:10.1145/1137856.1137877. short: D. Cohen Steiner, H. Edelsbrunner, D. Morozov, in:, ACM, 2006, pp. 119–126. conference: name: 'SCG: Symposium on Computational Geometry' date_created: 2018-12-11T12:03:58Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:44:18Z day: '01' doi: 10.1145/1137856.1137877 extern: 1 month: '06' page: 119 - 126 publication_status: published publisher: ACM publist_id: '2826' quality_controlled: 0 status: public title: Vines and vineyards by updating persistence in linear time type: conference year: '2006' ... --- _id: '3560' abstract: - lang: eng text: We continue the study of topological persistence [5] by investigat- ing the problem of simplifying a function f in a way that removes topological noise as determined by its persistence diagram [2]. To state our results, we call a function g an ε-simplification of another function f if ∥f − g∥∞ ≤ ε, and the persistence diagrams of g are the same as those of f except all points within L1-distance at most ε from the diagonal have been removed. We prove that for func- tions f on a 2-manifold such ε-simplification exists, and we give an algorithm to construct them in the piecewise linear case. acknowledgement: Partially supported by NSF under grant CCR-00-86013, by DARPA under grant HR0011-05-1-0007, and by the Lawrence Livermore National Laboratory under grant B543154. author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: 'Edelsbrunner H, Morozov D, Pascucci V. Persistence-sensitive simplification of functions on 2-manifolds. In: ACM; 2006:127-134. doi:10.1145/1137856.1137878' apa: 'Edelsbrunner, H., Morozov, D., & Pascucci, V. (2006). Persistence-sensitive simplification of functions on 2-manifolds (pp. 127–134). Presented at the SCG: Symposium on Computational Geometry, ACM. https://doi.org/10.1145/1137856.1137878' chicago: Edelsbrunner, Herbert, Dmitriy Morozov, and Valerio Pascucci. “Persistence-Sensitive Simplification of Functions on 2-Manifolds,” 127–34. ACM, 2006. https://doi.org/10.1145/1137856.1137878. ieee: 'H. Edelsbrunner, D. Morozov, and V. Pascucci, “Persistence-sensitive simplification of functions on 2-manifolds,” presented at the SCG: Symposium on Computational Geometry, 2006, pp. 127–134.' ista: 'Edelsbrunner H, Morozov D, Pascucci V. 2006. Persistence-sensitive simplification of functions on 2-manifolds. SCG: Symposium on Computational Geometry, 127–134.' mla: Edelsbrunner, Herbert, et al. Persistence-Sensitive Simplification of Functions on 2-Manifolds. ACM, 2006, pp. 127–34, doi:10.1145/1137856.1137878. short: H. Edelsbrunner, D. Morozov, V. Pascucci, in:, ACM, 2006, pp. 127–134. conference: name: 'SCG: Symposium on Computational Geometry' date_created: 2018-12-11T12:03:58Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:44:19Z day: '01' doi: 10.1145/1137856.1137878 extern: 1 main_file_link: - open_access: '0' url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.4465 month: '06' page: 127 - 134 publication_status: published publisher: ACM publist_id: '2825' quality_controlled: 0 status: public title: Persistence-sensitive simplification of functions on 2-manifolds type: conference year: '2006' ... --- _id: '3594' author: - first_name: Josephine full_name: Pemberton, Josephine M last_name: Pemberton - first_name: Graeme full_name: Swanson, Graeme M last_name: Swanson - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Suzanne full_name: Livingstone, Suzanne R last_name: Livingstone - first_name: Helen full_name: Senn, Helen V last_name: Senn citation: ama: Pemberton J, Swanson G, Barton NH, Livingstone S, Senn H. Hybridisation between red and sika deer in Scotland. Deer. 2006;13(9):22-26. apa: Pemberton, J., Swanson, G., Barton, N. H., Livingstone, S., & Senn, H. (2006). Hybridisation between red and sika deer in Scotland. Deer. BDS . chicago: Pemberton, Josephine, Graeme Swanson, Nicholas H Barton, Suzanne Livingstone, and Helen Senn. “Hybridisation between Red and Sika Deer in Scotland.” Deer. BDS , 2006. ieee: J. Pemberton, G. Swanson, N. H. Barton, S. Livingstone, and H. Senn, “Hybridisation between red and sika deer in Scotland,” Deer, vol. 13, no. 9. BDS , pp. 22–26, 2006. ista: Pemberton J, Swanson G, Barton NH, Livingstone S, Senn H. 2006. Hybridisation between red and sika deer in Scotland. Deer. 13(9), 22–26. mla: Pemberton, Josephine, et al. “Hybridisation between Red and Sika Deer in Scotland.” Deer, vol. 13, no. 9, BDS , 2006, pp. 22–26. short: J. Pemberton, G. Swanson, N.H. Barton, S. Livingstone, H. Senn, Deer 13 (2006) 22–26. date_created: 2018-12-11T12:04:08Z date_published: 2006-01-01T00:00:00Z date_updated: 2019-04-26T07:22:31Z day: '01' extern: 1 intvolume: ' 13' issue: '9' month: '01' page: 22 - 26 publication: Deer publication_status: published publisher: 'BDS ' publist_id: '2789' quality_controlled: 0 status: public title: Hybridisation between red and sika deer in Scotland type: review volume: 13 year: '2006' ... --- _id: '3609' abstract: - lang: eng text: Bombina bombina and B. variegata are two anciently diverged toad taxa that have adapted to different breeding habitats yet hybridize freely in zones of overlap where their parapatric distributions meet. Here, we report on a joint genetic and ecological analysis of a hybrid zone in the vicinity of Stryi in western Ukraine. We used five unlinked allozyme loci, two nuclear single nucleotide polymorphisms and a mitochondrial DNA haplotype as genetic markers. Parallel allele frequency clines with a sharp central step occur across a sharp ecotone, where transitions in aquatic habitat, elevation, and terrestrial vegetation coincide. The width of the hybrid zone, estimated as the inverse of the maximum gradient in allele frequency, is 2.3 km. This is the smallest of four estimates derived from different clinal transects across Europe. We argue that the narrow cline near Stryi is mainly due to a combination of habitat distribution and habitat preference. Adult toads show a preference for either ponds (B. bombina) or puddles (B. variegata), which is known to affect the distribution of genotypes within the hybrid zones. At Stryi, it should cause a reduction of the dispersal rate across the ecotone and thus narrow the cline. A detailed comparison of all five intensively studied Bombina transects lends support to the hypothesis that habitat distribution plus habitat preference can jointly affect the structure of hybrid zones and, ultimately, the resulting barriers to gene flow between differentiated gene pools. This study also represents a resampling of an area that was last studied more than 70 years ago. Our allele-frequency clines largely coincide with those that were described then on the basis of morphological variation. However, we found asymmetrical introgression of B. variegata genes into B. bombina territory along the bank of a river. author: - first_name: Alexey full_name: Yanchukov, Alexey last_name: Yanchukov - first_name: Sebastian full_name: Hofman, Sebastian last_name: Hofman - first_name: Jacek full_name: Szymura, Jacek M last_name: Szymura - first_name: Sergey full_name: Mezhzherin, Sergey V last_name: Mezhzherin - first_name: Sviatoslav full_name: Morozov-Leonov, Sviatoslav last_name: Morozov Leonov - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Beate full_name: Nürnberger, Beate last_name: Nürnberger citation: ama: 'Yanchukov A, Hofman S, Szymura J, et al. Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time. Evolution; International Journal of Organic Evolution. 2006;60(3):583-600. doi:10.1111/j.0014-3820.2006.tb01139.x' apa: 'Yanchukov, A., Hofman, S., Szymura, J., Mezhzherin, S., Morozov Leonov, S., Barton, N. H., & Nürnberger, B. (2006). Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2006.tb01139.x' chicago: 'Yanchukov, Alexey, Sebastian Hofman, Jacek Szymura, Sergey Mezhzherin, Sviatoslav Morozov Leonov, Nicholas H Barton, and Beate Nürnberger. “Hybridization of Bombina Bombina and B. Variegata (Anura, Discoglossidae) at a Sharp Ecotone in Western Ukraine: Comparisons across Transects and over Time.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.0014-3820.2006.tb01139.x.' ieee: 'A. Yanchukov et al., “Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time,” Evolution; International Journal of Organic Evolution, vol. 60, no. 3. Wiley-Blackwell, pp. 583–600, 2006.' ista: 'Yanchukov A, Hofman S, Szymura J, Mezhzherin S, Morozov Leonov S, Barton NH, Nürnberger B. 2006. Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time. Evolution; International Journal of Organic Evolution. 60(3), 583–600.' mla: 'Yanchukov, Alexey, et al. “Hybridization of Bombina Bombina and B. Variegata (Anura, Discoglossidae) at a Sharp Ecotone in Western Ukraine: Comparisons across Transects and over Time.” Evolution; International Journal of Organic Evolution, vol. 60, no. 3, Wiley-Blackwell, 2006, pp. 583–600, doi:10.1111/j.0014-3820.2006.tb01139.x.' short: A. Yanchukov, S. Hofman, J. Szymura, S. Mezhzherin, S. Morozov Leonov, N.H. Barton, B. Nürnberger, Evolution; International Journal of Organic Evolution 60 (2006) 583–600. date_created: 2018-12-11T12:04:13Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T07:44:38Z day: '01' doi: 10.1111/j.0014-3820.2006.tb01139.x extern: 1 intvolume: ' 60' issue: '3' month: '03' page: 583 - 600 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '2774' quality_controlled: 0 status: public title: 'Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time' type: journal_article volume: 60 year: '2006' ... --- _id: '3608' abstract: - lang: eng text: 'We study the evolution of inversions that capture locally adapted alleles when two populations are exchanging migrants or hybridizing. By suppressing recombination between the loci, a new inversion can spread. Neither drift nor coadaptation between the alleles (epistasis) is needed, so this local adaptation mechanism may apply to a broader range of genetic and demographic situations than alternative hypotheses that have been widely discussed. The mechanism can explain many features observed in inversion systems. It will drive an inversion to high frequency if there is no countervailing force, which could explain fixed differences observed between populations and species. An inversion can be stabilized at an intermediate frequency if it also happens to capture one or more deleterious recessive mutations, which could explain polymorphisms that are common in some species. This polymorphism can cycle in frequency with the changing selective advantage of the locally favored alleles. The mechanism can establish underdominant inversions that decrease heterokaryotype fitness by several percent if the cause of fitness loss is structural, while if the cause is genic there is no limit to the strength of underdominance that can result. The mechanism is expected to cause loci responsible for adaptive species-specific differences to map to inversions, as seen in recent QTL studies. We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests. ' author: - first_name: Mark full_name: Kirkpatrick, Mark last_name: Kirkpatrick - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Kirkpatrick M, Barton NH. Chromosome inversions, local adaptation, and speciation. Genetics. 2006;173(1):419-434. doi:10.1534/genetics.105.047985 apa: Kirkpatrick, M., & Barton, N. H. (2006). Chromosome inversions, local adaptation, and speciation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.105.047985 chicago: Kirkpatrick, Mark, and Nicholas H Barton. “Chromosome Inversions, Local Adaptation, and Speciation.” Genetics. Genetics Society of America, 2006. https://doi.org/10.1534/genetics.105.047985. ieee: M. Kirkpatrick and N. H. Barton, “Chromosome inversions, local adaptation, and speciation,” Genetics, vol. 173, no. 1. Genetics Society of America, pp. 419–434, 2006. ista: Kirkpatrick M, Barton NH. 2006. Chromosome inversions, local adaptation, and speciation. Genetics. 173(1), 419–434. mla: Kirkpatrick, Mark, and Nicholas H. Barton. “Chromosome Inversions, Local Adaptation, and Speciation.” Genetics, vol. 173, no. 1, Genetics Society of America, 2006, pp. 419–34, doi:10.1534/genetics.105.047985. short: M. Kirkpatrick, N.H. Barton, Genetics 173 (2006) 419–434. date_created: 2018-12-11T12:04:13Z date_published: 2006-05-01T00:00:00Z date_updated: 2021-01-12T07:44:37Z day: '01' doi: 10.1534/genetics.105.047985 extern: 1 intvolume: ' 173' issue: '1' month: '05' page: 419 - 434 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '2775' quality_controlled: 0 status: public title: Chromosome inversions, local adaptation, and speciation type: journal_article volume: 173 year: '2006' ... --- _id: '3610' abstract: - lang: eng text: For a model of diallelic loci with arbitrary epistasis, Barton and Turelli [2004. Effects of genetic drift on variance components under a general model of epistasis. Evolution 58, 2111–2132] gave results for variances among and within replicate lines obtained by inbreeding without selection. Here, we discuss the relation between their population genetic methods and classical quantitative genetic arguments. In particular, we consider the case of no dominance using classical identity by descent arguments, which generalizes their results from two alleles to multiple alleles. To clarify the connections between the alternative methods, we obtain the same results using an intermediate method, which explicitly identifies the statistical effects of sets of loci. We also discuss the effects of population bottlenecks on covariances among relatives. author: - first_name: William full_name: Hill, William G last_name: Hill - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Hill W, Barton NH, Turelli M. Prediction of effects of genetic drift on variance components under a general model of epistasis. Theoretical Population Biology. 2006;70(1):56-62. doi:10.1016/j.tpb.2005.10.001 apa: Hill, W., Barton, N. H., & Turelli, M. (2006). Prediction of effects of genetic drift on variance components under a general model of epistasis. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2005.10.001 chicago: Hill, William, Nicholas H Barton, and Michael Turelli. “Prediction of Effects of Genetic Drift on Variance Components under a General Model of Epistasis.” Theoretical Population Biology. Academic Press, 2006. https://doi.org/10.1016/j.tpb.2005.10.001. ieee: W. Hill, N. H. Barton, and M. Turelli, “Prediction of effects of genetic drift on variance components under a general model of epistasis,” Theoretical Population Biology, vol. 70, no. 1. Academic Press, pp. 56–62, 2006. ista: Hill W, Barton NH, Turelli M. 2006. Prediction of effects of genetic drift on variance components under a general model of epistasis. Theoretical Population Biology. 70(1), 56–62. mla: Hill, William, et al. “Prediction of Effects of Genetic Drift on Variance Components under a General Model of Epistasis.” Theoretical Population Biology, vol. 70, no. 1, Academic Press, 2006, pp. 56–62, doi:10.1016/j.tpb.2005.10.001. short: W. Hill, N.H. Barton, M. Turelli, Theoretical Population Biology 70 (2006) 56–62. date_created: 2018-12-11T12:04:14Z date_published: 2006-08-01T00:00:00Z date_updated: 2021-01-12T07:44:39Z day: '01' doi: 10.1016/j.tpb.2005.10.001 extern: 1 intvolume: ' 70' issue: '1' month: '08' page: 56 - 62 publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '2773' quality_controlled: 0 status: public title: Prediction of effects of genetic drift on variance components under a general model of epistasis type: journal_article volume: 70 year: '2006' ... --- _id: '3679' abstract: - lang: eng text: This paper describes a new system for "Finding Satellite Tracks” in astronomical images based on the modern geometric approach. There is an increasing need of using methods with solid mathematical and statistical foundation in astronomical image processing. Where the computational methods are serving in all disciplines of science, they are becoming popular in the field of astronomy as well. Currently different computational systems are required to be numerically optimized before to get applied on astronomical images. So at present there is no single system which solves the problems of astronomers using computational methods based on modern approaches. The system "Finding Satellite Tracks” is based on geometric matching method "Recognition by Adaptive Subdivision of Transformation Space (RAST)". alternative_title: - LNCS author: - first_name: Haider full_name: Ali,Haider last_name: Ali - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Ali H, Lampert C, Breuel T. Satellite tracks removal in astronomical images. In: Vol 4225. Springer; 2006:892-901. doi:10.1007/11892755_92' apa: 'Ali, H., Lampert, C., & Breuel, T. (2006). Satellite tracks removal in astronomical images (Vol. 4225, pp. 892–901). Presented at the CIARP: Iberoamerican Congress in Pattern Recognition, Springer. https://doi.org/10.1007/11892755_92' chicago: Ali, Haider, Christoph Lampert, and Thomas Breuel. “Satellite Tracks Removal in Astronomical Images,” 4225:892–901. Springer, 2006. https://doi.org/10.1007/11892755_92. ieee: 'H. Ali, C. Lampert, and T. Breuel, “Satellite tracks removal in astronomical images,” presented at the CIARP: Iberoamerican Congress in Pattern Recognition, 2006, vol. 4225, pp. 892–901.' ista: 'Ali H, Lampert C, Breuel T. 2006. Satellite tracks removal in astronomical images. CIARP: Iberoamerican Congress in Pattern Recognition, LNCS, vol. 4225, 892–901.' mla: Ali, Haider, et al. Satellite Tracks Removal in Astronomical Images. Vol. 4225, Springer, 2006, pp. 892–901, doi:10.1007/11892755_92. short: H. Ali, C. Lampert, T. Breuel, in:, Springer, 2006, pp. 892–901. conference: name: 'CIARP: Iberoamerican Congress in Pattern Recognition' date_created: 2018-12-11T12:04:35Z date_published: 2006-10-31T00:00:00Z date_updated: 2021-01-12T07:45:05Z day: '31' doi: 10.1007/11892755_92 extern: 1 intvolume: ' 4225' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/ali-ciarp2006.pdf month: '10' page: 892 - 901 publication_status: published publisher: Springer publist_id: '2700' quality_controlled: 0 status: public title: Satellite tracks removal in astronomical images type: conference volume: 4225 year: '2006' ... --- _id: '3677' abstract: - lang: eng text: We propose a video retrieval framework based on a novel combination of spatiograms and the Jensen-Shannon divergence, and validate its performance in two quantitative experiments on TRECVID BBC Rushes data. In the first experiment, color-based methods are tested by grouping redundant shots in an unsupervised clustering. Results of the second experiment show that motion-based spatiograms make a promising fast, compressed-domain descriptor for the detection of interview scenes. alternative_title: - TRECVID Notebook Papers and Slides author: - first_name: Adrian full_name: Ulges, Adrian last_name: Ulges - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Daniel full_name: Keysers,Daniel last_name: Keysers citation: ama: 'Ulges A, Lampert C, Keysers D. Spatiogram-based shot distances for video retrieval. In: NIST (National Institute of Standards and Technology, US Department of Commerce); 2006:1-10.' apa: Ulges, A., Lampert, C., & Keysers, D. (2006). Spatiogram-based shot distances for video retrieval (pp. 1–10). Presented at the TRECVID Workshop, NIST (National Institute of Standards and Technology, US Department of Commerce). chicago: Ulges, Adrian, Christoph Lampert, and Daniel Keysers. “Spatiogram-Based Shot Distances for Video Retrieval,” 1–10. NIST (National Institute of Standards and Technology, US Department of Commerce), 2006. ieee: A. Ulges, C. Lampert, and D. Keysers, “Spatiogram-based shot distances for video retrieval,” presented at the TRECVID Workshop, 2006, pp. 1–10. ista: Ulges A, Lampert C, Keysers D. 2006. Spatiogram-based shot distances for video retrieval. TRECVID Workshop, TRECVID Notebook Papers and Slides, , 1–10. mla: Ulges, Adrian, et al. Spatiogram-Based Shot Distances for Video Retrieval. NIST (National Institute of Standards and Technology, US Department of Commerce), 2006, pp. 1–10. short: A. Ulges, C. Lampert, D. Keysers, in:, NIST (National Institute of Standards and Technology, US Department of Commerce), 2006, pp. 1–10. conference: name: TRECVID Workshop date_created: 2018-12-11T12:04:34Z date_published: 2006-11-14T00:00:00Z date_updated: 2021-01-12T07:45:04Z day: '14' extern: 1 main_file_link: - open_access: '0' url: http://www-nlpir.nist.gov/projects/tvpubs/tv6.papers/dfki.pdf month: '11' page: 1 - 10 publication_status: published publisher: NIST (National Institute of Standards and Technology, US Department of Commerce) publist_id: '2702' quality_controlled: 0 status: public title: Spatiogram-based shot distances for video retrieval type: conference year: '2006' ... --- _id: '3680' abstract: - lang: eng text: The detection of counterfeit in printed documents is currently based mainly on built-in security features or on human expertise. We propose a classification system that supports non-expert users to distinguish original documents from PC-made forgeries by analyzing the printing technique used. Each letter in a document is classified using a support vector machine that has been trained to distinguish laser from inkjet printouts. A color-coded visualization helps the user to interpret the per-letter classification results author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Lin full_name: Mei,Lin last_name: Mei - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Lampert C, Mei L, Breuel T. Printing technique classification for document counterfeit detection. In: Vol 1. IEEE; 2006:639-634. doi:10.1109/ICCIAS.2006.294214' apa: 'Lampert, C., Mei, L., & Breuel, T. (2006). Printing technique classification for document counterfeit detection (Vol. 1, pp. 639–634). Presented at the CIS: Computational Intelligence and Security, IEEE. https://doi.org/10.1109/ICCIAS.2006.294214' chicago: Lampert, Christoph, Lin Mei, and Thomas Breuel. “Printing Technique Classification for Document Counterfeit Detection,” 1:639–634. IEEE, 2006. https://doi.org/10.1109/ICCIAS.2006.294214. ieee: 'C. Lampert, L. Mei, and T. Breuel, “Printing technique classification for document counterfeit detection,” presented at the CIS: Computational Intelligence and Security, 2006, vol. 1, pp. 639–634.' ista: 'Lampert C, Mei L, Breuel T. 2006. Printing technique classification for document counterfeit detection. CIS: Computational Intelligence and Security vol. 1, 639–634.' mla: Lampert, Christoph, et al. Printing Technique Classification for Document Counterfeit Detection. Vol. 1, IEEE, 2006, pp. 639–634, doi:10.1109/ICCIAS.2006.294214. short: C. Lampert, L. Mei, T. Breuel, in:, IEEE, 2006, pp. 639–634. conference: name: 'CIS: Computational Intelligence and Security' date_created: 2018-12-11T12:04:35Z date_published: 2006-11-03T00:00:00Z date_updated: 2021-01-12T07:45:06Z day: '03' doi: 10.1109/ICCIAS.2006.294214 extern: 1 intvolume: ' 1' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/lampert-cis2006.pdf month: '11' page: 639 - 634 publication_status: published publisher: IEEE publist_id: '2698' quality_controlled: 0 status: public title: Printing technique classification for document counterfeit detection type: conference volume: 1 year: '2006' ... --- _id: '3695' abstract: - lang: eng text: We give an analytical and geometrical treatment of what it means to separate a Gaussian kernel along arbitrary axes in Ropfn, and we present a separation scheme that allows us to efficiently implement anisotropic Gaussian convolution filters for data of arbitrary dimensionality. Based on our previous analysis we show that this scheme is optimal with regard to the number of memory accesses and interpolation operations needed. The proposed method relies on nonorthogonal convolution axes and works completely in image space. Thus, it avoids the need for a fast Fourier transform (FFT)-subroutine. Depending on the accuracy and speed requirements, different interpolation schemes and methods to implement the one-dimensional Gaussian (finite impulse response and infinite impulse response) can be integrated. Special emphasis is put on analyzing the performance and accuracy of the new method. In particular, we show that without any special optimization of the source code, it can perform anisotropic Gaussian filtering faster than methods relying on the FFT. author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Oliver full_name: Wirjadi,Oliver last_name: Wirjadi citation: ama: Lampert C, Wirjadi O. An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter. IEEE Transactions on Image Processing (TIP). 2006;15(11):3501-3513. doi: 10.1109/TIP.2006.877501 apa: Lampert, C., & Wirjadi, O. (2006). An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter. IEEE Transactions on Image Processing (TIP). IEEE. https://doi.org/ 10.1109/TIP.2006.877501 chicago: Lampert, Christoph, and Oliver Wirjadi. “An Optimal Non-Orthogonal Separation of the Anisotropic Gaussian Convolution Filter.” IEEE Transactions on Image Processing (TIP). IEEE, 2006. https://doi.org/ 10.1109/TIP.2006.877501 . ieee: C. Lampert and O. Wirjadi, “An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter,” IEEE Transactions on Image Processing (TIP), vol. 15, no. 11. IEEE, pp. 3501–3513, 2006. ista: Lampert C, Wirjadi O. 2006. An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter. IEEE Transactions on Image Processing (TIP). 15(11), 3501–3513. mla: Lampert, Christoph, and Oliver Wirjadi. “An Optimal Non-Orthogonal Separation of the Anisotropic Gaussian Convolution Filter.” IEEE Transactions on Image Processing (TIP), vol. 15, no. 11, IEEE, 2006, pp. 3501–13, doi: 10.1109/TIP.2006.877501 . short: C. Lampert, O. Wirjadi, IEEE Transactions on Image Processing (TIP) 15 (2006) 3501–3513. date_created: 2018-12-11T12:04:40Z date_published: 2006-11-01T00:00:00Z date_updated: 2021-01-12T07:49:01Z day: '01' doi: ' 10.1109/TIP.2006.877501 ' extern: 1 intvolume: ' 15' issue: '11' main_file_link: - open_access: '1' url: http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:386-kluedo-14003 month: '11' oa: 1 page: 3501 - 3513 publication: IEEE Transactions on Image Processing (TIP) publication_status: published publisher: IEEE publist_id: '2669' quality_controlled: 0 status: public title: An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter type: journal_article volume: 15 year: '2006' ... --- _id: '3693' abstract: - lang: eng text: Gaussian filtering in one, two or three dimensions is among the most commonly needed tasks in signal and image processing. Finite impulse response filters in the time domain with Gaussian masks are easy to implement in either floating or fixed point arithmetic, because Gaussian kernels are strictly positive and bounded. But these implementations are slow for large images or kernels. With the recursive IIR-filters and FFT-based methods, there are at least two alternative methods to perform Gaussian filtering in a faster way, but so far they are only applicable when floating-point hardware is available. In this paper, a fixed-point implementation of recursive Gaussian filtering is discussed and applied to isotropic and anisotropic image filtering by making use of a non-orthogonal separation scheme of the Gaussian filter. author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Oliver full_name: Wirjadi,Oliver last_name: Wirjadi citation: ama: 'Lampert C, Wirjadi O. Anisotropic Gaussian filtering using fixed point arithmetic. In: IEEE; 2006:1565-1568. doi:10.1109/ICIP.2006.312606' apa: 'Lampert, C., & Wirjadi, O. (2006). Anisotropic Gaussian filtering using fixed point arithmetic (pp. 1565–1568). Presented at the ICIP: IEEE International Conference on Image Processing, IEEE. https://doi.org/10.1109/ICIP.2006.312606' chicago: Lampert, Christoph, and Oliver Wirjadi. “Anisotropic Gaussian Filtering Using Fixed Point Arithmetic,” 1565–68. IEEE, 2006. https://doi.org/10.1109/ICIP.2006.312606. ieee: 'C. Lampert and O. Wirjadi, “Anisotropic Gaussian filtering using fixed point arithmetic,” presented at the ICIP: IEEE International Conference on Image Processing, 2006, pp. 1565–1568.' ista: 'Lampert C, Wirjadi O. 2006. Anisotropic Gaussian filtering using fixed point arithmetic. ICIP: IEEE International Conference on Image Processing, 1565–1568.' mla: Lampert, Christoph, and Oliver Wirjadi. Anisotropic Gaussian Filtering Using Fixed Point Arithmetic. IEEE, 2006, pp. 1565–68, doi:10.1109/ICIP.2006.312606. short: C. Lampert, O. Wirjadi, in:, IEEE, 2006, pp. 1565–1568. conference: name: 'ICIP: IEEE International Conference on Image Processing' date_created: 2018-12-11T12:04:39Z date_published: 2006-10-08T00:00:00Z date_updated: 2021-01-12T07:49:00Z day: '08' doi: 10.1109/ICIP.2006.312606 extern: 1 month: '10' page: 1565 - 1568 publication_status: published publisher: IEEE publist_id: '2670' quality_controlled: 0 status: public title: Anisotropic Gaussian filtering using fixed point arithmetic type: conference year: '2006' ... --- _id: '3692' author: - first_name: Daniel full_name: Keysers,Daniel last_name: Keysers - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Keysers D, Lampert C, Breuel T. Color image dequantization by constrained diffusion. In: Vol 6058. SPIE; 2006. doi:10.1117/12.648713' apa: Keysers, D., Lampert, C., & Breuel, T. (2006). Color image dequantization by constrained diffusion (Vol. 6058). Presented at the SPIE Electronic Imaging, SPIE. https://doi.org/10.1117/12.648713 chicago: Keysers, Daniel, Christoph Lampert, and Thomas Breuel. “Color Image Dequantization by Constrained Diffusion,” Vol. 6058. SPIE, 2006. https://doi.org/10.1117/12.648713. ieee: D. Keysers, C. Lampert, and T. Breuel, “Color image dequantization by constrained diffusion,” presented at the SPIE Electronic Imaging, 2006, vol. 6058. ista: Keysers D, Lampert C, Breuel T. 2006. Color image dequantization by constrained diffusion. SPIE Electronic Imaging vol. 6058. mla: Keysers, Daniel, et al. Color Image Dequantization by Constrained Diffusion. Vol. 6058, SPIE, 2006, doi:10.1117/12.648713. short: D. Keysers, C. Lampert, T. Breuel, in:, SPIE, 2006. conference: name: SPIE Electronic Imaging date_created: 2018-12-11T12:04:39Z date_published: 2006-01-15T00:00:00Z date_updated: 2019-05-10T12:19:52Z day: '15' doi: 10.1117/12.648713 extern: 1 intvolume: ' 6058' month: '01' publication_status: published publisher: SPIE publist_id: '2674' quality_controlled: 0 status: public title: Color image dequantization by constrained diffusion type: conference volume: 6058 year: '2006' ... --- _id: '3729' abstract: - lang: eng text: Measuring the visco-elastic properties of biological macromolecules constitutes an important step towards the understanding of dynamic biological processes, such as cell adhesion, muscle function, or plant cell wall stability. Force spectroscopy techniques based on the atomic force microscope (AFM) are increasingly used to study the complex visco-elastic response of (bio-)molecules on a single-molecule level. These experiments either require that the AFM cantilever is actively oscillated or that the molecule is clamped at constant force to monitor thermal cantilever motion. Here we demonstrate that the visco-elasticity of single bio-molecules can readily be extracted from the Brownian cantilever motion during conventional force-extension measurements. It is shown that the characteristics of the cantilever determine the signal-to-noise (S/N) ratio and time resolution. Using a small cantilever, the visco-elastic properties of single dextran molecules were resolved with a time resolution of 8.3 ms. The presented approach can be directly applied to probe the dynamic response of complex bio-molecular systems or proteins in force-extension experiments. author: - first_name: Christian full_name: Bippes, Christian A last_name: Bippes - first_name: Andrew full_name: Humphris, Andrew D last_name: Humphris - first_name: Martin full_name: Stark, Martin last_name: Stark - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Bippes C, Humphris A, Stark M, Mueller D, Janovjak HL. Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments. European Biophysics Journal. 2006;35(3):287-292. doi:10.1007/s00249-005-0023-9 apa: Bippes, C., Humphris, A., Stark, M., Mueller, D., & Janovjak, H. L. (2006). Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments. European Biophysics Journal. Springer. https://doi.org/10.1007/s00249-005-0023-9 chicago: Bippes, Christian, Andrew Humphris, Martin Stark, Daniel Mueller, and Harald L Janovjak. “Direct Measurement of Single-Molecule Visco-Elasticity in Atomic Force Microscope Force-Extension Experiments.” European Biophysics Journal. Springer, 2006. https://doi.org/10.1007/s00249-005-0023-9. ieee: C. Bippes, A. Humphris, M. Stark, D. Mueller, and H. L. Janovjak, “Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments,” European Biophysics Journal, vol. 35, no. 3. Springer, pp. 287–292, 2006. ista: Bippes C, Humphris A, Stark M, Mueller D, Janovjak HL. 2006. Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments. European Biophysics Journal. 35(3), 287–292. mla: Bippes, Christian, et al. “Direct Measurement of Single-Molecule Visco-Elasticity in Atomic Force Microscope Force-Extension Experiments.” European Biophysics Journal, vol. 35, no. 3, Springer, 2006, pp. 287–92, doi:10.1007/s00249-005-0023-9. short: C. Bippes, A. Humphris, M. Stark, D. Mueller, H.L. Janovjak, European Biophysics Journal 35 (2006) 287–292. date_created: 2018-12-11T12:04:51Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T07:51:46Z day: '01' doi: 10.1007/s00249-005-0023-9 extern: 1 intvolume: ' 35' issue: '3' month: '02' page: 287 - 292 publication: European Biophysics Journal publication_status: published publisher: Springer publist_id: '2500' quality_controlled: 0 status: public title: Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments type: journal_article volume: 35 year: '2006' ... --- _id: '3728' abstract: - lang: eng text: Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard–Jones contact interactions is applied to model the protein–membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins. author: - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak - first_name: Sławomir full_name: Filipek, Sławomir last_name: Filipek - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Krystiana full_name: Krzysko, Krystiana A last_name: Krzysko citation: ama: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2006;1758(4):537-544. doi:10.1016/j.bbamem.2006.03.028' apa: 'Cieplak, M., Filipek, S., Janovjak, H. L., & Krzysko, K. (2006). Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2006.03.028' chicago: 'Cieplak, Marek, Sławomir Filipek, Harald L Janovjak, and Krystiana Krzysko. “Pulling Single Bacteriorhodopsin out of a Membrane: Comparison of Simulation and Experiment.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier, 2006. https://doi.org/10.1016/j.bbamem.2006.03.028.' ieee: 'M. Cieplak, S. Filipek, H. L. Janovjak, and K. Krzysko, “Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment,” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1758, no. 4. Elsevier, pp. 537–544, 2006.' ista: 'Cieplak M, Filipek S, Janovjak HL, Krzysko K. 2006. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1758(4), 537–544.' mla: 'Cieplak, Marek, et al. “Pulling Single Bacteriorhodopsin out of a Membrane: Comparison of Simulation and Experiment.” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1758, no. 4, Elsevier, 2006, pp. 537–44, doi:10.1016/j.bbamem.2006.03.028.' short: M. Cieplak, S. Filipek, H.L. Janovjak, K. Krzysko, Biochimica et Biophysica Acta (BBA) - Biomembranes 1758 (2006) 537–544. date_created: 2018-12-11T12:04:50Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:51:46Z day: '01' doi: 10.1016/j.bbamem.2006.03.028 extern: 1 intvolume: ' 1758' issue: '4' month: '04' page: 537 - 544 publication: Biochimica et Biophysica Acta (BBA) - Biomembranes publication_status: published publisher: Elsevier publist_id: '2502' quality_controlled: 0 status: public title: 'Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment' type: journal_article volume: 1758 year: '2006' ... --- _id: '3722' author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: 'Janovjak HL, Mueller D. Rastersondenmikroskopie. In: Bioanalytik. Spektrum Akademischer Verlag; 2006.' apa: Janovjak, H. L., & Mueller, D. (2006). Rastersondenmikroskopie. In Bioanalytik. Spektrum Akademischer Verlag. chicago: Janovjak, Harald L, and Daniel Mueller. “Rastersondenmikroskopie.” In Bioanalytik. Spektrum Akademischer Verlag, 2006. ieee: H. L. Janovjak and D. Mueller, “Rastersondenmikroskopie,” in Bioanalytik, Spektrum Akademischer Verlag, 2006. ista: 'Janovjak HL, Mueller D. 2006.Rastersondenmikroskopie. In: Bioanalytik. .' mla: Janovjak, Harald L., and Daniel Mueller. “Rastersondenmikroskopie.” Bioanalytik, Spektrum Akademischer Verlag, 2006. short: H.L. Janovjak, D. Mueller, in:, Bioanalytik, Spektrum Akademischer Verlag, 2006. date_created: 2018-12-11T12:04:48Z date_published: 2006-06-16T00:00:00Z date_updated: 2021-01-12T07:51:44Z day: '16' extern: 1 month: '06' publication: Bioanalytik publication_status: published publisher: Spektrum Akademischer Verlag publist_id: '2508' quality_controlled: 0 status: public title: Rastersondenmikroskopie type: book_chapter year: '2006' ... --- _id: '3755' abstract: - lang: eng text: A primitive example of adaptation in gene expression is the balance between the rate of synthesis and degradation of cellular RNA, which allows rapid responses to environmental signals. Here, we investigate how multidrug efflux pump systems mediate the dynamics of a simple drug-inducible system in response to a steady level of inducer. Using fluorescence correlation spectroscopy, we measured in real time within a single bacterium the transcription activity at the RNA level of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated surface, we found that the acrAB-TolC promoter is steadily active. We also monitored the activity of the tet promoter to characterize the effect of this efflux system on the dynamics of drug-inducible transcription. We found that the transcriptional response of the tet promoter to a steady level of aTc rises and then falls back to its preinduction level. The rate of RNA degradation was constant throughout the transcriptional pulse, indicating that the modulation of intracellular inducer concentration alone can produce this pulsating response. Single-cell experiments together with numerical simulations suggest that such pulsating response in drug-inducible genetic systems is a property emerging from the dependence of drug-inducible transcription on multidrug efflux systems. author: - first_name: Thuc full_name: Le,Thuc T. last_name: Le - first_name: Thierry full_name: Emonet,Thierry last_name: Emonet - first_name: Sébastien full_name: Harlepp, Sébastien last_name: Harlepp - first_name: Calin C full_name: Calin Guet id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Philippe full_name: Cluzel,Philippe last_name: Cluzel citation: ama: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. 2006;90(9):3315-3321. doi:10.1529/biophysj.105.073353 apa: Le, T., Emonet, T., Harlepp, S., Guet, C. C., & Cluzel, P. (2006). Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.105.073353 chicago: Le, Thuc, Thierry Emonet, Sébastien Harlepp, Calin C Guet, and Philippe Cluzel. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” Biophysical Journal. Biophysical Society, 2006. https://doi.org/10.1529/biophysj.105.073353. ieee: T. Le, T. Emonet, S. Harlepp, C. C. Guet, and P. Cluzel, “Dynamical determinants of drug-inducible gene expression in a single bacterium,” Biophysical Journal, vol. 90, no. 9. Biophysical Society, pp. 3315–3321, 2006. ista: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. 2006. Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. 90(9), 3315–3321. mla: Le, Thuc, et al. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” Biophysical Journal, vol. 90, no. 9, Biophysical Society, 2006, pp. 3315–21, doi:10.1529/biophysj.105.073353. short: T. Le, T. Emonet, S. Harlepp, C.C. Guet, P. Cluzel, Biophysical Journal 90 (2006) 3315–3321. date_created: 2018-12-11T12:04:59Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:51:58Z day: '01' doi: 10.1529/biophysj.105.073353 extern: 1 intvolume: ' 90' issue: '9' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1432126/ month: '01' oa: 1 page: 3315 - 3321 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '2472' quality_controlled: 0 status: public title: Dynamical determinants of drug-inducible gene expression in a single bacterium type: journal_article volume: 90 year: '2006' ... --- _id: '3758' abstract: - lang: eng text: Control of physical simulation has become a popular topic in the field of computer graphics. Keyframe control has been applied to simulations of rigid bodies, smoke, liquid, flocks, and finite element-based elastic bodies. In this paper, we create a framework for controlling systems of interacting particles -- paying special attention to simulations of cloth and flocking behavior. We introduce a novel integrator-swapping approximation in order to apply the adjoint method to linearized implicit schemes appropriate for cloth simulation. This allows the control of cloth while avoiding computationally infeasible derivative calculations. Meanwhile, flocking control using the adjoint method is significantly more efficient than currently-used methods for constraining group behaviors, allowing the controlled simulation of greater numbers of agents in fewer optimization iterations. article_processing_charge: No author: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Peter full_name: Mucha, Peter last_name: Mucha - first_name: Greg full_name: Turk, Greg last_name: Turk citation: ama: 'Wojtan C, Mucha P, Turk G. Keyframe control of complex particle systems using the adjoint method. In: ACM; 2006:15-23.' apa: 'Wojtan, C., Mucha, P., & Turk, G. (2006). Keyframe control of complex particle systems using the adjoint method (pp. 15–23). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, ACM.' chicago: Wojtan, Chris, Peter Mucha, and Greg Turk. “Keyframe Control of Complex Particle Systems Using the Adjoint Method,” 15–23. ACM, 2006. ieee: 'C. Wojtan, P. Mucha, and G. Turk, “Keyframe control of complex particle systems using the adjoint method,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 2006, pp. 15–23.' ista: 'Wojtan C, Mucha P, Turk G. 2006. Keyframe control of complex particle systems using the adjoint method. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 15–23.' mla: Wojtan, Chris, et al. Keyframe Control of Complex Particle Systems Using the Adjoint Method. ACM, 2006, pp. 15–23. short: C. Wojtan, P. Mucha, G. Turk, in:, ACM, 2006, pp. 15–23. conference: name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation' date_created: 2018-12-11T12:05:00Z date_published: 2006-09-01T00:00:00Z date_updated: 2023-02-23T11:41:22Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: http://www.amath.unc.edu/Faculty/mucha/Reprints/SCAclothcontrolpreprint.pdf month: '09' oa_version: None page: 15 - 23 publication_status: published publisher: ACM publist_id: '2469' status: public title: Keyframe control of complex particle systems using the adjoint method type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2006' ... --- _id: '3818' abstract: - lang: eng text: Rigorous analysis of synaptic transmission in the central nervous system requires access to presynaptic terminals. However, cortical terminals have been largely inaccessible to presynaptic patch-clamp recording, due to their small size. Using improved patch-clamp techniques in brain slices, we recorded from mossy fiber terminals in the CA3 region of the hippocampus, which have a diameter of 2-5 microm. The major steps of improvement were the enhanced visibility provided by high-numerical aperture objectives and infrared illumination, the development of vibratomes with minimal vertical blade vibrations and the use of sucrose-based solutions for storage and cutting. Based on these improvements, we describe a protocol that allows us to routinely record from hippocampal mossy fiber boutons. Presynaptic recordings can be obtained in slices from both rats and mice. Presynaptic recordings can be also obtained in slices from transgenic mice in which terminals are labeled with enhanced green fluorescent protein. author: - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Liyi full_name: Li, Liyi last_name: Li - first_name: Jörg full_name: Geiger, Jörg R last_name: Geiger - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. 2006;1(4):2075-2081. doi:10.1038/nprot.2006.312 apa: Bischofberger, J., Engel, D., Li, L., Geiger, J., & Jonas, P. M. (2006). Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.312 chicago: Bischofberger, Josef, Dominique Engel, Liyi Li, Jörg Geiger, and Peter M Jonas. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.312 . ieee: J. Bischofberger, D. Engel, L. Li, J. Geiger, and P. M. Jonas, “Patch-clamp recording from mossy fiber terminals in hippocampal slices,” Nature Protocols, vol. 1, no. 4. Nature Publishing Group, pp. 2075–81, 2006. ista: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. 2006. Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. 1(4), 2075–81. mla: Bischofberger, Josef, et al. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.” Nature Protocols, vol. 1, no. 4, Nature Publishing Group, 2006, pp. 2075–81, doi:10.1038/nprot.2006.312 . short: J. Bischofberger, D. Engel, L. Li, J. Geiger, P.M. Jonas, Nature Protocols 1 (2006) 2075–81. date_created: 2018-12-11T12:05:20Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:25Z day: '01' doi: '10.1038/nprot.2006.312 ' extern: 1 intvolume: ' 1' issue: '4' month: '01' page: 2075 - 81 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '2392' quality_controlled: 0 status: public title: Patch-clamp recording from mossy fiber terminals in hippocampal slices type: journal_article volume: 1 year: '2006' ... --- _id: '3890' abstract: - lang: eng text: We consider two-player infinite games played on graphs. The games are concurrent, in that at each state the players choose their moves simultaneously and independently, and stochastic, in that the moves determine a probability distribution for the successor state. The value of a game is the maximal probability with which a player can guarantee the satisfaction of her objective. We show that the values of concurrent games with w-regular objectives expressed as parity conditions can be decided in NP boolean AND coNP. This result substantially improves the best known previous bound of 3EXPTIME. It also shows that the full class of concurrent parity games is no harder than the special case of turn-based stochastic reachability games, for which NP boolean AND coNP is the best known bound. While the previous, more restricted NP boolean AND coNP results for graph games relied on the existence of particularly simple (pure memoryless) optimal strategies, in concurrent games with parity objectives optimal strategies may not exist, and epsilon-optimal strategies (which achieve the value of the game within a parameter epsilon > 0) require in general both randomization and infinite memory. Hence our proof must rely on a more detailed analysis of strategies and, in addition to the main result, yields two results that are interesting on their own. First, we show that there exist epsilon-optimal strategies that in the limit coincide with memoryless strategies; this parallels the celebrated result of Mertens-Neyman for concurrent games with limit-average objectives. Second, we complete the characterization of the memory requirements for epsilon-optimal strategies for concurrent games with parity conditions, by showing that memoryless strategies suffice for epsilon-optimality for coBachi conditions. acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: de Alfaro, Luca last_name: De Alfaro - 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, De Alfaro L, Henzinger TA. The complexity of quantitative concurrent parity games. In: SIAM; 2006:678-687. doi:10.1145/1109557.1109631' apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). The complexity of quantitative concurrent parity games (pp. 678–687). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1145/1109557.1109631' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “The Complexity of Quantitative Concurrent Parity Games,” 678–87. SIAM, 2006. https://doi.org/10.1145/1109557.1109631. ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of quantitative concurrent parity games,” presented at the SODA: Symposium on Discrete Algorithms, 2006, pp. 678–687.' ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. The complexity of quantitative concurrent parity games. SODA: Symposium on Discrete Algorithms, 678–687.' mla: Chatterjee, Krishnendu, et al. The Complexity of Quantitative Concurrent Parity Games. SIAM, 2006, pp. 678–87, doi:10.1145/1109557.1109631. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, SIAM, 2006, pp. 678–687. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T12:05:43Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:59Z day: '01' doi: 10.1145/1109557.1109631 extern: 1 month: '01' page: 678 - 687 publication_status: published publisher: SIAM publist_id: '2273' quality_controlled: 0 status: public title: The complexity of quantitative concurrent parity games type: conference year: '2006' ... --- _id: '3889' abstract: - lang: eng text: We study observation-based strategies for two-player turn-based games on graphs with omega-regular objectives. An observation-based strategy relies on imperfect information about the history of a play, namely, on the past sequence of observations. Such games occur in the synthesis of a controller that does not see the private state of the plant. Our main results are twofold. First, we give a fixed-point algorithm for computing the set of states from which a player can win with a deterministic observation-based strategy for any omega-regular objective. The fixed point is computed in the lattice of antichains of state sets. This algorithm has the advantages of being directed by the objective and of avoiding an explicit subset construction on the game graph. Second, we give an algorithm for computing the set of states from which a player can win with probability 1 with a randomized observation-based strategy for a Buchi objective. This set is of interest because in the absence of perfect information, randomized strategies are more powerful than deterministic ones. We show that our algorithms are optimal by proving matching lower bounds. acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR-0234690, by the SNSF under the Indo-Swiss Joint Research Programme, and by the FRFC project “Centre Fédéré en Vérification” funded by the FNRS under grant 2.4530.02. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: 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: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. Algorithms for omega-regular games with imperfect information. In: Vol 4207. Springer; 2006:287-302. doi:10.1007/11874683_19' apa: 'Chatterjee, K., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Algorithms for omega-regular games with imperfect information (Vol. 4207, pp. 287–302). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_19' chicago: Chatterjee, Krishnendu, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Algorithms for Omega-Regular Games with Imperfect Information,” 4207:287–302. Springer, 2006. https://doi.org/10.1007/11874683_19. ieee: 'K. Chatterjee, L. Doyen, T. A. Henzinger, and J. Raskin, “Algorithms for omega-regular games with imperfect information,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 287–302.' ista: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. 2006. Algorithms for omega-regular games with imperfect information. CSL: Computer Science Logic, LNCS, vol. 4207, 287–302.' mla: Chatterjee, Krishnendu, et al. Algorithms for Omega-Regular Games with Imperfect Information. Vol. 4207, Springer, 2006, pp. 287–302, doi:10.1007/11874683_19. short: K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006, pp. 287–302. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:05:43Z date_published: 2006-11-13T00:00:00Z date_updated: 2021-01-12T07:52:59Z day: '13' doi: 10.1007/11874683_19 extern: 1 intvolume: ' 4207' month: '11' page: 287 - 302 publication_status: published publisher: Springer publist_id: '2276' quality_controlled: 0 status: public title: Algorithms for omega-regular games with imperfect information type: conference volume: 4207 year: '2006' ... --- _id: '3891' abstract: - lang: eng text: 'We study infinite stochastic games played by two-players over a finite state space, with objectives specified by sets of infinite traces. The games are concurrent (players make moves simultaneously and independently), stochastic (the next state is determined by a probability distribution that depends on the current state and chosen moves of the players) and infinite (proceeds for infinite number of rounds). The analysis of concurrent stochastic games can be classified into: quantitative analysis, analyzing the optimum value of the game; and qualitative analysis, analyzing the set of states with optimum value 1. We consider concurrent games with tail objectives, i.e., objectives that are independent of the finite-prefix of traces, and show that the class of tail objectives are strictly richer than the omega-regular objectives. We develop new proof techniques to extend several properties of concurrent games with omega-regular objectives to concurrent games with tail objectives. We prove the positive limit-one property for tail objectives, that states for all concurrent games if the optimum value for a player is positive for a tail objective Phi at some state, then there is a state where the optimum value is 1 for Phi, for the player. We also show that the optimum values of zero-sum (strictly conflicting objectives) games with tail objectives can be related to equilibrium values of nonzero-sum (not strictly conflicting objectives) games with simpler reachability objectives. A consequence of our analysis presents a polynomial time reduction of the quantitative analysis of tail objectives to the qualitative analysis for the sub-class of one-player stochastic games (Markov decision processes).' alternative_title: - 'LNCS ' author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Chatterjee K. Concurrent games with tail objectives. In: Vol 4207. Springer; 2006:256-270. doi:10.1007/11874683_17' apa: 'Chatterjee, K. (2006). Concurrent games with tail objectives (Vol. 4207, pp. 256–270). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_17' chicago: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives,” 4207:256–70. Springer, 2006. https://doi.org/10.1007/11874683_17. ieee: 'K. Chatterjee, “Concurrent games with tail objectives,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 256–270.' ista: 'Chatterjee K. 2006. Concurrent games with tail objectives. CSL: Computer Science Logic, LNCS , vol. 4207, 256–270.' mla: Chatterjee, Krishnendu. Concurrent Games with Tail Objectives. Vol. 4207, Springer, 2006, pp. 256–70, doi:10.1007/11874683_17. short: K. Chatterjee, in:, Springer, 2006, pp. 256–270. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:05:44Z date_published: 2006-09-28T00:00:00Z date_updated: 2021-01-12T07:53:00Z day: '28' doi: 10.1007/11874683_17 extern: 1 intvolume: ' 4207' month: '09' page: 256 - 270 publication_status: published publisher: Springer publist_id: '2272' quality_controlled: 0 status: public title: Concurrent games with tail objectives type: conference volume: 4207 year: '2006' ... --- _id: '3888' 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 omega-regular winning conditions specified as Rabin or Streett objectives. These games are NP-complete and coNP-complete, respectively. The value of the game for a player at a state s given an objective Phi is the maximal probability with which the player can guarantee the satisfaction of Phi from s. We present a strategy-improvement algorithm to compute values in stochastic Rabin games, where an improvement step involves solving Markov decision processes (MDPs) and nonstochastic Rabin games. The algorithm also computes values for stochastic Streett games but does not directly yield an optimal strategy for Streett objectives. We then show how to obtain an optimal strategy for Streett objectives by solving certain nonstochastic Streett games. acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR-0234690, and by the SNSF under the Indo-Swiss Joint Research Programme. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Henzinger TA. Strategy improvement for stochastic Rabin and Streett games. In: Vol 4137. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2006:375-389. doi:10.1007/11817949_25' apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement for stochastic Rabin and Streett games (Vol. 4137, pp. 375–389). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11817949_25' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement for Stochastic Rabin and Streett Games,” 4137:375–89. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006. https://doi.org/10.1007/11817949_25. ieee: 'K. Chatterjee and T. A. Henzinger, “Strategy improvement for stochastic Rabin and Streett games,” presented at the CONCUR: Concurrency Theory, 2006, vol. 4137, pp. 375–389.' ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement for stochastic Rabin and Streett games. CONCUR: Concurrency Theory, LNCS, vol. 4137, 375–389.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement for Stochastic Rabin and Streett Games. Vol. 4137, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006, pp. 375–89, doi:10.1007/11817949_25. short: K. Chatterjee, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006, pp. 375–389. conference: name: 'CONCUR: Concurrency Theory' date_created: 2018-12-11T12:05:43Z date_published: 2006-08-10T00:00:00Z date_updated: 2021-01-12T07:52:58Z day: '10' doi: 10.1007/11817949_25 extern: 1 intvolume: ' 4137' month: '08' page: 375 - 389 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '2278' quality_controlled: 0 status: public title: Strategy improvement for stochastic Rabin and Streett games type: conference volume: 4137 year: '2006' ... --- _id: '3908' abstract: - lang: eng text: 'It is commonly believed that both the average length and the frequency of microsatellites correlate with genome size. We have estimated the frequency and the average length for 69 perfect dinucleotide microsatellites in an insect with an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae). Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat arrays are 1.4 to 2 times longer than in other insect species. The average repeat number in C. biguttulus lies in the range of higher vertebrates. Natural populations are highly variable. At least 30 alleles per locus were found and the expected heterozygosity is above 0.95 at all three loci studied. In contrast, the observed heterozygosity is much lower (≤0.51), which could be caused by long null alleles.' author: - first_name: Jana full_name: Ustinova, Jana last_name: Ustinova - first_name: Roland full_name: Achmann, Roland last_name: Achmann - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Frieder full_name: Mayer, Frieder last_name: Mayer citation: ama: 'Ustinova J, Achmann R, Cremer S, Mayer F. Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. 2006;62(2):158-167. doi:10.1007/s00239-005-0022-6' apa: 'Ustinova, J., Achmann, R., Cremer, S., & Mayer, F. (2006). Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. Springer. https://doi.org/10.1007/s00239-005-0022-6' chicago: 'Ustinova, Jana, Roland Achmann, Sylvia Cremer, and Frieder Mayer. “Long Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution. Springer, 2006. https://doi.org/10.1007/s00239-005-0022-6.' ieee: 'J. Ustinova, R. Achmann, S. Cremer, and F. Mayer, “Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus,” Journal of Molecular Evolution, vol. 62, no. 2. Springer, pp. 158–167, 2006.' ista: 'Ustinova J, Achmann R, Cremer S, Mayer F. 2006. Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. 62(2), 158–167.' mla: 'Ustinova, Jana, et al. “Long Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution, vol. 62, no. 2, Springer, 2006, pp. 158–67, doi:10.1007/s00239-005-0022-6.' short: J. Ustinova, R. Achmann, S. Cremer, F. Mayer, Journal of Molecular Evolution 62 (2006) 158–167. date_created: 2018-12-11T12:05:49Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T07:53:07Z day: '01' doi: 10.1007/s00239-005-0022-6 extern: '1' intvolume: ' 62' issue: '2' language: - iso: eng month: '02' oa_version: None page: 158 - 167 publication: Journal of Molecular Evolution publication_status: published publisher: Springer publist_id: '2242' status: public title: 'Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2006' ... --- _id: '3934' abstract: - lang: eng text: T cells develop in the thymus in a highly specialized cellular and extracellular microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly found in the medulla of the human thymic lobules. Using high-resolution light microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like structure, together with other typical basement membrane components including collagen type IV, nidogen and perlecan. Other interstitial matrix components, such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated with these structures. Three-dimensional (3D) confocal microscopy suggested a tubular structure, whereas immunoelectron and transmission electron microscopy showed that the core of these tubes contained fibrillar collagens enwrapped by the LN-5-containing membrane. These medullary conduits are surrounded by thymic epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and tenascin-C. Dendritic cells were also detected in close vicinity to the conduits. Both of these stromal cell types express major histocompatibility complex (MHC) class II molecules capable of antigen presentation. The conduits are connected to blood vessels but, with an average diameter of 2 mum, they are too small to transport cells. However, evidence is provided that smaller molecules such as a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in the conduits. These results clearly demonstrate that a conduit system, which is also known from secondary lymphatic organs such as lymph nodes and spleen, is present in the medulla of the human thymus, and that it might serve to transport small blood-borne molecules or chemokines to defined locations within the medulla. author: - first_name: Mihaela full_name: Drumea-Mirancea, Mihaela last_name: Drumea Mirancea - first_name: Johannes full_name: Wessels, Johannes T last_name: Wessels - first_name: Claudia full_name: Müller, Claudia A last_name: Müller - first_name: Mike full_name: Essl, Mike last_name: Essl - first_name: Johannes full_name: Eble, Johannes A last_name: Eble - first_name: Eva full_name: Tolosa, Eva last_name: Tolosa - first_name: Manuel full_name: Koch, Manuel last_name: Koch - first_name: Dieter full_name: Reinhardt, Dieter P last_name: Reinhardt - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Lydia full_name: Sorokin, Lydia last_name: Sorokin - first_name: York full_name: Stierhof, York-Dieter last_name: Stierhof - first_name: Heinz full_name: Schwarz, Heinz last_name: Schwarz - first_name: Gerd full_name: Klein, Gerd last_name: Klein citation: ama: 'Drumea Mirancea M, Wessels J, Müller C, et al. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 2006;119(Pt 7):1396-1405. doi:10.1242/​jcs.02840' apa: 'Drumea Mirancea, M., Wessels, J., Müller, C., Essl, M., Eble, J., Tolosa, E., … Klein, G. (2006). Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/​jcs.02840' chicago: 'Drumea Mirancea, Mihaela, Johannes Wessels, Claudia Müller, Mike Essl, Johannes Eble, Eva Tolosa, Manuel Koch, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/​jcs.02840.' ieee: 'M. Drumea Mirancea et al., “Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules,” Journal of Cell Science, vol. 119, no. Pt 7. Company of Biologists, pp. 1396–1405, 2006.' ista: 'Drumea Mirancea M, Wessels J, Müller C, Essl M, Eble J, Tolosa E, Koch M, Reinhardt D, Sixt MK, Sorokin L, Stierhof Y, Schwarz H, Klein G. 2006. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 119(Pt 7), 1396–1405.' mla: 'Drumea Mirancea, Mihaela, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science, vol. 119, no. Pt 7, Company of Biologists, 2006, pp. 1396–405, doi:10.1242/​jcs.02840.' short: M. Drumea Mirancea, J. Wessels, C. Müller, M. Essl, J. Eble, E. Tolosa, M. Koch, D. Reinhardt, M.K. Sixt, L. Sorokin, Y. Stierhof, H. Schwarz, G. Klein, Journal of Cell Science 119 (2006) 1396–1405. date_created: 2018-12-11T12:05:58Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:53:18Z day: '01' doi: 10.1242/​jcs.02840 extern: 1 intvolume: ' 119' issue: Pt 7 month: '04' page: 1396 - 1405 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '2192' quality_controlled: 0 status: public title: 'Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules' type: journal_article volume: 119 year: '2006' ... --- _id: '3935' abstract: - lang: eng text: Integrins regulate cell behavior through the assembly of multiprotein complexes at the site of cell adhesion. Parvins are components of such a multiprotein complex. They consist of three members (alpha-, beta-, and gamma-parvin), form a functional complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin has been reported to be expressed in hematopoietic organs. In the present study, we report the expression pattern of the parvins in hematopoietic cells and the phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent antibody response and lymphocyte and dendritic cell migration. These data indicate that despite the high expression of gamma-parvin in hematopoietic cells it must play a more subtle role for blood cell homeostasis. author: - first_name: Haiyan full_name: Chu, Haiyan last_name: Chu - first_name: Ingo full_name: Thievessen, Ingo last_name: Thievessen - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Ari full_name: Waisman, Ari last_name: Waisman - first_name: Attila full_name: Braun, Attila last_name: Braun - first_name: Angelika full_name: Noegel, Angelika A last_name: Noegel - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler citation: ama: Chu H, Thievessen I, Sixt MK, et al. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 2006;26(5):1817-1825. doi:10.1128/MCB.26.5.1817-1825.2006 apa: Chu, H., Thievessen, I., Sixt, M. K., Lämmermann, T., Waisman, A., Braun, A., … Fässler, R. (2006). γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. American Society for Microbiology. https://doi.org/10.1128/MCB.26.5.1817-1825.2006 chicago: Chu, Haiyan, Ingo Thievessen, Michael K Sixt, Tim Lämmermann, Ari Waisman, Attila Braun, Angelika Noegel, and Reinhard Fässler. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology. American Society for Microbiology, 2006. https://doi.org/10.1128/MCB.26.5.1817-1825.2006. ieee: H. Chu et al., “γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response,” Molecular and Cellular Biology, vol. 26, no. 5. American Society for Microbiology, pp. 1817–1825, 2006. ista: Chu H, Thievessen I, Sixt MK, Lämmermann T, Waisman A, Braun A, Noegel A, Fässler R. 2006. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 26(5), 1817–1825. mla: Chu, Haiyan, et al. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology, vol. 26, no. 5, American Society for Microbiology, 2006, pp. 1817–25, doi:10.1128/MCB.26.5.1817-1825.2006. short: H. Chu, I. Thievessen, M.K. Sixt, T. Lämmermann, A. Waisman, A. Braun, A. Noegel, R. Fässler, Molecular and Cellular Biology 26 (2006) 1817–1825. date_created: 2018-12-11T12:05:58Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T07:53:18Z day: '01' doi: 10.1128/MCB.26.5.1817-1825.2006 extern: 1 intvolume: ' 26' issue: '5' month: '03' page: 1817 - 1825 publication: Molecular and Cellular Biology publication_status: published publisher: American Society for Microbiology publist_id: '2193' quality_controlled: 0 status: public title: γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response type: journal_article volume: 26 year: '2006' ... --- _id: '3936' abstract: - lang: eng text: At least eight of the twelve known members of the beta1 integrin family are expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1 has received most attention as a main factor mediating firm adhesion to the endothelium during blood cell extravasation. Therapeutic trials are ongoing into the use of antibodies and small molecule inhibitors to target this interaction and hence obtain anti-inflammatory effects. However, extravasation is only one possible process that is mediated by beta1 integrins and there is evidence that they also mediate leukocyte retention and positioning in the tissue, lymphocyte activation and possibly migration within the interstitium. Genetic mouse models where integrins are selectively deleted on blood cells have been used to investigate these functions and further studies will be invaluable to critically evaluate therapeutic trials. author: - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Martina full_name: Bauer, Martina last_name: Bauer - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler citation: ama: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 2006;18(5):482-490. doi:10.1016/j.ceb.2006.08.007' apa: 'Sixt, M. K., Bauer, M., Lämmermann, T., & Fässler, R. (2006). β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2006.08.007' chicago: 'Sixt, Michael K, Martina Bauer, Tim Lämmermann, and Reinhard Fässler. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology. Elsevier, 2006. https://doi.org/10.1016/j.ceb.2006.08.007.' ieee: 'M. K. Sixt, M. Bauer, T. Lämmermann, and R. Fässler, “β1 integrins: zip codes and signaling relay for blood cells,” Current Opinion in Cell Biology, vol. 18, no. 5. Elsevier, pp. 482–490, 2006.' ista: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. 2006. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 18(5), 482–490.' mla: 'Sixt, Michael K., et al. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology, vol. 18, no. 5, Elsevier, 2006, pp. 482–90, doi:10.1016/j.ceb.2006.08.007.' short: M.K. Sixt, M. Bauer, T. Lämmermann, R. Fässler, Current Opinion in Cell Biology 18 (2006) 482–490. date_created: 2018-12-11T12:05:59Z date_published: 2006-10-01T00:00:00Z date_updated: 2021-01-12T07:53:19Z day: '01' doi: 10.1016/j.ceb.2006.08.007 extern: 1 intvolume: ' 18' issue: '5' month: '10' page: 482 - 490 publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '2191' quality_controlled: 0 status: public title: 'β1 integrins: zip codes and signaling relay for blood cells' type: journal_article volume: 18 year: '2006' ... --- _id: '4140' abstract: - lang: eng text: Wnt11 is a key signal, determining cell polarization and migration during vertebrate gastrulation. It is known that Wnt11 functionally interacts with several signaling components, the homologues of which control planar cell polarity in Drosophila melanogaster. Although in D. melanogaster these components are thought to polarize cells by asymmetrically localizing at the plasma membrane, it is not yet clear whether their subcellular localization plays a similarly important role in vertebrates. We show that in zebrafish embryonic cells, Wnt11 locally functions at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase cell contact persistence. This increase in cell contact persistence is mediated by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo at the plasma membrane, and it does not require the activity of further downstream effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence to coordinate cell movements during gastrulation. article_processing_charge: No author: - first_name: Sabine full_name: Witzel, Sabine last_name: Witzel - first_name: Vitaly full_name: Zimyanin, Vitaly last_name: Zimyanin - first_name: Filipa full_name: Carreira Barbosa, Filipa last_name: Carreira Barbosa - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada - 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: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. 2006;175(5):791-802. doi:10.1083/jcb.200606017 apa: Witzel, S., Zimyanin, V., Carreira Barbosa, F., Tada, M., & Heisenberg, C.-P. J. (2006). Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.200606017 chicago: Witzel, Sabine, Vitaly Zimyanin, Filipa Carreira Barbosa, Masazumi Tada, and Carl-Philipp J Heisenberg. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology. Rockefeller University Press, 2006. https://doi.org/10.1083/jcb.200606017. ieee: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, and C.-P. J. Heisenberg, “Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane,” Journal of Cell Biology, vol. 175, no. 5. Rockefeller University Press, pp. 791–802, 2006. ista: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. 2006. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. 175(5), 791–802. mla: Witzel, Sabine, et al. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology, vol. 175, no. 5, Rockefeller University Press, 2006, pp. 791–802, doi:10.1083/jcb.200606017. short: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, C.-P.J. Heisenberg, Journal of Cell Biology 175 (2006) 791–802. date_created: 2018-12-11T12:07:11Z date_published: 2006-12-04T00:00:00Z date_updated: 2021-01-12T07:54:48Z day: '04' doi: 10.1083/jcb.200606017 extern: '1' intvolume: ' 175' issue: '5' language: - iso: eng month: '12' oa_version: None page: 791 - 802 publication: Journal of Cell Biology publication_status: published publisher: Rockefeller University Press publist_id: '1980' status: public title: Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 175 year: '2006' ... --- _id: '4145' abstract: - lang: eng text: The detection of microRNAs (miRNAs) at single-cell resolution is important for studying the role of these posttranscriptional regulators. Here, we use a dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics of specific miRNAs in individual live cells. This approach reveals, for example, that in the developing mouse central nervous system,, miR-124a is expressed not only in postmitotic neurons but also in neuronal progenitor cells. Collectively, our results demonstrate that acute administration of DFRS plasmids.offers an alternative to previous in situ hybridization and transgenic approaches and allows the monitoring of miRNA appearance and disappearance in defined cell lineages during vertebrate development. article_processing_charge: No author: - first_name: Davide full_name: Tonelli, Davide last_name: Tonelli - first_name: Frederico full_name: Calegari, Frederico last_name: Calegari - first_name: Ji full_name: Fei, Ji last_name: Fei - first_name: Tadashi full_name: Nomura, Tadashi last_name: Nomura - first_name: Noriko full_name: Osumi, Noriko last_name: Osumi - 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: Wieland full_name: Huttner, Wieland last_name: Huttner citation: ama: Tonelli D, Calegari F, Fei J, et al. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 2006;41(6):727-732. doi:10.2144/000112296 apa: Tonelli, D., Calegari, F., Fei, J., Nomura, T., Osumi, N., Heisenberg, C.-P. J., & Huttner, W. (2006). Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. Informa Healthcare. https://doi.org/10.2144/000112296 chicago: Tonelli, Davide, Frederico Calegari, Ji Fei, Tadashi Nomura, Noriko Osumi, Carl-Philipp J Heisenberg, and Wieland Huttner. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques. Informa Healthcare, 2006. https://doi.org/10.2144/000112296. ieee: D. Tonelli et al., “Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid,” Biotechniques, vol. 41, no. 6. Informa Healthcare, pp. 727–732, 2006. ista: Tonelli D, Calegari F, Fei J, Nomura T, Osumi N, Heisenberg C-PJ, Huttner W. 2006. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 41(6), 727–732. mla: Tonelli, Davide, et al. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques, vol. 41, no. 6, Informa Healthcare, 2006, pp. 727–32, doi:10.2144/000112296. short: D. Tonelli, F. Calegari, J. Fei, T. Nomura, N. Osumi, C.-P.J. Heisenberg, W. Huttner, Biotechniques 41 (2006) 727–732. date_created: 2018-12-11T12:07:12Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:54:50Z day: '01' doi: 10.2144/000112296 extern: '1' intvolume: ' 41' issue: '6' language: - iso: eng month: '12' oa_version: None page: 727 - 732 publication: Biotechniques publication_status: published publisher: Informa Healthcare publist_id: '1974' status: public title: Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 41 year: '2006' ... --- _id: '4176' abstract: - lang: eng text: 'During vertebrate gastrulation, a well-orchestrated series of morphogenetic changes leads to the formation of the three germ layers: the ectoderm, mesoderm and endoderm. The analysis of gene expression patterns during gastrulation has been central to the identification of genes involved in germ layer formation. However, many proteins are regulated on a translational or post-translational level and are thus undetectable by gene expression analysis. Therefore, we developed a 2D-gel-based comparative proteomic approach to target proteins involved in germ layer morphogenesis during zebrafish gastrulation. Proteomes of ectodermal and mesendodermal progenitor cells were compared and 35 significantly regulated proteins were identified by mass spectrometry, including several proteins with predicted functions in cytoskeletal organization. A comparison of our proteomic results with data obtained in an accompanying microarray-based gene expression analysis revealed no significant overlap, confirming the complementary nature of proteomics and transcriptomics. The regulation of ezrin2, which was identified based on a reduction in spot intensity in mesendodermal cells, was independently validated. Furthermore, we show that ezrin2 is activated by phosphorylation in mesendodermal cells and is required for proper germ layer morphogenesis. We demonstrate the feasibility of proteomics in zebrafish, concluding that proteomics is a valuable tool for analysis of early development.' article_processing_charge: No author: - first_name: Vinzenz full_name: Link, Vinzenz last_name: Link - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: Irinka full_name: Castanon, Irinka last_name: Castanon - first_name: Petra full_name: Stockinger, Petra last_name: Stockinger - first_name: Andrej full_name: Shevchenko, Andrej last_name: Shevchenko - 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: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. 2006;119(10):2073-2083. doi:10.1242/jcs.02928 apa: Link, V., Carvalho, L., Castanon, I., Stockinger, P., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02928 chicago: Link, Vinzenz, Lara Carvalho, Irinka Castanon, Petra Stockinger, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02928. ieee: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, and C.-P. J. Heisenberg, “Identification of regulators of germ layer morphogenesis using proteomics in zebrafish,” Journal of Cell Science, vol. 119, no. 10. Company of Biologists, pp. 2073–2083, 2006. ista: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. 2006. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. 119(10), 2073–2083. mla: Link, Vinzenz, et al. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science, vol. 119, no. 10, Company of Biologists, 2006, pp. 2073–83, doi:10.1242/jcs.02928. short: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, C.-P.J. Heisenberg, Journal of Cell Science 119 (2006) 2073–2083. date_created: 2018-12-11T12:07:24Z date_published: 2006-05-15T00:00:00Z date_updated: 2021-01-12T07:55:04Z day: '15' doi: 10.1242/jcs.02928 extern: '1' intvolume: ' 119' issue: '10' language: - iso: eng month: '05' oa_version: None page: 2073 - 2083 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '1944' status: public title: Identification of regulators of germ layer morphogenesis using proteomics in zebrafish type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2006' ... --- _id: '4173' abstract: - lang: eng text: 'Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.' article_processing_charge: No author: - first_name: Vinzenz full_name: Link, Vinzenz last_name: Link - first_name: Andrej full_name: Shevchenko, Andrej last_name: Shevchenko - 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: Link V, Shevchenko A, Heisenberg C-PJ. Proteomics of early zebrafish embryos. BMC Developmental Biology. 2006;6:1-9. doi:10.1186/1471-213X-6-1 apa: Link, V., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Proteomics of early zebrafish embryos. BMC Developmental Biology. BioMed Central. https://doi.org/10.1186/1471-213X-6-1 chicago: Link, Vinzenz, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology. BioMed Central, 2006. https://doi.org/10.1186/1471-213X-6-1. ieee: V. Link, A. Shevchenko, and C.-P. J. Heisenberg, “Proteomics of early zebrafish embryos,” BMC Developmental Biology, vol. 6. BioMed Central, pp. 1–9, 2006. ista: Link V, Shevchenko A, Heisenberg C-PJ. 2006. Proteomics of early zebrafish embryos. BMC Developmental Biology. 6, 1–9. mla: Link, Vinzenz, et al. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology, vol. 6, BioMed Central, 2006, pp. 1–9, doi:10.1186/1471-213X-6-1. short: V. Link, A. Shevchenko, C.-P.J. Heisenberg, BMC Developmental Biology 6 (2006) 1–9. date_created: 2018-12-11T12:07:23Z date_published: 2006-01-13T00:00:00Z date_updated: 2021-01-12T07:55:02Z day: '13' doi: 10.1186/1471-213X-6-1 extern: '1' intvolume: ' 6' language: - iso: eng main_file_link: - open_access: '1' url: http://www.biomedcentral.com/1471-213X/6/1 month: '01' oa: 1 oa_version: None page: 1 - 9 publication: BMC Developmental Biology publication_status: published publisher: BioMed Central publist_id: '1945' status: public title: Proteomics of early zebrafish embryos 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: '2006' ... --- _id: '4178' abstract: - lang: eng text: Detailed reconstruction of the spatiotemporal history of embryonic cells is key to understanding tissue formation processes but is often complicated by the large number of cells involved, particularly so in vertebrates. Through a combination of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed the movement of mesencephalic and metencephalic cell populations in the early zebrafish embryo. To facilitate the analysis of our cell tracking data, we have created TracePilot, a software tool that allows interactive manipulation and visualization of tracking data. We demonstrate its utility by showing novel visualizations of cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot) is Java-based, available free of charge, and has a program structure that allows the incorporation of additional analysis tools. article_processing_charge: No author: - first_name: Tobias full_name: Langenberg, Tobias last_name: Langenberg - first_name: Tadeusz full_name: Dracz, Tadeusz last_name: Dracz - first_name: Andrew full_name: Oates, Andrew last_name: Oates - 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: Michael full_name: Brand, Michael last_name: Brand citation: ama: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. 2006;235(4):928-933. doi:10.1002/dvdy.20692 apa: Langenberg, T., Dracz, T., Oates, A., Heisenberg, C.-P. J., & Brand, M. (2006). Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. Wiley-Blackwell. https://doi.org/10.1002/dvdy.20692 chicago: Langenberg, Tobias, Tadeusz Dracz, Andrew Oates, Carl-Philipp J Heisenberg, and Michael Brand. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” Developmental Dynamics. Wiley-Blackwell, 2006. https://doi.org/10.1002/dvdy.20692. ieee: T. Langenberg, T. Dracz, A. Oates, C.-P. J. Heisenberg, and M. Brand, “Analysis and visualization of cell movement in the developing zebrafish brain,” Developmental Dynamics, vol. 235, no. 4. Wiley-Blackwell, pp. 928–933, 2006. ista: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. 2006. Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. 235(4), 928–933. mla: Langenberg, Tobias, et al. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” Developmental Dynamics, vol. 235, no. 4, Wiley-Blackwell, 2006, pp. 928–33, doi:10.1002/dvdy.20692. short: T. Langenberg, T. Dracz, A. Oates, C.-P.J. Heisenberg, M. Brand, Developmental Dynamics 235 (2006) 928–933. date_created: 2018-12-11T12:07:25Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:55:04Z day: '01' doi: 10.1002/dvdy.20692 extern: '1' intvolume: ' 235' issue: '4' language: - iso: eng month: '04' oa_version: None page: 928 - 933 publication: Developmental Dynamics publication_status: published publisher: Wiley-Blackwell publist_id: '1940' status: public title: Analysis and visualization of cell movement in the developing zebrafish brain type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 235 year: '2006' ... --- _id: '4184' abstract: - lang: eng text: Epithelial morphogenesis depends on coordinated changes in cell shape, a process that is still poorly understood. During zebrafish epiboly and Drosophila dorsal closure, cell-shape changes at the epithelial margin are of critical importance. Here evidence is provided for a conserved mechanism of local actin and myosin 2 recruitment during theses events. It was found that during epiboly of the zebrafish embryo, the movement of the outer epithelium (enveloping layer) over the yolk cell surface involves the constriction of marginal cells. This process depends on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm requires the Ste20-like kinase Msn1, an orthologue of Drosophila Misshapen. Similarly, in Drosophila, actin and myosin 2 localization and cell constriction at the margin of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus, this study has characterized a conserved mechanism underlying coordinated cell-shape changes during epithelial morphogenesis. article_processing_charge: No author: - first_name: Mathias full_name: Köppen, Mathias last_name: Köppen - first_name: Beatriz full_name: Fernández, Beatriz last_name: Fernández - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: António full_name: Jacinto, António last_name: Jacinto - 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: 'Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. 2006;133(14):2671-2681. doi:doi: 10.1242/dev.02439' apa: 'Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., & Heisenberg, C.-P. J. (2006). Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. Company of Biologists. https://doi.org/doi: 10.1242/dev.02439' chicago: 'Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and Carl-Philipp J Heisenberg. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” Development. Company of Biologists, 2006. https://doi.org/doi: 10.1242/dev.02439.' ieee: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg, “Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila,” Development, vol. 133, no. 14. Company of Biologists, pp. 2671–2681, 2006. ista: Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2006. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. 133(14), 2671–2681. mla: 'Köppen, Mathias, et al. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” Development, vol. 133, no. 14, Company of Biologists, 2006, pp. 2671–81, doi:doi: 10.1242/dev.02439.' short: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Development 133 (2006) 2671–2681. date_created: 2018-12-11T12:07:27Z date_published: 2006-07-15T00:00:00Z date_updated: 2021-01-12T07:55:08Z day: '15' doi: 'doi: 10.1242/dev.02439' extern: '1' intvolume: ' 133' issue: '14' language: - iso: eng month: '07' oa_version: None page: 2671 - 2681 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1935' status: public title: Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 133 year: '2006' ... --- _id: '4218' abstract: - lang: eng text: The molecular and cellular mechanisms governing cell motility and directed migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate that zebrafish primordial germ cells whose migration is guided by SDF-1 generate bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed at sites of higher levels of free calcium where activation of myosin contraction occurs. Separation of the acto-myosin cortex from the plasma membrane at these sites is followed by a flow of cytoplasm into the forming bleb. We propose that polarized activation of the receptor CXCR4 leads to a rise in free calcium that in turn activates myosin contraction in the part of the cell responding to higher levels of the ligand SDF-1. The biased formation of new protrusions in a particular region of the cell in response to SDF-1 defines the leading edge and the direction of cell migration. article_processing_charge: No author: - first_name: Heiko full_name: Blaser, Heiko last_name: Blaser - first_name: Michal full_name: Reichman Fried, Michal last_name: Reichman Fried - first_name: Irinka full_name: Castanon, Irinka last_name: Castanon - first_name: Karin full_name: Dumstrei, Karin last_name: Dumstrei - first_name: Florence full_name: Marlow, Florence last_name: Marlow - first_name: Koichi full_name: Kawakami, Koichi last_name: Kawakami - first_name: Lilianna full_name: Solnica Krezel, Lilianna last_name: Solnica Krezel - 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: Erez full_name: Raz, Erez last_name: Raz citation: ama: 'Blaser H, Reichman Fried M, Castanon I, et al. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. 2006;11(5):613-627. doi:10.1016/j.devcel.2006.09.023' apa: 'Blaser, H., Reichman Fried, M., Castanon, I., Dumstrei, K., Marlow, F., Kawakami, K., … Raz, E. (2006). Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2006.09.023' chicago: 'Blaser, Heiko, Michal Reichman Fried, Irinka Castanon, Karin Dumstrei, Florence Marlow, Koichi Kawakami, Lilianna Solnica Krezel, Carl-Philipp J Heisenberg, and Erez Raz. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell. Cell Press, 2006. https://doi.org/10.1016/j.devcel.2006.09.023.' ieee: 'H. Blaser et al., “Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow,” Developmental Cell, vol. 11, no. 5. Cell Press, pp. 613–627, 2006.' ista: 'Blaser H, Reichman Fried M, Castanon I, Dumstrei K, Marlow F, Kawakami K, Solnica Krezel L, Heisenberg C-PJ, Raz E. 2006. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. 11(5), 613–627.' mla: 'Blaser, Heiko, et al. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell, vol. 11, no. 5, Cell Press, 2006, pp. 613–27, doi:10.1016/j.devcel.2006.09.023.' short: H. Blaser, M. Reichman Fried, I. Castanon, K. Dumstrei, F. Marlow, K. Kawakami, L. Solnica Krezel, C.-P.J. Heisenberg, E. Raz, Developmental Cell 11 (2006) 613–627. date_created: 2018-12-11T12:07:39Z date_published: 2006-11-06T00:00:00Z date_updated: 2021-01-12T07:55:23Z day: '06' doi: 10.1016/j.devcel.2006.09.023 extern: '1' intvolume: ' 11' issue: '5' language: - iso: eng month: '11' oa_version: None page: 613 - 627 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '1898' status: public title: 'Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2006' ... --- _id: '4237' abstract: - lang: eng text: The growth function of populations is central in biomathematics. The main dogma is the existence of density-dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the Population. One important class of regulatory functions is the theta-logistic, which generalizes the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalizes many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter rho and a competition coefficient theta. Distinct sign combinations of these parameters reproduce not only the family of theta-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population. (c) 2005 Elsevier Ltd. All rights reserved. article_processing_charge: No author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. 2006;238(2):245-256. doi:3802 apa: de Vladar, H. (2006). Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. Elsevier. https://doi.org/3802 chicago: Vladar, Harold de. “Density-Dependence as a Size-Independent Regulatory Mechanism.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/3802. ieee: H. de Vladar, “Density-dependence as a size-independent regulatory mechanism,” Journal of Theoretical Biology, vol. 238, no. 2. Elsevier, pp. 245–256, 2006. ista: de Vladar H. 2006. Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. 238(2), 245–256. mla: de Vladar, Harold. “Density-Dependence as a Size-Independent Regulatory Mechanism.” Journal of Theoretical Biology, vol. 238, no. 2, Elsevier, 2006, pp. 245–56, doi:3802. short: H. de Vladar, Journal of Theoretical Biology 238 (2006) 245–256. date_created: 2018-12-11T12:07:46Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:55:31Z day: '01' doi: '3802' extern: '1' intvolume: ' 238' issue: '2' language: - iso: eng month: '01' oa_version: None page: 245 - 256 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '1878' status: public title: Density-dependence as a size-independent regulatory mechanism type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 238 year: '2006' ... --- _id: '4235' author: - first_name: Harold full_name: Harold Vladar id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 - first_name: J. full_name: González,J. A last_name: González citation: ama: de Vladar H, González J. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. 2006:91-109. apa: de Vladar, H., & González, J. (2006). Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. Elsevier. chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology. Elsevier, 2006. ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence of immunological activity and therapy,” Journal of Theoretical Biology. Elsevier, pp. 91–109, 2006. ista: de Vladar H, González J. 2006. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology., 91–109. mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology, Elsevier, 2006, pp. 91–109. short: H. de Vladar, J. González, Journal of Theoretical Biology (2006) 91–109. date_created: 2018-12-11T12:07:45Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:55:30Z day: '01' extern: 1 month: '01' page: 91 - 109 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '1879' quality_controlled: 0 status: public title: Dynamic response of cancer under the influence of immunological activity and therapy type: journal_article year: '2006' ... --- _id: '4248' abstract: - lang: eng text: 'In finite populations, genetic drift generates interference between selected loci, causing advantageous alleles to be found more often on different chromosomes than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson effect” generates indirect selection to increase recombination rates. We present a new method to quantify the strength of this selection. Our model represents a new beneficial allele (A) entering a population as a single copy, while another beneficial allele (B) is sweeping at another locus. A third locus affects the recombination rate between selected loci. Using a branching process model, we calculate the probability distribution of the number of copies of A on the different genetic backgrounds, after it is established but while it is still rare. Then, we use a deterministic model to express the change in frequency of the recombination modifier, due to hitchhiking, as A goes to fixation. We show that this method can give good estimates of selection for recombination. Moreover, it shows that recombination is selected through two different effects: it increases the fixation probability of new alleles, and it accelerates selective sweeps. The relative importance of these two effects depends on the relative times of occurrence of the beneficial alleles.' author: - first_name: Denis full_name: Roze, Denis last_name: Roze - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Roze D, Barton NH. The Hill-Robertson effect and the evolution of recombination. Genetics. 2006;173(3):1793-1811. doi:10.1534/genetics.106.058586 apa: Roze, D., & Barton, N. H. (2006). The Hill-Robertson effect and the evolution of recombination. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.106.058586 chicago: Roze, Denis, and Nicholas H Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” Genetics. Genetics Society of America, 2006. https://doi.org/10.1534/genetics.106.058586 . ieee: D. Roze and N. H. Barton, “The Hill-Robertson effect and the evolution of recombination,” Genetics, vol. 173, no. 3. Genetics Society of America, pp. 1793–1811, 2006. ista: Roze D, Barton NH. 2006. The Hill-Robertson effect and the evolution of recombination. Genetics. 173(3), 1793–1811. mla: Roze, Denis, and Nicholas H. Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” Genetics, vol. 173, no. 3, Genetics Society of America, 2006, pp. 1793–811, doi:10.1534/genetics.106.058586 . short: D. Roze, N.H. Barton, Genetics 173 (2006) 1793–1811. date_created: 2018-12-11T12:07:50Z date_published: 2006-07-01T00:00:00Z date_updated: 2021-01-12T07:55:36Z day: '01' doi: '10.1534/genetics.106.058586 ' extern: 1 intvolume: ' 173' issue: '3' month: '07' page: 1793 - 1811 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '1854' quality_controlled: 0 status: public title: The Hill-Robertson effect and the evolution of recombination type: journal_article volume: 173 year: '2006' ... --- _id: '4250' abstract: - lang: eng text: A recent analysis has shown that divergence between human and chimpanzee varies greatly across the genome. Although this is consistent with ‘hybridisation’ between the diverging human and chimp lineages, such observations can be explained more simply by the null model of allopatric speciation. author: - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Evolutionary Biology: How did the human species form? Current Biology. 2006;16(16):647-650. doi:10.1016/j.cub.2006.07.032' apa: 'Barton, N. H. (2006). Evolutionary Biology: How did the human species form? Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2006.07.032' chicago: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” Current Biology. Cell Press, 2006. https://doi.org/10.1016/j.cub.2006.07.032.' ieee: 'N. H. Barton, “Evolutionary Biology: How did the human species form?,” Current Biology, vol. 16, no. 16. Cell Press, pp. 647–650, 2006.' ista: 'Barton NH. 2006. Evolutionary Biology: How did the human species form? Current Biology. 16(16), 647–650.' mla: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” Current Biology, vol. 16, no. 16, Cell Press, 2006, pp. 647–50, doi:10.1016/j.cub.2006.07.032.' short: N.H. Barton, Current Biology 16 (2006) 647–650. date_created: 2018-12-11T12:07:51Z date_published: 2006-08-22T00:00:00Z date_updated: 2019-04-26T07:22:41Z day: '22' doi: 10.1016/j.cub.2006.07.032 extern: 1 intvolume: ' 16' issue: '16' month: '08' page: 647 - 650 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '1850' quality_controlled: 0 status: public title: 'Evolutionary Biology: How did the human species form?' type: review volume: 16 year: '2006' ... --- _id: '4359' alternative_title: - LNCS 3855 author: - first_name: Thomas full_name: Thomas Wies id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Viktor full_name: Kuncak, Viktor last_name: Kuncak - first_name: Patrick full_name: Lam,Patrick last_name: Lam - first_name: Andreas full_name: Podelski,Andreas last_name: Podelski - first_name: Martin full_name: Rinard,Martin last_name: Rinard citation: ama: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. Field Constraint Analysis. In: Springer; 2006:157-173. doi:1551' apa: 'Wies, T., Kuncak, V., Lam, P., Podelski, A., & Rinard, M. (2006). Field Constraint Analysis (pp. 157–173). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Springer. https://doi.org/1551' chicago: Wies, Thomas, Viktor Kuncak, Patrick Lam, Andreas Podelski, and Martin Rinard. “Field Constraint Analysis,” 157–73. Springer, 2006. https://doi.org/1551. ieee: 'T. Wies, V. Kuncak, P. Lam, A. Podelski, and M. Rinard, “Field Constraint Analysis,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, 2006, pp. 157–173.' ista: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. 2006. Field Constraint Analysis. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS 3855, , 157–173.' mla: Wies, Thomas, et al. Field Constraint Analysis. Springer, 2006, pp. 157–73, doi:1551. short: T. Wies, V. Kuncak, P. Lam, A. Podelski, M. Rinard, in:, Springer, 2006, pp. 157–173. conference: name: 'VMCAI: Verification, Model Checking and Abstract Interpretation' date_created: 2018-12-11T12:08:27Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:23Z day: '01' doi: '1551' extern: 1 month: '01' page: 157 - 173 publication_status: published publisher: Springer publist_id: '1097' quality_controlled: 0 status: public title: Field Constraint Analysis type: conference year: '2006' ... --- _id: '4373' alternative_title: - LNCS author: - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Dejan Nickovic id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Amir full_name: Pnueli,Amir last_name: Pnueli citation: ama: 'Maler O, Nickovic D, Pnueli A. Real Time Temporal Logic: Past, Present, Future. In: Springer; 2006:2-16. doi:1571' apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). Real Time Temporal Logic: Past, Present, Future (pp. 2–16). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1571' chicago: 'Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Real Time Temporal Logic: Past, Present, Future,” 2–16. Springer, 2006. https://doi.org/1571.' ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “Real Time Temporal Logic: Past, Present, Future,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 2–16.' ista: 'Maler O, Nickovic D, Pnueli A. 2006. Real Time Temporal Logic: Past, Present, Future. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 2–16.' mla: 'Maler, Oded, et al. Real Time Temporal Logic: Past, Present, Future. Springer, 2006, pp. 2–16, doi:1571.' short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 2–16. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:31Z date_published: 2006-01-23T00:00:00Z date_updated: 2021-01-12T07:56:29Z day: '23' doi: '1571' extern: 1 month: '01' page: 2 - 16 publication_status: published publisher: Springer publist_id: '1084' quality_controlled: 0 status: public title: 'Real Time Temporal Logic: Past, Present, Future' type: conference year: '2006' ... --- _id: '4374' alternative_title: - LNCS author: - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Dejan Nickovic id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Amir full_name: Pnueli,Amir last_name: Pnueli citation: ama: 'Maler O, Nickovic D, Pnueli A. From MITL to Timed Automata. In: Springer; 2006:274-289. doi:1570' apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). From MITL to Timed Automata (pp. 274–289). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1570' chicago: Maler, Oded, Dejan Nickovic, and Amir Pnueli. “From MITL to Timed Automata,” 274–89. Springer, 2006. https://doi.org/1570. ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “From MITL to Timed Automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 274–289.' ista: 'Maler O, Nickovic D, Pnueli A. 2006. From MITL to Timed Automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 274–289.' mla: Maler, Oded, et al. From MITL to Timed Automata. Springer, 2006, pp. 274–89, doi:1570. short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 274–289. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:31Z date_published: 2006-10-19T00:00:00Z date_updated: 2021-01-12T07:56:30Z day: '19' doi: '1570' extern: 1 month: '10' page: 274 - 289 publication_status: published publisher: Springer publist_id: '1085' quality_controlled: 0 status: public title: From MITL to Timed Automata type: conference year: '2006' ... --- _id: '4406' abstract: - lang: eng text: We propose and evaluate a new algorithm for checking the universality of nondeterministic finite automata. In contrast to the standard algorithm, which uses the subset construction to explicitly determinize the automaton, we keep the determinization step implicit. Our algorithm computes the least fixed point of a monotone function on the lattice of antichains of state sets. We evaluate the performance of our algorithm experimentally using the random automaton model recently proposed by Tabakov and Vardi. We show that on the difficult instances of this probabilistic model, the antichain algorithm outperforms the standard one by several orders of magnitude. We also show how variations of the antichain method can be used for solving the language-inclusion problem for nondeterministic finite automata, and the emptiness problem for alternating finite automata. acknowledgement: This research was supported in part by the NSF grants CCR-0234690 and CCR-0225610, and the Belgian FNRS grant 2.4530.02 of the FRFC project “Centre Fédéré en Vérification.” alternative_title: - LNCS author: - first_name: Martin full_name: De Wulf, Martin last_name: De Wulf - 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: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. Antichains: A new algorithm for checking universality of finite automata. In: Vol 4144. Springer; 2006:17-30. doi:10.1007/11817963_5' apa: 'De Wulf, M., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Antichains: A new algorithm for checking universality of finite automata (Vol. 4144, pp. 17–30). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/11817963_5' chicago: 'De Wulf, Martin, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Antichains: A New Algorithm for Checking Universality of Finite Automata,” 4144:17–30. Springer, 2006. https://doi.org/10.1007/11817963_5.' ieee: 'M. De Wulf, L. Doyen, T. A. Henzinger, and J. Raskin, “Antichains: A new algorithm for checking universality of finite automata,” presented at the CAV: Computer Aided Verification, 2006, vol. 4144, pp. 17–30.' ista: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. 2006. Antichains: A new algorithm for checking universality of finite automata. CAV: Computer Aided Verification, LNCS, vol. 4144, 17–30.' mla: 'De Wulf, Martin, et al. Antichains: A New Algorithm for Checking Universality of Finite Automata. Vol. 4144, Springer, 2006, pp. 17–30, doi:10.1007/11817963_5.' short: M. De Wulf, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006, pp. 17–30. conference: name: 'CAV: Computer Aided Verification' date_created: 2018-12-11T12:08:41Z date_published: 2006-08-08T00:00:00Z date_updated: 2021-01-12T07:56:45Z day: '08' doi: 10.1007/11817963_5 extern: 1 intvolume: ' 4144' month: '08' page: 17 - 30 publication_status: published publisher: Springer publist_id: '326' quality_controlled: 0 status: public title: 'Antichains: A new algorithm for checking universality of finite automata' type: conference volume: 4144 year: '2006' ... --- _id: '4401' alternative_title: - LNCS author: - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur - first_name: Pavol full_name: Pavol Cerny id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Steve full_name: Zdancewic,Steve last_name: Zdancewic citation: ama: 'Alur R, Cerny P, Zdancewic S. Preserving Secrecy Under Refinement. In: Springer; 2006:107-118. doi:1543' apa: 'Alur, R., Cerny, P., & Zdancewic, S. (2006). Preserving Secrecy Under Refinement (pp. 107–118). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/1543' chicago: Alur, Rajeev, Pavol Cerny, and Steve Zdancewic. “Preserving Secrecy Under Refinement,” 107–18. Springer, 2006. https://doi.org/1543. ieee: 'R. Alur, P. Cerny, and S. Zdancewic, “Preserving Secrecy Under Refinement,” presented at the ICALP: Automata, Languages and Programming, 2006, pp. 107–118.' ista: 'Alur R, Cerny P, Zdancewic S. 2006. Preserving Secrecy Under Refinement. ICALP: Automata, Languages and Programming, LNCS, , 107–118.' mla: Alur, Rajeev, et al. Preserving Secrecy Under Refinement. Springer, 2006, pp. 107–18, doi:1543. short: R. Alur, P. Cerny, S. Zdancewic, in:, Springer, 2006, pp. 107–118. conference: name: 'ICALP: Automata, Languages and Programming' date_created: 2018-12-11T12:08:40Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:42Z day: '01' doi: '1543' extern: 1 month: '01' page: 107 - 118 publication_status: published publisher: Springer publist_id: '1054' quality_controlled: 0 status: public title: Preserving Secrecy Under Refinement type: conference year: '2006' ... --- _id: '4437' abstract: - lang: eng text: The synthesis of reactive systems requires the solution of two-player games on graphs with ω-regular objectives. When the objective is specified by a linear temporal logic formula or nondeterministic Büchi automaton, then previous algorithms for solving the game require the construction of an equivalent deterministic automaton. However, determinization for automata on infinite words is extremely complicated, and current implementations fail to produce deterministic automata even for relatively small inputs. We show how to construct, from a given nondeterministic Büchi automaton, an equivalent nondeterministic parity automaton that is good for solving games with objective . The main insight is that a nondeterministic automaton is good for solving games if it fairly simulates the equivalent deterministic automaton. In this way, we omit the determinization step in game solving and reactive synthesis. The fact that our automata are nondeterministic makes them surprisingly simple, amenable to symbolic implementation, and allows an incremental search for winning strategies. acknowledgement: This research was supported in part by the Swiss National Science Foundation. 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: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: 'Henzinger TA, Piterman N. Solving games without determinization. In: Vol 4207. Springer; 2006:395-410. doi:10.1007/11874683_26' apa: 'Henzinger, T. A., & Piterman, N. (2006). Solving games without determinization (Vol. 4207, pp. 395–410). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_26' chicago: Henzinger, Thomas A, and Nir Piterman. “Solving Games without Determinization,” 4207:395–410. Springer, 2006. https://doi.org/10.1007/11874683_26. ieee: 'T. A. Henzinger and N. Piterman, “Solving games without determinization,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 395–410.' ista: 'Henzinger TA, Piterman N. 2006. Solving games without determinization. CSL: Computer Science Logic, LNCS, vol. 4207, 395–410.' mla: Henzinger, Thomas A., and Nir Piterman. Solving Games without Determinization. Vol. 4207, Springer, 2006, pp. 395–410, doi:10.1007/11874683_26. short: T.A. Henzinger, N. Piterman, in:, Springer, 2006, pp. 395–410. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:08:51Z date_published: 2006-09-20T00:00:00Z date_updated: 2021-01-12T07:56:58Z day: '20' doi: 10.1007/11874683_26 extern: 1 intvolume: ' 4207' month: '09' page: 395 - 410 publication_status: published publisher: Springer publist_id: '295' quality_controlled: 0 status: public title: Solving games without determinization type: conference volume: 4207 year: '2006' ... --- _id: '4436' abstract: - lang: eng text: We present an assume-guarantee interface algebra for real-time components. In our formalism a component implements a set of task sequences that share a resource. A component interface consists of an arrival rate function and a latency for each task sequence, and a capacity function for the shared resource. The interface specifies that the component guarantees certain task latencies depending on assumptions about task arrival rates and allocated resource capacities. Our algebra defines compatibility and refinement relations on interfaces. Interface compatibility can be checked on partial designs, even when some component interfaces are yet unknown. In this case interface composition computes as new assumptions the weakest constraints on the unknown components that are necessary to satisfy the specified guarantees. Interface refinement is defined in a way that ensures that compatible interfaces can be refined and implemented independently. Our algebra thus formalizes an interface-based design methodology that supports both the incremental addition of new components and the independent stepwise refinement of existing components. We demonstrate the flexibility and efficiency of the framework through simulation experiments. 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: Slobodan full_name: Matic, Slobodan last_name: Matic citation: ama: 'Henzinger TA, Matic S. An interface algebra for real-time components. In: IEEE; 2006:253-266. doi:10.1109/RTAS.2006.11' apa: 'Henzinger, T. A., & Matic, S. (2006). An interface algebra for real-time components (pp. 253–266). Presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, IEEE. https://doi.org/10.1109/RTAS.2006.11' chicago: Henzinger, Thomas A, and Slobodan Matic. “An Interface Algebra for Real-Time Components,” 253–66. IEEE, 2006. https://doi.org/10.1109/RTAS.2006.11. ieee: 'T. A. Henzinger and S. Matic, “An interface algebra for real-time components,” presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, 2006, pp. 253–266.' ista: 'Henzinger TA, Matic S. 2006. An interface algebra for real-time components. RTAS: Real-time and Embedded Technology and Applications Symposium, 253–266.' mla: Henzinger, Thomas A., and Slobodan Matic. An Interface Algebra for Real-Time Components. IEEE, 2006, pp. 253–66, doi:10.1109/RTAS.2006.11. short: T.A. Henzinger, S. Matic, in:, IEEE, 2006, pp. 253–266. conference: name: 'RTAS: Real-time and Embedded Technology and Applications Symposium' date_created: 2018-12-11T12:08:50Z date_published: 2006-04-24T00:00:00Z date_updated: 2021-01-12T07:56:57Z day: '24' doi: 10.1109/RTAS.2006.11 extern: 1 month: '04' page: 253 - 266 publication_status: published publisher: IEEE publist_id: '294' quality_controlled: 0 status: public title: An interface algebra for real-time components type: conference year: '2006' ... --- _id: '4432' abstract: - lang: eng text: We add freeze quantifiers to the game logic ATL in order to specify real-time objectives for games played on timed structures. We define the semantics of the resulting logic TATL by restricting the players to physically meaningful strategies, which do not prevent time from diverging. We show that TATL can be model checked over timed automaton games. We also specify timed optimization problems for physically meaningful strategies, and we show that for timed automaton games, the optimal answers can be approximated to within any degree of precision. acknowledgement: This research was supported in part by the NSF grants CCR-0208875, CCR-0225610, and CCR-0234690. 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: Vinayak full_name: Prabhu, Vinayak S last_name: Prabhu citation: ama: 'Henzinger TA, Prabhu V. Timed alternating-time temporal logic. In: Vol 4202. Springer; 2006:1-17. doi:10.1007/11867340_1' apa: 'Henzinger, T. A., & Prabhu, V. (2006). Timed alternating-time temporal logic (Vol. 4202, pp. 1–17). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/10.1007/11867340_1' chicago: Henzinger, Thomas A, and Vinayak Prabhu. “Timed Alternating-Time Temporal Logic,” 4202:1–17. Springer, 2006. https://doi.org/10.1007/11867340_1. ieee: 'T. A. Henzinger and V. Prabhu, “Timed alternating-time temporal logic,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, vol. 4202, pp. 1–17.' ista: 'Henzinger TA, Prabhu V. 2006. Timed alternating-time temporal logic. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 4202, 1–17.' mla: Henzinger, Thomas A., and Vinayak Prabhu. Timed Alternating-Time Temporal Logic. Vol. 4202, Springer, 2006, pp. 1–17, doi:10.1007/11867340_1. short: T.A. Henzinger, V. Prabhu, in:, Springer, 2006, pp. 1–17. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:49Z date_published: 2006-09-19T00:00:00Z date_updated: 2021-01-12T07:56:56Z day: '19' doi: 10.1007/11867340_1 extern: 1 intvolume: ' 4202' month: '09' page: 1 - 17 publication_status: published publisher: Springer publist_id: '296' quality_controlled: 0 status: public title: Timed alternating-time temporal logic type: conference volume: 4202 year: '2006' ... --- _id: '4431' abstract: - lang: eng text: 'We summarize some current trends in embedded systems design and point out some of their characteristics, such as the chasm between analytical and computational models, and the gap between safety-critical and best-effort engineering practices. We call for a coherent scientific foundation for embedded systems design, and we discuss a few key demands on such a foundation: the need for encompassing several manifestations of heterogeneity, and the need for constructivity in design. We believe that the development of a satisfactory Embedded Systems Design Science provides a timely challenge and opportunity for reinvigorating computer science.' acknowledgement: Supported in part by the ARTIST2 European Network of Excellence on Embedded Systems Design, by the NSF ITR Center on Hybrid and Embedded Software Systems (CHESS), and by the SNSF NCCR on Mobile Information and Communication Systems (MICS). 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: Joseph full_name: Sifakis, Joseph last_name: Sifakis citation: ama: 'Henzinger TA, Sifakis J. The embedded systems design challenge. In: Vol 4085. Springer; 2006:1-15. doi:10.1007/11813040_1' apa: 'Henzinger, T. A., & Sifakis, J. (2006). The embedded systems design challenge (Vol. 4085, pp. 1–15). Presented at the FM: Formal Methods, Springer. https://doi.org/10.1007/11813040_1' chicago: Henzinger, Thomas A, and Joseph Sifakis. “The Embedded Systems Design Challenge,” 4085:1–15. Springer, 2006. https://doi.org/10.1007/11813040_1. ieee: 'T. A. Henzinger and J. Sifakis, “The embedded systems design challenge,” presented at the FM: Formal Methods, 2006, vol. 4085, pp. 1–15.' ista: 'Henzinger TA, Sifakis J. 2006. The embedded systems design challenge. FM: Formal Methods, LNCS, vol. 4085, 1–15.' mla: Henzinger, Thomas A., and Joseph Sifakis. The Embedded Systems Design Challenge. Vol. 4085, Springer, 2006, pp. 1–15, doi:10.1007/11813040_1. short: T.A. Henzinger, J. Sifakis, in:, Springer, 2006, pp. 1–15. conference: name: 'FM: Formal Methods' date_created: 2018-12-11T12:08:49Z date_published: 2006-08-10T00:00:00Z date_updated: 2021-01-12T07:56:55Z day: '10' doi: 10.1007/11813040_1 extern: 1 intvolume: ' 4085' month: '08' page: 1 - 15 publication_status: published publisher: Springer publist_id: '301' quality_controlled: 0 status: public title: The embedded systems design challenge type: conference volume: 4085 year: '2006' ... --- _id: '4451' abstract: - lang: eng text: One source of complexity in the μ-calculus is its ability to specify an unbounded number of switches between universal (AX) and existential (EX) branching modes. We therefore study the problems of satisfiability, validity, model checking, and implication for the universal and existential fragments of the μ-calculus, in which only one branching mode is allowed. The universal fragment is rich enough to express most specifications of interest, and therefore improved algorithms are of practical importance. We show that while the satisfiability and validity problems become indeed simpler for the existential and universal fragments, this is, unfortunately, not the case for model checking and implication. We also show the corresponding results for the alternation-free fragment of the μ-calculus, where no alternations between least and greatest fixed points are allowed. Our results imply that efforts to find a polynomial-time model-checking algorithm for the μ-calculus can be replaced by efforts to find such an algorithm for the universal or existential fragment. 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: Orna full_name: Kupferman, Orna last_name: Kupferman - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: Henzinger TA, Kupferman O, Majumdar R. On the universal and existential fragments of the mu-calculus. Theoretical Computer Science. 2006;354(2):173-186. doi:10.1016/j.tcs.2005.11.015 apa: Henzinger, T. A., Kupferman, O., & Majumdar, R. (2006). On the universal and existential fragments of the mu-calculus. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2005.11.015 chicago: Henzinger, Thomas A, Orna Kupferman, and Ritankar Majumdar. “On the Universal and Existential Fragments of the Mu-Calculus.” Theoretical Computer Science. Elsevier, 2006. https://doi.org/10.1016/j.tcs.2005.11.015. ieee: T. A. Henzinger, O. Kupferman, and R. Majumdar, “On the universal and existential fragments of the mu-calculus,” Theoretical Computer Science, vol. 354, no. 2. Elsevier, pp. 173–186, 2006. ista: Henzinger TA, Kupferman O, Majumdar R. 2006. On the universal and existential fragments of the mu-calculus. Theoretical Computer Science. 354(2), 173–186. mla: Henzinger, Thomas A., et al. “On the Universal and Existential Fragments of the Mu-Calculus.” Theoretical Computer Science, vol. 354, no. 2, Elsevier, 2006, pp. 173–86, doi:10.1016/j.tcs.2005.11.015. short: T.A. Henzinger, O. Kupferman, R. Majumdar, Theoretical Computer Science 354 (2006) 173–186. date_created: 2018-12-11T12:08:55Z date_published: 2006-03-28T00:00:00Z date_updated: 2021-01-12T07:57:04Z day: '28' doi: 10.1016/j.tcs.2005.11.015 extern: 1 intvolume: ' 354' issue: '2' month: '03' page: 173 - 186 publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '276' quality_controlled: 0 status: public title: On the universal and existential fragments of the mu-calculus type: journal_article volume: 354 year: '2006' ... --- _id: '4523' abstract: - lang: eng text: We consider the problem if a given program satisfies a specified safety property. Interesting programs have infinite state spaces, with inputs ranging over infinite domains, and for these programs the property checking problem is undecidable. Two broad approaches to property checking are testing and verification. Testing tries to find inputs and executions which demonstrate violations of the property. Verification tries to construct a formal proof which shows that all executions of the program satisfy the property. Testing works best when errors are easy to find, but it is often difficult to achieve sufficient coverage for correct programs. On the other hand, verification methods are most successful when proofs are easy to find, but they are often inefficient at discovering errors. We propose a new algorithm, Synergy, which combines testing and verification. Synergy unifies several ideas from the literature, including counterexample-guided model checking, directed testing, and partition refinement.This paper presents a description of the Synergy algorithm, its theoretical properties, a comparison with related algorithms, and a prototype implementation called Yogi. author: - first_name: Bhargav full_name: Gulavani, Bhargav S last_name: Gulavani - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Yamini full_name: Kannan, Yamini last_name: Kannan - first_name: Aditya full_name: Nori, Aditya V last_name: Nori - first_name: Sriram full_name: Rajamani, Sriram K last_name: Rajamani citation: ama: 'Gulavani B, Henzinger TA, Kannan Y, Nori A, Rajamani S. Synergy: A new algorithm for property checking. In: ACM; 2006:117-127. doi:10.1145/1181775.1181790' apa: 'Gulavani, B., Henzinger, T. A., Kannan, Y., Nori, A., & Rajamani, S. (2006). Synergy: A new algorithm for property checking (pp. 117–127). Presented at the FSE: Foundations of Software Engineering, ACM. https://doi.org/10.1145/1181775.1181790' chicago: 'Gulavani, Bhargav, Thomas A Henzinger, Yamini Kannan, Aditya Nori, and Sriram Rajamani. “Synergy: A New Algorithm for Property Checking,” 117–27. ACM, 2006. https://doi.org/10.1145/1181775.1181790.' ieee: 'B. Gulavani, T. A. Henzinger, Y. Kannan, A. Nori, and S. Rajamani, “Synergy: A new algorithm for property checking,” presented at the FSE: Foundations of Software Engineering, 2006, pp. 117–127.' ista: 'Gulavani B, Henzinger TA, Kannan Y, Nori A, Rajamani S. 2006. Synergy: A new algorithm for property checking. FSE: Foundations of Software Engineering, 117–127.' mla: 'Gulavani, Bhargav, et al. Synergy: A New Algorithm for Property Checking. ACM, 2006, pp. 117–27, doi:10.1145/1181775.1181790.' short: B. Gulavani, T.A. Henzinger, Y. Kannan, A. Nori, S. Rajamani, in:, ACM, 2006, pp. 117–127. conference: name: 'FSE: Foundations of Software Engineering' date_created: 2018-12-11T12:09:18Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:59:26Z day: '01' doi: 10.1145/1181775.1181790 extern: 1 month: '01' page: 117 - 127 publication_status: published publisher: ACM publist_id: '206' quality_controlled: 0 status: public title: 'Synergy: A new algorithm for property checking' type: conference year: '2006' ... --- _id: '4526' abstract: - lang: eng text: 'We designed and implemented a new programming language called Hierarchical Timing Language (HTL) for hard realtime systems. Critical timing constraints are specified within the language,and ensured by the compiler. Programs in HTL are extensible in two dimensions without changing their timing behavior: new program modules can be added, and individual program tasks can be refined. The mechanism supporting time invariance under parallel composition is that different program modules communicate at specified instances of time. Time invariance under refinement is achieved by conservative scheduling of the top level. HTL is a coordination language, in that individual tasks can be implemented in "foreign" languages. As a case study, we present a distributed HTL implementation of an automotive steer-by-wire controller.' author: - 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: Alberto full_name: Sangiovanni-Vincentelli, Alberto last_name: Sangiovanni Vincentelli citation: ama: 'Ghosal A, Henzinger TA, Iercan D, Kirsch C, Sangiovanni Vincentelli A. A hierarchical coordination language for interacting real-time tasks. In: ACM; 2006:132-141. doi:10.1145/1176887.1176907' apa: 'Ghosal, A., Henzinger, T. A., Iercan, D., Kirsch, C., & Sangiovanni Vincentelli, A. (2006). A hierarchical coordination language for interacting real-time tasks (pp. 132–141). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1176887.1176907' chicago: Ghosal, Arkadeb, Thomas A Henzinger, Daniel Iercan, Christoph Kirsch, and Alberto Sangiovanni Vincentelli. “A Hierarchical Coordination Language for Interacting Real-Time Tasks,” 132–41. ACM, 2006. https://doi.org/10.1145/1176887.1176907. ieee: 'A. Ghosal, T. A. Henzinger, D. Iercan, C. Kirsch, and A. Sangiovanni Vincentelli, “A hierarchical coordination language for interacting real-time tasks,” presented at the EMSOFT: Embedded Software , 2006, pp. 132–141.' ista: 'Ghosal A, Henzinger TA, Iercan D, Kirsch C, Sangiovanni Vincentelli A. 2006. A hierarchical coordination language for interacting real-time tasks. EMSOFT: Embedded Software , 132–141.' mla: Ghosal, Arkadeb, et al. A Hierarchical Coordination Language for Interacting Real-Time Tasks. ACM, 2006, pp. 132–41, doi:10.1145/1176887.1176907. short: A. Ghosal, T.A. Henzinger, D. Iercan, C. Kirsch, A. Sangiovanni Vincentelli, in:, ACM, 2006, pp. 132–141. conference: name: 'EMSOFT: Embedded Software ' date_created: 2018-12-11T12:09:18Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:59:27Z day: '01' doi: 10.1145/1176887.1176907 extern: 1 month: '01' page: 132 - 141 publication_status: published publisher: ACM publist_id: '201' quality_controlled: 0 status: public title: A hierarchical coordination language for interacting real-time tasks type: conference year: '2006' ... --- _id: '4528' abstract: - lang: eng text: Computational modeling of biological systems is becoming increasingly common as scientists attempt to understand biological phenomena in their full complexity. Here we distinguish between two types of biological models mathematical and computational - according to their different representations of biological phenomena and their diverse potential. We call the approach of constructing computational models of biological systems executable biology, as it focuses on the design of executable computer algorithms that mimic biological phenomena. We give an overview of the main modeling efforts in this direction, and discuss some of the new challenges that executable biology poses for computer science and biology. We argue that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research, driving biology towards a more precise engineering discipline. 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 citation: ama: 'Fisher J, Henzinger TA. Executable biology. In: IEEE; 2006:1675-1682. doi:10.1109/WSC.2006.322942' apa: 'Fisher, J., & Henzinger, T. A. (2006). Executable biology (pp. 1675–1682). Presented at the WSC: Winter Simulation Conference, IEEE. https://doi.org/10.1109/WSC.2006.322942' chicago: Fisher, Jasmin, and Thomas A Henzinger. “Executable Biology,” 1675–82. IEEE, 2006. https://doi.org/10.1109/WSC.2006.322942. ieee: 'J. Fisher and T. A. Henzinger, “Executable biology,” presented at the WSC: Winter Simulation Conference, 2006, pp. 1675–1682.' ista: 'Fisher J, Henzinger TA. 2006. Executable biology. WSC: Winter Simulation Conference, 1675–1682.' mla: Fisher, Jasmin, and Thomas A. Henzinger. Executable Biology. IEEE, 2006, pp. 1675–82, doi:10.1109/WSC.2006.322942. short: J. Fisher, T.A. Henzinger, in:, IEEE, 2006, pp. 1675–1682. conference: name: 'WSC: Winter Simulation Conference' date_created: 2018-12-11T12:09:19Z date_published: 2006-12-03T00:00:00Z date_updated: 2021-01-12T07:59:28Z day: '03' doi: 10.1109/WSC.2006.322942 extern: 1 month: '12' page: 1675 - 1682 publication_status: published publisher: IEEE publist_id: '197' quality_controlled: 0 status: public title: Executable biology type: conference year: '2006' ... --- _id: '4539' abstract: - lang: eng text: Games on graphs with ω-regular objectives provide a model for the control and synthesis of reactive systems. Every ω-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Büchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett (fairness) objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound. acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Henzinger TA. Finitary winning in omega-regular games. In: Vol 3920. Springer; 2006:257-271. doi:10.1007/11691372_17' apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Finitary winning in omega-regular games (Vol. 3920, pp. 257–271). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Springer. https://doi.org/10.1007/11691372_17' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Finitary Winning in Omega-Regular Games,” 3920:257–71. Springer, 2006. https://doi.org/10.1007/11691372_17. ieee: 'K. Chatterjee and T. A. Henzinger, “Finitary winning in omega-regular games,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, 2006, vol. 3920, pp. 257–271.' ista: 'Chatterjee K, Henzinger TA. 2006. Finitary winning in omega-regular games. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 3920, 257–271.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Finitary Winning in Omega-Regular Games. Vol. 3920, Springer, 2006, pp. 257–71, doi:10.1007/11691372_17. short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2006, pp. 257–271. conference: name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' date_created: 2018-12-11T12:09:22Z date_published: 2006-03-15T00:00:00Z date_updated: 2021-01-12T07:59:32Z day: '15' doi: 10.1007/11691372_17 extern: 1 intvolume: ' 3920' month: '03' page: 257 - 271 publication_status: published publisher: Springer publist_id: '183' quality_controlled: 0 status: public title: Finitary winning in omega-regular games type: conference volume: 3920 year: '2006' ... --- _id: '4538' 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. These games lie in NP ∩ coNP. We present a strategy improvement algorithm for stochastic parity games; this is the first non-brute-force algorithm for solving these games. From the strategy improvement algorithm we obtain a randomized subexponential-time algorithm to solve such games. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Henzinger TA. Strategy improvement and randomized subexponential algorithms for stochastic parity games. In: Vol 3884. Springer; 2006:512-523. doi:10.1007/11672142_42' apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement and randomized subexponential algorithms for stochastic parity games (Vol. 3884, pp. 512–523). Presented at the STACS: Theoretical Aspects of Computer Science, Springer. https://doi.org/10.1007/11672142_42' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement and Randomized Subexponential Algorithms for Stochastic Parity Games,” 3884:512–23. Springer, 2006. https://doi.org/10.1007/11672142_42. ieee: 'K. Chatterjee and T. A. Henzinger, “Strategy improvement and randomized subexponential algorithms for stochastic parity games,” presented at the STACS: Theoretical Aspects of Computer Science, 2006, vol. 3884, pp. 512–523.' ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement and randomized subexponential algorithms for stochastic parity games. STACS: Theoretical Aspects of Computer Science, LNCS, vol. 3884, 512–523.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement and Randomized Subexponential Algorithms for Stochastic Parity Games. Vol. 3884, Springer, 2006, pp. 512–23, doi:10.1007/11672142_42. short: K. Chatterjee, T.A. Henzinger, in:, Springer, 2006, pp. 512–523. conference: name: 'STACS: Theoretical Aspects of Computer Science' date_created: 2018-12-11T12:09:22Z date_published: 2006-02-14T00:00:00Z date_updated: 2021-01-12T07:59:32Z day: '14' doi: 10.1007/11672142_42 extern: 1 intvolume: ' 3884' month: '02' page: 512 - 523 publication_status: published publisher: Springer publist_id: '184' quality_controlled: 0 status: public title: Strategy improvement and randomized subexponential algorithms for stochastic parity games type: conference volume: 3884 year: '2006' ... --- _id: '4551' abstract: - lang: eng text: "We consider Markov decision processes (MDPs) with multiple discounted reward objectives. Such MDPs occur in design problems where one wishes to simultaneously optimize several criteria, for example, latency and power. The possible trade-offs between the different objectives are characterized by the Pareto curve. We show that every Pareto-optimal point can be achieved by a memoryless strategy; however, unlike in the single-objective case, the memoryless strategy may require randomization. Moreover, we show that the Pareto curve can be approximated in polynomial time in the size of the MDP. Additionally, we study the problem if a given value vector is realizable by any strategy, and show that it can be decided in polynomial time; but the question whether it is realizable by a deterministic memoryless strategy is NP-complete. These results provide efficient algorithms for design exploration in MDP models with multiple objectives.\nThis research was supported in part by the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202. " acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: 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. Markov decision processes with multiple objectives. In: Vol 3884. Springer; 2006:325-336. doi:10.1007/11672142_26' apa: 'Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2006). Markov decision processes with multiple objectives (Vol. 3884, pp. 325–336). Presented at the STACS: Theoretical Aspects of Computer Science, Springer. https://doi.org/10.1007/11672142_26' chicago: Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Markov Decision Processes with Multiple Objectives,” 3884:325–36. Springer, 2006. https://doi.org/10.1007/11672142_26. ieee: 'K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Markov decision processes with multiple objectives,” presented at the STACS: Theoretical Aspects of Computer Science, 2006, vol. 3884, pp. 325–336.' ista: 'Chatterjee K, Majumdar R, Henzinger TA. 2006. Markov decision processes with multiple objectives. STACS: Theoretical Aspects of Computer Science, LNCS, vol. 3884, 325–336.' mla: Chatterjee, Krishnendu, et al. Markov Decision Processes with Multiple Objectives. Vol. 3884, Springer, 2006, pp. 325–36, doi:10.1007/11672142_26. short: K. Chatterjee, R. Majumdar, T.A. Henzinger, in:, Springer, 2006, pp. 325–336. conference: name: 'STACS: Theoretical Aspects of Computer Science' date_created: 2018-12-11T12:09:26Z date_published: 2006-02-14T00:00:00Z date_updated: 2021-01-12T07:59:38Z day: '14' doi: 10.1007/11672142_26 extern: 1 intvolume: ' 3884' month: '02' page: 325 - 336 publication_status: published publisher: Springer publist_id: '161' quality_controlled: 0 status: public title: Markov decision processes with multiple objectives type: conference volume: 3884 year: '2006' ... --- _id: '4550' abstract: - lang: eng text: 'In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent''s payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it sometimes suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of ω-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium.' 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 - first_name: Marcin full_name: Jurdziński, Marcin last_name: Jurdziński citation: ama: Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. Theoretical Computer Science. 2006;365(1-2):67-82. doi:10.1016/j.tcs.2006.07.032 apa: Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2006). Games with secure equilibria. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2006.07.032 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games with Secure Equilibria.” Theoretical Computer Science. Elsevier, 2006. https://doi.org/10.1016/j.tcs.2006.07.032. ieee: K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,” Theoretical Computer Science, vol. 365, no. 1–2. Elsevier, pp. 67–82, 2006. ista: Chatterjee K, Henzinger TA, Jurdziński M. 2006. Games with secure equilibria. Theoretical Computer Science. 365(1–2), 67–82. mla: Chatterjee, Krishnendu, et al. “Games with Secure Equilibria.” Theoretical Computer Science, vol. 365, no. 1–2, Elsevier, 2006, pp. 67–82, doi:10.1016/j.tcs.2006.07.032. short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, Theoretical Computer Science 365 (2006) 67–82. date_created: 2018-12-11T12:09:26Z date_published: 2006-08-07T00:00:00Z date_updated: 2021-01-12T07:59:38Z day: '07' doi: 10.1016/j.tcs.2006.07.032 extern: 1 intvolume: ' 365' issue: 1-2 month: '08' page: 67 - 82 publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '164' quality_controlled: 0 status: public title: Games with secure equilibria type: journal_article volume: 365 year: '2006' ... --- _id: '4549' abstract: - lang: eng text: We present a compositional theory of system verification, where specifications assign real-numbered costs to systems. These costs can express a wide variety of quantitative system properties, such as resource consumption, price, or a measure of how well a system satisfies its specification. The theory supports the composition of systems and specifications, and the hiding of variables. Boolean refinement relations are replaced by real-numbered distances between descriptions of a system at different levels of detail. We show that the classical Boolean rules for compositional reasoning have quantitative counterparts in our setting. While our general theory allows costs to be specified by arbitrary cost functions, we also consider a class of linear cost functions, which give rise to an instance of our framework where all operations are computable in polynomial time. acknowledgement: Supported in part by the NSF grants CCR-0234690, CCR-0208875, and CCR-0225610; by the NSF grant CCR-0132780 and ARP grant SC20051123. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: de Alfaro, Luca last_name: De Alfaro - first_name: Marco full_name: Faella, Marco last_name: Faella - 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: Mariëlle full_name: Stoelinga, Mariëlle last_name: Stoelinga citation: ama: 'Chatterjee K, De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Compositional quantitative reasoning. In: IEEE; 2006:179-188. doi:10.1109/QEST.2006.11' apa: 'Chatterjee, K., De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga, M. (2006). Compositional quantitative reasoning (pp. 179–188). Presented at the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2006.11' chicago: Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Compositional Quantitative Reasoning,” 179–88. IEEE, 2006. https://doi.org/10.1109/QEST.2006.11. ieee: 'K. Chatterjee, L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Compositional quantitative reasoning,” presented at the QEST: Quantitative Evaluation of Systems, 2006, pp. 179–188.' ista: 'Chatterjee K, De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2006. Compositional quantitative reasoning. QEST: Quantitative Evaluation of Systems, 179–188.' mla: Chatterjee, Krishnendu, et al. Compositional Quantitative Reasoning. IEEE, 2006, pp. 179–88, doi:10.1109/QEST.2006.11. short: K. Chatterjee, L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:, IEEE, 2006, pp. 179–188. conference: name: 'QEST: Quantitative Evaluation of Systems' date_created: 2018-12-11T12:09:26Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T07:59:37Z day: '01' doi: 10.1109/QEST.2006.11 extern: 1 month: '09' page: 179 - 188 publication_status: published publisher: IEEE publist_id: '163' quality_controlled: 0 status: public title: Compositional quantitative reasoning type: conference year: '2006' ... --- _id: '4552' abstract: - lang: eng text: 'A concurrent reachability game is a two-player game played on a graph: at each state, the players simultaneously and independently select moves; the two moves determine jointly a probability distribution over the successor states. The objective for player 1 consists in reaching a set of target states; the objective for player 2 is to prevent this, so that the game is zero-sum. Our contributions are two-fold. First, we present a simple proof of the fact that in concurrent reachability games, for all epsilon > 0, memoryless epsilon-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an epsilon-optimal strategy achieves the objective with probability within epsilon of the value of the game. In contrast to previous proofs of this fact, which rely on the limit behavior of discounted games using advanced Puisieux series analysis, our proof is elementary and combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives.' author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: de Alfaro, Luca last_name: De Alfaro - 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, De Alfaro L, Henzinger TA. Strategy improvement for concurrent reachability games. In: IEEE; 2006:291-300. doi:10.1109/QEST.2006.48' apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). Strategy improvement for concurrent reachability games (pp. 291–300). Presented at the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2006.48' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy Improvement for Concurrent Reachability Games,” 291–300. IEEE, 2006. https://doi.org/10.1109/QEST.2006.48. ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for concurrent reachability games,” presented at the QEST: Quantitative Evaluation of Systems, 2006, pp. 291–300.' ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. Strategy improvement for concurrent reachability games. QEST: Quantitative Evaluation of Systems, 291–300.' mla: Chatterjee, Krishnendu, et al. Strategy Improvement for Concurrent Reachability Games. IEEE, 2006, pp. 291–300, doi:10.1109/QEST.2006.48. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, IEEE, 2006, pp. 291–300. conference: name: 'QEST: Quantitative Evaluation of Systems' date_created: 2018-12-11T12:09:26Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:59:39Z day: '01' doi: 10.1109/QEST.2006.48 extern: 1 month: '01' page: 291 - 300 publication_status: published publisher: IEEE publist_id: '162' quality_controlled: 0 status: public title: Strategy improvement for concurrent reachability games type: conference year: '2006' ... --- _id: '4574' abstract: - lang: eng text: Many software model checkers are based on predicate abstraction. If the verification goal depends on pointer structures, the approach does not work well, because it is difficult to find adequate predicate abstractions for the heap. In contrast, shape analysis, which uses graph-based heap abstractions, can provide a compact representation of recursive data structures. We integrate shape analysis into the software model checker Blast. Because shape analysis is expensive, we do not apply it globally. Instead, we ensure that, like predicates, shape graphs are computed and stored locally, only where necessary for proving the verification goal. To achieve this, we extend lazy abstraction refinement, which so far has been used only for predicate abstractions, to three-valued logical structures. This approach does not only increase the precision of model checking, but it also increases the efficiency of shape analysis. We implemented the technique by extending Blast with calls to Tvla. alternative_title: - LNCS 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. Lazy shape analysis. In: Vol 4144. Springer; 2006:532-546. doi:10.1007/11817963_48' apa: 'Beyer, D., Henzinger, T. A., & Théoduloz, G. (2006). Lazy shape analysis (Vol. 4144, pp. 532–546). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/11817963_48' chicago: Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Lazy Shape Analysis,” 4144:532–46. Springer, 2006. https://doi.org/10.1007/11817963_48. ieee: 'D. Beyer, T. A. Henzinger, and G. Théoduloz, “Lazy shape analysis,” presented at the CAV: Computer Aided Verification, 2006, vol. 4144, pp. 532–546.' ista: 'Beyer D, Henzinger TA, Théoduloz G. 2006. Lazy shape analysis. CAV: Computer Aided Verification, LNCS, vol. 4144, 532–546.' mla: Beyer, Dirk, et al. Lazy Shape Analysis. Vol. 4144, Springer, 2006, pp. 532–46, doi:10.1007/11817963_48. short: D. Beyer, T.A. Henzinger, G. Théoduloz, in:, Springer, 2006, pp. 532–546. conference: name: 'CAV: Computer Aided Verification' date_created: 2018-12-11T12:09:33Z date_published: 2006-08-08T00:00:00Z date_updated: 2021-01-12T07:59:49Z day: '08' doi: 10.1007/11817963_48 extern: 1 intvolume: ' 4144' month: '08' page: 532 - 546 publication_status: published publisher: Springer publist_id: '133' quality_controlled: 0 status: public title: Lazy shape analysis type: conference volume: 4144 year: '2006' ... --- _id: '573' abstract: - lang: eng text: 'Mitchison and Jozsa recently suggested that the "chained-Zeno" counterfactual computation protocol recently proposed by Hosten et al. is counterfactual for only one output of the computer. This claim was based on the existing abstract algebraic definition of counterfactual computation, and indeed according to this definition, their argument is correct. However, a more general definition (physically adequate) for counterfactual computation is implicitly assumed by Hosten et. al. Here we explain in detail why the protocol is counterfactual and how the "history tracking" method of the existing description inadequately represents the physics underlying the protocol. Consequently, we propose a modified definition of counterfactual computation. Finally, we comment on one of the most interesting aspects of the error-correcting protocol. ' 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: Matthew full_name: Rakher, Matthew last_name: Rakher - first_name: Julio full_name: Barreiro, Julio last_name: Barreiro - first_name: Nicholas full_name: Peters, Nicholas last_name: Peters - first_name: Paul full_name: Kwiat, Paul last_name: Kwiat citation: ama: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual computation revisited. 2006. apa: Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2006). Counterfactual computation revisited. ArXiv. chicago: Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Computation Revisited.” ArXiv, 2006. ieee: O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual computation revisited.” ArXiv, 2006. ista: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2006. Counterfactual computation revisited. mla: Hosten, Onur, et al. Counterfactual Computation Revisited. ArXiv, 2006. short: O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, (2006). date_created: 2018-12-11T11:47:16Z date_published: 2006-08-06T00:00:00Z date_updated: 2020-05-12T08:23:52Z day: '06' extern: '1' external_id: arxiv: - '0607101' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/quant-ph/0607101 month: '08' oa: 1 oa_version: Preprint page: '12' publication_status: published publisher: ArXiv publist_id: '7241' status: public title: Counterfactual computation revisited type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2006' ... --- _id: '574' abstract: - lang: eng text: 'Vaidman, in a recent article adopts the method of ''quantum weak measurements in pre- and postselected ensembles'' to ascertain whether or not the chained-Zeno counterfactual computation scheme proposed by Hosten et al. is counterfactual; which has been the topic of a debate on the definition of counterfactuality. We disagree with his conclusion, which brings up some interesting aspects of quantum weak measurements and some concerns about the way they are interpreted. ' 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. Weak measurements and counterfactual computation. 2006. apa: Hosten, O., & Kwiat, P. (2006). Weak measurements and counterfactual computation. ArXiv. chicago: Hosten, Onur, and Paul Kwiat. “Weak Measurements and Counterfactual Computation.” ArXiv, 2006. ieee: O. Hosten and P. Kwiat, “Weak measurements and counterfactual computation.” ArXiv, 2006. ista: Hosten O, Kwiat P. 2006. Weak measurements and counterfactual computation. mla: Hosten, Onur, and Paul Kwiat. Weak Measurements and Counterfactual Computation. ArXiv, 2006. short: O. Hosten, P. Kwiat, (2006). date_created: 2018-12-11T11:47:16Z date_published: 2006-12-19T00:00:00Z date_updated: 2020-05-12T08:18:01Z day: '19' extern: '1' external_id: arxiv: - '0612159' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/quant-ph/0612159 month: '12' oa: 1 oa_version: Preprint page: '2' publication_status: published publisher: ArXiv publist_id: '7240' status: public title: Weak measurements and counterfactual computation type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2006' ... --- _id: '578' abstract: - lang: eng text: A source of single photons allows secure quantum key distribution, in addition, to being a critical resource for linear optics quantum computing. We describe our progress on deterministically creating single photons from spontaneous parametric downconversion, an extension of the Pittman, Jacobs and Franson scheme [Phys. Rev A, v66, 042303 (2002)]. Their idea was to conditionally prepare single photons by measuring one member of a spontaneously emitted photon pair and storing the remaining conditionally prepared photon until a predetermined time, when it would be "deterministically" released from storage. Our approach attempts to improve upon this by recycling the pump pulse in order to decrease the possibility of multiple-pair generation, while maintaining a high probability of producing a single pair. Many of the challenges we discuss are central to other quantum information technologies, including the need for low-loss optical storage, switching and detection, and fast feed-forward control. alternative_title: - Proc. SPIE author: - first_name: Nicholas full_name: Peters, Nicholas A last_name: Peters - first_name: Keith full_name: Arnold, Keith J last_name: Arnold - first_name: Aaron full_name: VanDevender, Aaron P last_name: Vandevender - first_name: Evan full_name: Jeffrey, Evan R last_name: Jeffrey - first_name: Radhika full_name: Rangarajan, Radhika last_name: Rangarajan - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Julio full_name: Barreiro, Julio T last_name: Barreiro - first_name: Joseph full_name: Altepeter, Joseph B last_name: Altepeter - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: 'Peters N, Arnold K, Vandevender A, et al. Towards a quasi-deterministic single-photon source. In: Vol 6305. SPIE; 2006. doi:10.1117/12.684702' apa: Peters, N., Arnold, K., Vandevender, A., Jeffrey, E., Rangarajan, R., Hosten, O., … Kwiat, P. (2006). Towards a quasi-deterministic single-photon source (Vol. 6305). Presented at the Quantum Communications and Quantum Imaging, SPIE. https://doi.org/10.1117/12.684702 chicago: Peters, Nicholas, Keith Arnold, Aaron Vandevender, Evan Jeffrey, Radhika Rangarajan, Onur Hosten, Julio Barreiro, Joseph Altepeter, and Paul Kwiat. “Towards a Quasi-Deterministic Single-Photon Source,” Vol. 6305. SPIE, 2006. https://doi.org/10.1117/12.684702. ieee: N. Peters et al., “Towards a quasi-deterministic single-photon source,” presented at the Quantum Communications and Quantum Imaging, 2006, vol. 6305. ista: Peters N, Arnold K, Vandevender A, Jeffrey E, Rangarajan R, Hosten O, Barreiro J, Altepeter J, Kwiat P. 2006. Towards a quasi-deterministic single-photon source. Quantum Communications and Quantum Imaging, Proc. SPIE, vol. 6305. mla: Peters, Nicholas, et al. Towards a Quasi-Deterministic Single-Photon Source. Vol. 6305, SPIE, 2006, doi:10.1117/12.684702. short: N. Peters, K. Arnold, A. Vandevender, E. Jeffrey, R. Rangarajan, O. Hosten, J. Barreiro, J. Altepeter, P. Kwiat, in:, SPIE, 2006. conference: name: Quantum Communications and Quantum Imaging date_created: 2018-12-11T11:47:17Z date_published: 2006-01-01T00:00:00Z date_updated: 2020-07-14T12:47:11Z day: '01' doi: 10.1117/12.684702 extern: 1 intvolume: ' 6305' month: '01' publication_status: published publisher: SPIE publist_id: '7234' quality_controlled: 0 status: public title: Towards a quasi-deterministic single-photon source type: conference volume: 6305 year: '2006' ... --- _id: '577' abstract: - lang: eng text: Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) are high-efficiency single-photon detectors which have multi-photon counting capability. While both the VLPCs and the SSPMs have inferred internal quantum efficiencies above 93%, the actual measured values for both the detectors were in fact limited to less than 88%, attributed to in-coupling losses. We are currently improving this overall detection efficiency via a) custom anti-reflection coating the detectors and the in-coupling fibers, b) implementing a novel cryogenic design to reduce transmission losses and, c) using low-noise electronics to obtain a better signal-to-noise ratio. alternative_title: - Proceedings of SPIE author: - first_name: Radhika full_name: Rangarajan, Radhika last_name: Rangarajan - first_name: Joseph full_name: Altepeter, Joseph B last_name: Altepeter - first_name: Evan full_name: Jeffrey, Evan R last_name: Jeffrey - first_name: Micah full_name: Stoutimore, Micah J last_name: Stoutimore - first_name: Nicholas full_name: Peters, Nicholas A last_name: Peters - 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 G last_name: Kwiat citation: ama: 'Rangarajan R, Altepeter J, Jeffrey E, et al. High-efficiency single-photon detectors. In: Vol 6372. SPIE; 2006. doi:10.1117/12.686117' apa: Rangarajan, R., Altepeter, J., Jeffrey, E., Stoutimore, M., Peters, N., Hosten, O., & Kwiat, P. (2006). High-efficiency single-photon detectors (Vol. 6372). Presented at the Unknown (978-081946470-5), SPIE. https://doi.org/10.1117/12.686117 chicago: Rangarajan, Radhika, Joseph Altepeter, Evan Jeffrey, Micah Stoutimore, Nicholas Peters, Onur Hosten, and Paul Kwiat. “High-Efficiency Single-Photon Detectors,” Vol. 6372. SPIE, 2006. https://doi.org/10.1117/12.686117. ieee: R. Rangarajan et al., “High-efficiency single-photon detectors,” presented at the Unknown (978-081946470-5), 2006, vol. 6372. ista: Rangarajan R, Altepeter J, Jeffrey E, Stoutimore M, Peters N, Hosten O, Kwiat P. 2006. High-efficiency single-photon detectors. Unknown (978-081946470-5), Proceedings of SPIE, vol. 6372. mla: Rangarajan, Radhika, et al. High-Efficiency Single-Photon Detectors. Vol. 6372, SPIE, 2006, doi:10.1117/12.686117. short: R. Rangarajan, J. Altepeter, E. Jeffrey, M. Stoutimore, N. Peters, O. Hosten, P. Kwiat, in:, SPIE, 2006. conference: name: Unknown (978-081946470-5) date_created: 2018-12-11T11:47:17Z date_published: 2006-01-01T00:00:00Z date_updated: 2020-07-14T12:47:11Z day: '01' doi: 10.1117/12.686117 extern: 1 intvolume: ' 6372' month: '01' publication_status: published publisher: SPIE publist_id: '7233' quality_controlled: 0 status: public title: High-efficiency single-photon detectors type: conference volume: 6372 year: '2006' ... --- _id: '579' abstract: - lang: eng text: 'The logic underlying the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to surprising effects. Counterfactual computation constitutes a striking example: the potential outcome of a quantum computation can be inferred, even if the computer is not run 1. Relying on similar arguments to interaction-free measurements 2 (or quantum interrogation3), counterfactual computation is accomplished by putting the computer in a superposition of ''running'' and ''not running'' states, and then interfering the two histories. Conditional on the as-yet-unknown outcome of the computation, it is sometimes possible to counterfactually infer information about the solution. Here we demonstrate counterfactual computation, implementing Grover''s search algorithm with an all-optical approach4. It was believed that the overall probability of such counterfactual inference is intrinsically limited1,5, so that it could not perform better on average than random guesses. However, using a novel ''chained'' version of the quantum Zeno effect6, we show how to boost the counterfactual inference probability to unity, thereby beating the random guessing limit. Our methods are general and apply to any physical system, as illustrated by a discussion of trapped-ion systems. Finally, we briefly show that, in certain circumstances, counterfactual computation can eliminate errors induced by decoherence. ' author: - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Matthew full_name: Rakher, Matthew T last_name: Rakher - first_name: Julio full_name: Barreiro, Julio T last_name: Barreiro - first_name: Nicholas full_name: Peters, Nicholas A last_name: Peters - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual quantum computation through quantum interrogation. Nature. 2006;439(7079):949-952. doi:10.1038/nature04523 apa: Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2006). Counterfactual quantum computation through quantum interrogation. Nature. Nature Publishing Group. https://doi.org/10.1038/nature04523 chicago: Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Quantum Computation through Quantum Interrogation.” Nature. Nature Publishing Group, 2006. https://doi.org/10.1038/nature04523. ieee: O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual quantum computation through quantum interrogation,” Nature, vol. 439, no. 7079. Nature Publishing Group, pp. 949–952, 2006. ista: Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2006. Counterfactual quantum computation through quantum interrogation. Nature. 439(7079), 949–952. mla: Hosten, Onur, et al. “Counterfactual Quantum Computation through Quantum Interrogation.” Nature, vol. 439, no. 7079, Nature Publishing Group, 2006, pp. 949–52, doi:10.1038/nature04523. short: O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, Nature 439 (2006) 949–952. date_created: 2018-12-11T11:47:18Z date_published: 2006-02-23T00:00:00Z date_updated: 2021-01-12T08:03:29Z day: '23' doi: 10.1038/nature04523 extern: 1 intvolume: ' 439' issue: '7079' month: '02' page: 949 - 952 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '7235' quality_controlled: 0 status: public title: Counterfactual quantum computation through quantum interrogation type: journal_article volume: 439 year: '2006' ... --- _id: '583' abstract: - lang: eng text: Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) facilitate efficient single-photon detection. We are attempting to improve their efficiency, previously limited to < 88% by coupling losses, via anti-reflection coatings, better electronics and cryogenics. author: - first_name: Radhika full_name: Rangarajan, Radhika last_name: Rangarajan - first_name: Nicholas full_name: Peters, Nicholas A last_name: Peters - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Joseph full_name: Altepeter, Joseph B last_name: Altepeter - first_name: Evan full_name: Jeffrey, Evan R last_name: Jeffrey - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: 'Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. Improved single-photon detection. In: IEEE; 2006. doi:10.1109/CLEO.2006.4628641' apa: 'Rangarajan, R., Peters, N., Hosten, O., Altepeter, J., Jeffrey, E., & Kwiat, P. (2006). Improved single-photon detection. Presented at the CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference, IEEE. https://doi.org/10.1109/CLEO.2006.4628641' chicago: Rangarajan, Radhika, Nicholas Peters, Onur Hosten, Joseph Altepeter, Evan Jeffrey, and Paul Kwiat. “Improved Single-Photon Detection.” IEEE, 2006. https://doi.org/10.1109/CLEO.2006.4628641. ieee: 'R. Rangarajan, N. Peters, O. Hosten, J. Altepeter, E. Jeffrey, and P. Kwiat, “Improved single-photon detection,” presented at the CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference, 2006.' ista: 'Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. 2006. Improved single-photon detection. CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference.' mla: Rangarajan, Radhika, et al. Improved Single-Photon Detection. IEEE, 2006, doi:10.1109/CLEO.2006.4628641. short: R. Rangarajan, N. Peters, O. Hosten, J. Altepeter, E. Jeffrey, P. Kwiat, in:, IEEE, 2006. conference: name: 'CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference' date_created: 2018-12-11T11:47:19Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T08:03:43Z day: '01' doi: 10.1109/CLEO.2006.4628641 extern: 1 month: '01' publication_status: published publisher: IEEE publist_id: '7232' quality_controlled: 0 status: public title: Improved single-photon detection type: conference year: '2006' ... --- _id: '6151' author: - first_name: Iris full_name: Salecker, Iris last_name: Salecker - first_name: Michael full_name: Häusser, Michael last_name: Häusser - 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: 'Salecker I, Häusser M, de Bono M. On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits. EMBO reports. 2006;7(6):585-589. doi:10.1038/sj.embor.7400713' apa: 'Salecker, I., Häusser, M., & de Bono, M. (2006). On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits. EMBO Reports. Wiley. https://doi.org/10.1038/sj.embor.7400713' chicago: 'Salecker, Iris, Michael Häusser, and Mario de Bono. “On the Axonal Road to Circuit Function and Behaviour: Workshop on the Assembly and Function of Neuronal Circuits.” EMBO Reports. Wiley, 2006. https://doi.org/10.1038/sj.embor.7400713.' ieee: 'I. Salecker, M. Häusser, and M. de Bono, “On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits,” EMBO reports, vol. 7, no. 6. Wiley, pp. 585–589, 2006.' ista: 'Salecker I, Häusser M, de Bono M. 2006. On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits. EMBO reports. 7(6), 585–589.' mla: 'Salecker, Iris, et al. “On the Axonal Road to Circuit Function and Behaviour: Workshop on the Assembly and Function of Neuronal Circuits.” EMBO Reports, vol. 7, no. 6, Wiley, 2006, pp. 585–89, doi:10.1038/sj.embor.7400713.' short: I. Salecker, M. Häusser, M. de Bono, EMBO Reports 7 (2006) 585–589. date_created: 2019-03-21T08:50:43Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T08:06:23Z day: '01' doi: 10.1038/sj.embor.7400713 extern: '1' external_id: pmid: - '16729018' intvolume: ' 7' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://europepmc.org/articles/pmc1479602 month: '06' oa: 1 oa_version: Published Version page: 585-589 pmid: 1 publication: EMBO reports publication_identifier: issn: - 1469-221X - 1469-3178 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2006' ... --- _id: '6152' author: - first_name: Candida full_name: Rogers, Candida last_name: Rogers - first_name: Annelie full_name: Persson, Annelie last_name: Persson - first_name: Benny full_name: Cheung, Benny last_name: Cheung - 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: Rogers C, Persson A, Cheung B, de Bono M. Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans. Current Biology. 2006;16(7):649-659. doi:10.1016/j.cub.2006.03.023 apa: Rogers, C., Persson, A., Cheung, B., & de Bono, M. (2006). Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2006.03.023 chicago: Rogers, Candida, Annelie Persson, Benny Cheung, and Mario de Bono. “Behavioral Motifs and Neural Pathways Coordinating O2 Responses and Aggregation in C. Elegans.” Current Biology. Elsevier, 2006. https://doi.org/10.1016/j.cub.2006.03.023. ieee: C. Rogers, A. Persson, B. Cheung, and M. de Bono, “Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans,” Current Biology, vol. 16, no. 7. Elsevier, pp. 649–659, 2006. ista: Rogers C, Persson A, Cheung B, de Bono M. 2006. Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans. Current Biology. 16(7), 649–659. mla: Rogers, Candida, et al. “Behavioral Motifs and Neural Pathways Coordinating O2 Responses and Aggregation in C. Elegans.” Current Biology, vol. 16, no. 7, Elsevier, 2006, pp. 649–59, doi:10.1016/j.cub.2006.03.023. short: C. Rogers, A. Persson, B. Cheung, M. de Bono, Current Biology 16 (2006) 649–659. date_created: 2019-03-21T09:15:27Z date_published: 2006-04-04T00:00:00Z date_updated: 2021-01-12T08:06:23Z day: '04' doi: 10.1016/j.cub.2006.03.023 extern: '1' external_id: pmid: - '16581509' intvolume: ' 16' issue: '7' language: - iso: eng month: '04' oa_version: None page: 649-659 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2006' ... --- _id: '7328' abstract: - lang: eng text: An experimental technique for measuring the current density distribution with a resolution smaller than the channel/rib scale of the flow field in polymer electrolyte fuel cells (PEFCs) is presented. The electron conductors in a plane perpendicular to the channel direction are considered as two-dimensional resistors. Hence, the current density is obtained from the solution of Laplace's equation with the potentials at current collector and reaction layer as boundary conditions. Using ohmic drop for calculating the local current, detailed knowledge of all resistances involved is of prime importance. In particular, the contact resistance between the gas diffusion layer (GDL) and flow field rib, as well as GDL bulk conductivity, are strongly dependent on clamping pressure. They represent a substantial amount of the total ohmic drop and therefore require careful consideration. The detailed experimental setup as well as the concise procedure for quantitative data evaluation is described. Finally, the method is applied successfully to a cell operated on pure oxygen and air up to high current densities. The results show that electrical and ionic resistances seem to govern the current distribution at low current regimes, whereas mass transport limitations locally hamper the current production at high loads. article_number: A2158 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: Mathias full_name: Reum, Mathias last_name: Reum - first_name: Jörg full_name: Evertz, Jörg last_name: Evertz - first_name: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: Freunberger SA, Reum M, Evertz J, Wokaun A, Büchi FN. Measuring the current distribution in PEFCs with sub-millimeter resolution. Journal of The Electrochemical Society. 2006;153(11). doi:10.1149/1.2345591 apa: Freunberger, S. A., Reum, M., Evertz, J., Wokaun, A., & Büchi, F. N. (2006). Measuring the current distribution in PEFCs with sub-millimeter resolution. Journal of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2345591 chicago: Freunberger, Stefan Alexander, Mathias Reum, Jörg Evertz, Alexander Wokaun, and Felix N. Büchi. “Measuring the Current Distribution in PEFCs with Sub-Millimeter Resolution.” Journal of The Electrochemical Society. The Electrochemical Society, 2006. https://doi.org/10.1149/1.2345591. ieee: S. A. Freunberger, M. Reum, J. Evertz, A. Wokaun, and F. N. Büchi, “Measuring the current distribution in PEFCs with sub-millimeter resolution,” Journal of The Electrochemical Society, vol. 153, no. 11. The Electrochemical Society, 2006. ista: Freunberger SA, Reum M, Evertz J, Wokaun A, Büchi FN. 2006. Measuring the current distribution in PEFCs with sub-millimeter resolution. Journal of The Electrochemical Society. 153(11), A2158. mla: Freunberger, Stefan Alexander, et al. “Measuring the Current Distribution in PEFCs with Sub-Millimeter Resolution.” Journal of The Electrochemical Society, vol. 153, no. 11, A2158, The Electrochemical Society, 2006, doi:10.1149/1.2345591. short: S.A. Freunberger, M. Reum, J. Evertz, A. Wokaun, F.N. Büchi, Journal of The Electrochemical Society 153 (2006). date_created: 2020-01-15T12:23:12Z date_published: 2006-09-20T00:00:00Z date_updated: 2021-01-12T08:13:06Z day: '20' doi: 10.1149/1.2345591 extern: '1' intvolume: ' 153' issue: '11' language: - iso: eng month: '09' 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: Measuring the current distribution in PEFCs with sub-millimeter resolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 153 year: '2006' ... --- _id: '7327' abstract: - lang: eng text: "Propagation of performance changes to adjacent cells in polymer electrolyte fuel cell stacks is studied by means of voltage monitoring and local current density measurements in peripheral cells of the stack. A technical fuel cell stack has been modified by implementing two independent reactant and coolant supplies in order to deliberately change the performance of one cell (anomalous cell) and study the coupling phenomena to adjacent cells (coupling cells), while keeping the working conditions of the later cell-group unaltered.\r\nTwo anomalies are studied: (i) air starvation and (ii) thermal anomaly, in a single anomalous cell in the stack and their coupling to adjacent cells. The results have shown that anomalies inducing considerable changes in the local current density of the anomalous cell (such as air starvation) propagate to adjacent cells affecting their performance. The propagation of local current density changes takes place via the common bipolar plate due to its finite thickness and in-plane conductivity. Consequently, anomalies which do not strongly influence the local current density distribution (such as a thermal anomaly under the studied working conditions) do not propagate to adjacent cells." article_processing_charge: No article_type: original 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: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: Santis M, Freunberger SA, Papra M, Wokaun A, Büchi FN. Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks. Journal of Power Sources. 2006;161(2):1076-1083. doi:10.1016/j.jpowsour.2006.06.007 apa: Santis, M., Freunberger, S. A., Papra, M., Wokaun, A., & Büchi, F. N. (2006). Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2006.06.007 chicago: Santis, Marco, Stefan Alexander Freunberger, Matthias Papra, Alexander Wokaun, and Felix N. Büchi. “Experimental Investigation of Coupling Phenomena in Polymer Electrolyte Fuel Cell Stacks.” Journal of Power Sources. Elsevier, 2006. https://doi.org/10.1016/j.jpowsour.2006.06.007. ieee: M. Santis, S. A. Freunberger, M. Papra, A. Wokaun, and F. N. Büchi, “Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks,” Journal of Power Sources, vol. 161, no. 2. Elsevier, pp. 1076–1083, 2006. ista: Santis M, Freunberger SA, Papra M, Wokaun A, Büchi FN. 2006. Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks. Journal of Power Sources. 161(2), 1076–1083. mla: Santis, Marco, et al. “Experimental Investigation of Coupling Phenomena in Polymer Electrolyte Fuel Cell Stacks.” Journal of Power Sources, vol. 161, no. 2, Elsevier, 2006, pp. 1076–83, doi:10.1016/j.jpowsour.2006.06.007. short: M. Santis, S.A. Freunberger, M. Papra, A. Wokaun, F.N. Büchi, Journal of Power Sources 161 (2006) 1076–1083. date_created: 2020-01-15T12:22:56Z date_published: 2006-10-27T00:00:00Z date_updated: 2021-01-12T08:13:06Z day: '27' doi: 10.1016/j.jpowsour.2006.06.007 extern: '1' intvolume: ' 161' issue: '2' language: - iso: eng month: '10' oa_version: None page: 1076-1083 publication: Journal of Power Sources publication_identifier: issn: - 0378-7753 publication_status: published publisher: Elsevier status: public title: Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 161 year: '2006' ... --- _id: '7326' abstract: - lang: eng text: 'Often the properties of a single cell are considered as representative for a complete polymer electrolyte fuel cell stack or even a fuel cell system. In some cases this comes close, however, in many real cases differences on several scales become important. Cell interaction phenomena in fuel cell stacks that arise from inequalities between adjacent cells are investigated in detail experimentally. For that, a specialized 2-cell stack with advanced localized diagnostics was developed. The results show that inequalities propagate by electrical coupling, inhomogeneous cell polarization and inducing in-plane current in the common bipolar plate. The effects of the different loss-mechanisms are analyzed and quantified. ' article_processing_charge: No author: - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi - 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: Marco full_name: Santis, Marco last_name: Santis citation: ama: 'Büchi FN, Freunberger SA, Santis M. What is learned beyond the scale of single cells? In: ECS Transactions. Vol 3. ECS; 2006:963-968. doi:10.1149/1.2356215' apa: 'Büchi, F. N., Freunberger, S. A., & Santis, M. (2006). What is learned beyond the scale of single cells? In ECS Transactions (Vol. 3, pp. 963–968). Cancun, Mexico: ECS. https://doi.org/10.1149/1.2356215' chicago: Büchi, Felix N., Stefan Alexander Freunberger, and Marco Santis. “What Is Learned beyond the Scale of Single Cells?” In ECS Transactions, 3:963–68. ECS, 2006. https://doi.org/10.1149/1.2356215. ieee: F. N. Büchi, S. A. Freunberger, and M. Santis, “What is learned beyond the scale of single cells?,” in ECS Transactions, Cancun, Mexico, 2006, vol. 3, no. 1, pp. 963–968. ista: Büchi FN, Freunberger SA, Santis M. 2006. What is learned beyond the scale of single cells? ECS Transactions. ECS Meeting vol. 3, 963–968. mla: Büchi, Felix N., et al. “What Is Learned beyond the Scale of Single Cells?” ECS Transactions, vol. 3, no. 1, ECS, 2006, pp. 963–68, doi:10.1149/1.2356215. short: F.N. Büchi, S.A. Freunberger, M. Santis, in:, ECS Transactions, ECS, 2006, pp. 963–968. conference: end_date: 2006-11-03 location: Cancun, Mexico name: ECS Meeting start_date: 2006-10-29 date_created: 2020-01-15T12:22:44Z date_published: 2006-11-03T00:00:00Z date_updated: 2021-01-12T08:13:05Z day: '03' doi: 10.1149/1.2356215 extern: '1' intvolume: ' 3' issue: '1' language: - iso: eng month: '11' oa_version: None page: 963-968 publication: ECS Transactions publication_status: published publisher: ECS quality_controlled: '1' status: public title: What is learned beyond the scale of single cells? type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2006' ... --- _id: '7329' abstract: - lang: eng text: A novel measurement principle for measuring the current distribution in polymer electrolyte fuel cells (PEFCs) is introduced. It allows, in contrast to all other known techniques, for the first time for a resolution smaller than the channel/rib scale of the flow field in PEFCs. The current density is obtained by considering the electron conductors in the cell as a two-dimensional resistor with the voltage drop caused by the current. The method was applied to a cell operated on oxygen up to high current densities. The results show that the ohmic resistances govern the current distribution in the low current regime, whereas mass transport limitations hamper the current production under the land at high loads. 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: Mathias full_name: Reum, Mathias last_name: Reum - first_name: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: Freunberger SA, Reum M, Wokaun A, Büchi FN. Expanding current distribution measurement in PEFCs to sub-millimeter resolution. Electrochemistry Communications. 2006;8(9):1435-1438. doi:10.1016/j.elecom.2006.05.032 apa: Freunberger, S. A., Reum, M., Wokaun, A., & Büchi, F. N. (2006). Expanding current distribution measurement in PEFCs to sub-millimeter resolution. Electrochemistry Communications. Elsevier. https://doi.org/10.1016/j.elecom.2006.05.032 chicago: Freunberger, Stefan Alexander, Mathias Reum, Alexander Wokaun, and Felix N. Büchi. “Expanding Current Distribution Measurement in PEFCs to Sub-Millimeter Resolution.” Electrochemistry Communications. Elsevier, 2006. https://doi.org/10.1016/j.elecom.2006.05.032. ieee: S. A. Freunberger, M. Reum, A. Wokaun, and F. N. Büchi, “Expanding current distribution measurement in PEFCs to sub-millimeter resolution,” Electrochemistry Communications, vol. 8, no. 9. Elsevier, pp. 1435–1438, 2006. ista: Freunberger SA, Reum M, Wokaun A, Büchi FN. 2006. Expanding current distribution measurement in PEFCs to sub-millimeter resolution. Electrochemistry Communications. 8(9), 1435–1438. mla: Freunberger, Stefan Alexander, et al. “Expanding Current Distribution Measurement in PEFCs to Sub-Millimeter Resolution.” Electrochemistry Communications, vol. 8, no. 9, Elsevier, 2006, pp. 1435–38, doi:10.1016/j.elecom.2006.05.032. short: S.A. Freunberger, M. Reum, A. Wokaun, F.N. Büchi, Electrochemistry Communications 8 (2006) 1435–1438. date_created: 2020-01-15T12:23:22Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T08:13:06Z day: '01' doi: 10.1016/j.elecom.2006.05.032 extern: '1' intvolume: ' 8' issue: '9' language: - iso: eng month: '09' oa_version: None page: 1435-1438 publication: Electrochemistry Communications publication_identifier: issn: - 1388-2481 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Expanding current distribution measurement in PEFCs to sub-millimeter resolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2006' ... --- _id: '7330' abstract: - lang: eng text: Polymer electrolyte fuel cells (PE fuel cells) working with air at low stoichiometries (<2.0) and standard electrochemical components show a high degree of inhomogeneity in the current density distribution over the active area. An inhomogeneous current density distribution leads to a non-uniform utilization of the active area, which could negatively affect the time of life of the cells. Furthermore, it is also believed to lower cell performance. In this work, the homogenization of the current density, realized by means of tailored cathodes with along-the-air-channel redistributed catalyst loadings, is investigated. The air stoichiometry range for which a homogenization of the current density is achieved depends upon the gradient with which the catalyst is redistributed along the air channel. A gentle increasing catalyst loading profile homogenizes the current density at relatively higher air stoichiometries, while a steeper profile is suited better for lower air stoichiometries. The results show that a homogenization of the current density by means of redistributed catalyst loading has negative effects on cell performance. Model calculations corroborate the experimental findings on homogenization of the current density and deliver an explanation for the decrease in cell performance. article_processing_charge: No article_type: original author: - first_name: M. full_name: Santis, M. 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: A. full_name: Reiner, A. last_name: Reiner - first_name: F.N. full_name: Büchi, F.N. last_name: Büchi citation: ama: Santis M, Freunberger SA, Reiner A, Büchi FN. Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients. Electrochimica Acta. 2006;51(25):5383-5393. doi:10.1016/j.electacta.2006.02.008 apa: Santis, M., Freunberger, S. A., Reiner, A., & Büchi, F. N. (2006). Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2006.02.008 chicago: Santis, M., Stefan Alexander Freunberger, A. Reiner, and F.N. Büchi. “Homogenization of the Current Density in Polymer Electrolyte Fuel Cells by In-Plane Cathode Catalyst Gradients.” Electrochimica Acta. Elsevier, 2006. https://doi.org/10.1016/j.electacta.2006.02.008. ieee: M. Santis, S. A. Freunberger, A. Reiner, and F. N. Büchi, “Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients,” Electrochimica Acta, vol. 51, no. 25. Elsevier, pp. 5383–5393, 2006. ista: Santis M, Freunberger SA, Reiner A, Büchi FN. 2006. Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients. Electrochimica Acta. 51(25), 5383–5393. mla: Santis, M., et al. “Homogenization of the Current Density in Polymer Electrolyte Fuel Cells by In-Plane Cathode Catalyst Gradients.” Electrochimica Acta, vol. 51, no. 25, Elsevier, 2006, pp. 5383–93, doi:10.1016/j.electacta.2006.02.008. short: M. Santis, S.A. Freunberger, A. Reiner, F.N. Büchi, Electrochimica Acta 51 (2006) 5383–5393. date_created: 2020-01-15T12:23:34Z date_published: 2006-07-01T00:00:00Z date_updated: 2021-01-12T08:13:07Z day: '01' doi: 10.1016/j.electacta.2006.02.008 extern: '1' intvolume: ' 51' issue: '25' language: - iso: eng month: '07' oa_version: None page: 5383-5393 publication: Electrochimica Acta publication_identifier: issn: - 0013-4686 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2006' ... --- _id: '7332' abstract: - lang: eng text: A quasi-two-dimensional, along-the-channel mass and heat-transfer model for a proton exchange membrane fuel cell (PEFC) is described and validated against experimental current distribution data. The model is formulated in a dimensional manner, i.e., local transport phenomena are treated one-dimensional in through-plane direction and coupled in-plane by convective transport in the gas and coolant channels. Thus, a two-dimensional slice running through the repetitive unit of a cell from the anode channel via membrane-electrode assembly (MEA) and cathode channel to the coolant channel and from inlet to outlet is modeled. The aim of the work is to elucidate the influence of operating conditions such as feed gas humidities and stoichiometric ratios on the along-the-channel current density distribution and to identify the distinct underlying voltage loss mechanisms. Furthermore, a complicated technical flow field is modeled by a combination of co- and counterflow subdomains and compared with experimental current densities. article_number: A396 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: Marco full_name: Santis, Marco last_name: Santis - 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 citation: ama: Freunberger SA, Santis M, Schneider IA, Wokaun A, Büchi FN. In-plane effects in large-scale PEMFCs. Journal of The Electrochemical Society. 2006;153(2). doi:10.1149/1.2150150 apa: Freunberger, S. A., Santis, M., Schneider, I. A., Wokaun, A., & Büchi, F. N. (2006). In-plane effects in large-scale PEMFCs. Journal of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2150150 chicago: Freunberger, Stefan Alexander, Marco Santis, Ingo A. Schneider, Alexander Wokaun, and Felix N. Büchi. “In-Plane Effects in Large-Scale PEMFCs.” Journal of The Electrochemical Society. The Electrochemical Society, 2006. https://doi.org/10.1149/1.2150150. ieee: S. A. Freunberger, M. Santis, I. A. Schneider, A. Wokaun, and F. N. Büchi, “In-plane effects in large-scale PEMFCs,” Journal of The Electrochemical Society, vol. 153, no. 2. The Electrochemical Society, 2006. ista: Freunberger SA, Santis M, Schneider IA, Wokaun A, Büchi FN. 2006. In-plane effects in large-scale PEMFCs. Journal of The Electrochemical Society. 153(2), A396. mla: Freunberger, Stefan Alexander, et al. “In-Plane Effects in Large-Scale PEMFCs.” Journal of The Electrochemical Society, vol. 153, no. 2, A396, The Electrochemical Society, 2006, doi:10.1149/1.2150150. short: S.A. Freunberger, M. Santis, I.A. Schneider, A. Wokaun, F.N. Büchi, Journal of The Electrochemical Society 153 (2006). date_created: 2020-01-15T12:24:00Z date_published: 2006-01-04T00:00:00Z date_updated: 2021-01-12T08:13:08Z day: '04' doi: 10.1149/1.2150150 extern: '1' intvolume: ' 153' issue: '2' language: - iso: eng month: '01' 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: In-plane effects in large-scale PEMFCs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 153 year: '2006' ... --- _id: '7331' abstract: - lang: eng text: A previously developed mathematical model for water management and current density distribution in a polymer electrolyte fuel cell (PEFCs) is employed to investigate the effects of cooling strategies on cell performance. The model describes a two-dimensional slice through the cell along the channels and through the entire cell sandwich including the coolant channels and the bipolar plate. Arbitrary flow arrangements of fuel, oxidant, and coolant stream directions can be described. Due to the serious impact of temperature on all processes in the PEFC, both the relative direction of the coolant stream to the gas streams and its mass flow turns out to significantly affect the cell performance. Besides influencing the electrochemical reaction and all kinds of mass transfer temperature, variations predominantly alter the local membrane hydration distribution and subseqently its conductivity. article_number: A909 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: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: 'Freunberger SA, Wokaun A, Büchi FN. In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance. Journal of The Electrochemical Society. 2006;153(5). doi:10.1149/1.2185282' apa: 'Freunberger, S. A., Wokaun, A., & Büchi, F. N. (2006). In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance. Journal of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2185282' chicago: 'Freunberger, Stefan Alexander, Alexander Wokaun, and Felix N. Büchi. “In-Plane Effects in Large-Scale PEFCs: II. The Influence of Cooling Strategy on Cell Performance.” Journal of The Electrochemical Society. The Electrochemical Society, 2006. https://doi.org/10.1149/1.2185282.' ieee: 'S. A. Freunberger, A. Wokaun, and F. N. Büchi, “In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance,” Journal of The Electrochemical Society, vol. 153, no. 5. The Electrochemical Society, 2006.' ista: 'Freunberger SA, Wokaun A, Büchi FN. 2006. In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance. Journal of The Electrochemical Society. 153(5), A909.' mla: 'Freunberger, Stefan Alexander, et al. “In-Plane Effects in Large-Scale PEFCs: II. The Influence of Cooling Strategy on Cell Performance.” Journal of The Electrochemical Society, vol. 153, no. 5, A909, The Electrochemical Society, 2006, doi:10.1149/1.2185282.' short: S.A. Freunberger, A. Wokaun, F.N. Büchi, Journal of The Electrochemical Society 153 (2006). date_created: 2020-01-15T12:23:46Z date_published: 2006-03-27T00:00:00Z date_updated: 2021-01-12T08:13:08Z day: '27' doi: 10.1149/1.2185282 extern: '1' intvolume: ' 153' issue: '5' language: - iso: eng month: '03' 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: 'In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 153 year: '2006' ... --- _id: '854' abstract: - lang: eng text: Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch - the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene. acknowledgement: |- FAK is supported by the NSF Graduate Research Fellowship. We thank the Natural History Museum, North-Eastern Research Center, Far Eastern Branch of the Russian Academy of Sciences for photographic material ofM. primigenius leg, V. A. Nikishina for artwork and technical support, Y.B. Yurov, G. Dvoryanchikov, N. Riazanskaya and T. Kolesnikova for technical support, K. Mehren and C. Gray for elephant specimens, and V. Y. Solovyev for help with artwork of animal images. author: - first_name: Evgeny full_name: Rogaev, Evgeny I last_name: Rogaev - first_name: Yuri full_name: Moliaka, Yuri K last_name: Moliaka - first_name: Boris full_name: Malyarchuk, Boris A last_name: Malyarchuk - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Miroslava full_name: Derenko, Miroslava V last_name: Derenko - first_name: Ilya full_name: Chumakov, Ilya M last_name: Chumakov - first_name: Anastasia full_name: Grigorenko, Anastasia P last_name: Grigorenko citation: ama: Rogaev E, Moliaka Y, Malyarchuk B, et al. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 2006;4(3):0403-0410. doi:10.1371/journal.pbio.0040073 apa: Rogaev, E., Moliaka, Y., Malyarchuk, B., Kondrashov, F., Derenko, M., Chumakov, I., & Grigorenko, A. (2006). Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.0040073 chicago: Rogaev, Evgeny, Yuri Moliaka, Boris Malyarchuk, Fyodor Kondrashov, Miroslava Derenko, Ilya Chumakov, and Anastasia Grigorenko. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology. Public Library of Science, 2006. https://doi.org/10.1371/journal.pbio.0040073. ieee: E. Rogaev et al., “Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius,” PLoS Biology, vol. 4, no. 3. Public Library of Science, pp. 0403–0410, 2006. ista: Rogaev E, Moliaka Y, Malyarchuk B, Kondrashov F, Derenko M, Chumakov I, Grigorenko A. 2006. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 4(3), 0403–0410. mla: Rogaev, Evgeny, et al. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology, vol. 4, no. 3, Public Library of Science, 2006, pp. 0403–10, doi:10.1371/journal.pbio.0040073. short: E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov, A. Grigorenko, PLoS Biology 4 (2006) 0403–0410. date_created: 2018-12-11T11:48:51Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T08:19:58Z day: '01' doi: 10.1371/journal.pbio.0040073 extern: 1 intvolume: ' 4' issue: '3' month: '03' page: 0403 - 0410 publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '6794' quality_controlled: 0 status: public title: Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius type: journal_article volume: 4 year: '2006' ...