--- _id: '1687' abstract: - lang: eng text: Guided cell movement is essential for development and integrity of animals and crucially involved in cellular immune responses. Leukocytes are professional migratory cells that can navigate through most types of tissues and sense a wide range of directional cues. The responses of these cells to attractants have been mainly explored in tissue culture settings. How leukocytes make directional decisions in situ, within the challenging environment of a tissue maze, is less understood. Here we review recent advances in how leukocytes sense chemical cues in complex tissue settings and make links with paradigms of directed migration in development and Dictyostelium discoideum amoebae. author: - first_name: Milka full_name: Sarris, Milka last_name: Sarris - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Sarris M, Sixt MK. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 2015;36(10):93-102. doi:10.1016/j.ceb.2015.08.001' apa: 'Sarris, M., & Sixt, M. K. (2015). Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.08.001' chicago: 'Sarris, Milka, and Michael K Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.08.001.' ieee: 'M. Sarris and M. K. Sixt, “Navigating in tissue mazes: Chemoattractant interpretation in complex environments,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 93–102, 2015.' ista: 'Sarris M, Sixt MK. 2015. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 36(10), 93–102.' mla: 'Sarris, Milka, and Michael K. Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 93–102, doi:10.1016/j.ceb.2015.08.001.' short: M. Sarris, M.K. Sixt, Current Opinion in Cell Biology 36 (2015) 93–102. date_created: 2018-12-11T11:53:28Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:52:31Z day: '01' ddc: - '570' department: - _id: MiSi doi: 10.1016/j.ceb.2015.08.001 ec_funded: 1 file: - access_level: open_access checksum: c29973924b790aab02fdd91857759cfb content_type: application/pdf creator: system date_created: 2018-12-12T10:11:21Z date_updated: 2020-07-14T12:45:12Z file_id: '4875' file_name: IST-2016-445-v1+1_1-s2.0-S0955067415001064-main.pdf file_size: 797964 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 36' issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '10' oa: 1 oa_version: Published Version page: 93 - 102 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '5458' pubrep_id: '445' quality_controlled: '1' scopus_import: 1 status: public title: 'Navigating in tissue mazes: Chemoattractant interpretation in complex environments' 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: 36 year: '2015' ... --- _id: '1685' abstract: - lang: eng text: "Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph is a subgraph of G such that cutting Σ along G yields a topological disk. We provide a fixed parameter tractable approximation scheme for the problem of computing the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε) approximation of the shortest cut graph in time f(ε, g)n3.\r\nOur techniques first rely on the computation of a spanner for the problem using the technique of brick decompositions, to reduce the problem to the case of bounded tree-width. Then, to solve the bounded tree-width case, we introduce a variant of the surface-cut decomposition of Rué, Sau and Thilikos, which may be of independent interest." alternative_title: - LNCS author: - first_name: Vincent full_name: Cohen Addad, Vincent last_name: Cohen Addad - first_name: Arnaud N full_name: De Mesmay, Arnaud N id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87 last_name: De Mesmay citation: ama: 'Cohen Addad V, de Mesmay AN. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. In: Vol 9294. Springer; 2015:386-398. doi:10.1007/978-3-662-48350-3_33' apa: 'Cohen Addad, V., & de Mesmay, A. N. (2015). A fixed parameter tractable approximation scheme for the optimal cut graph of a surface (Vol. 9294, pp. 386–398). Presented at the ESA: European Symposium on Algorithms, Patras, Greece: Springer. https://doi.org/10.1007/978-3-662-48350-3_33' chicago: Cohen Addad, Vincent, and Arnaud N de Mesmay. “A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface,” 9294:386–98. Springer, 2015. https://doi.org/10.1007/978-3-662-48350-3_33. ieee: 'V. Cohen Addad and A. N. de Mesmay, “A fixed parameter tractable approximation scheme for the optimal cut graph of a surface,” presented at the ESA: European Symposium on Algorithms, Patras, Greece, 2015, vol. 9294, pp. 386–398.' ista: 'Cohen Addad V, de Mesmay AN. 2015. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. ESA: European Symposium on Algorithms, LNCS, vol. 9294, 386–398.' mla: Cohen Addad, Vincent, and Arnaud N. de Mesmay. A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface. Vol. 9294, Springer, 2015, pp. 386–98, doi:10.1007/978-3-662-48350-3_33. short: V. Cohen Addad, A.N. de Mesmay, in:, Springer, 2015, pp. 386–398. conference: end_date: 2015-09-16 location: Patras, Greece name: 'ESA: European Symposium on Algorithms' start_date: 2015-09-14 date_created: 2018-12-11T11:53:27Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:31Z day: '01' department: - _id: UlWa doi: 10.1007/978-3-662-48350-3_33 ec_funded: 1 intvolume: ' 9294' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1507.01688 month: '09' oa: 1 oa_version: Preprint page: 386 - 398 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5462' quality_controlled: '1' scopus_import: 1 status: public title: A fixed parameter tractable approximation scheme for the optimal cut graph of a surface type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9294 year: '2015' ... --- _id: '1688' abstract: - lang: eng text: 'We estimate the selection constant in the following geometric selection theorem by Pach: For every positive integer d, there is a constant (Formula presented.) such that whenever (Formula presented.) are n-element subsets of (Formula presented.), we can find a point (Formula presented.) and subsets (Formula presented.) for every i∈[d+1], each of size at least cdn, such that p belongs to all rainbowd-simplices determined by (Formula presented.) simplices with one vertex in each Yi. We show a super-exponentially decreasing upper bound (Formula presented.). The ideas used in the proof of the upper bound also help us to prove Pach’s theorem with (Formula presented.), which is a lower bound doubly exponentially decreasing in d (up to some polynomial in the exponent). For comparison, Pach’s original approach yields a triply exponentially decreasing lower bound. On the other hand, Fox, Pach, and Suk recently obtained a hypergraph density result implying a proof of Pach’s theorem with (Formula presented.). In our construction for the upper bound, we use the fact that the minimum solid angle of every d-simplex is super-exponentially small. This fact was previously unknown and might be of independent interest. For the lower bound, we improve the ‘separation’ part of the argument by showing that in one of the key steps only d+1 separations are necessary, compared to 2d separations in the original proof. We also provide a measure version of Pach’s theorem.' acknowledgement: R. K. was supported by the Russian Foundation for Basic Research Grant 15-31-20403 (mol_a_ved) and grant 15-01-99563. J. K., Z. P., and M. T. were partially supported by ERC Advanced Research Grant No. 267165 (DISCONV) and by the project CE-ITI (GAČR P202/12/G061) of the Czech Science Foundation. J. K. was also partially supported by Swiss National Science Foundation Grants 200021-137574 and 200020-14453. P. P., Z. P., and M. T. were partially supported by the Charles University Grant GAUK 421511. P. P. was also partially supported by the Charles University Grant SVV-2014-260107. Z. P. was also partially supported by the Charles University Grant SVV-2014-260103. author: - first_name: Roman full_name: Karasev, Roman last_name: Karasev - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl - first_name: Pavel full_name: Paták, Pavel last_name: Paták - first_name: Zuzana full_name: Patakova, Zuzana last_name: Patakova orcid: 0000-0002-3975-1683 - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 citation: ama: Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 2015;54(3):610-636. doi:10.1007/s00454-015-9720-z apa: Karasev, R., Kynčl, J., Paták, P., Patakova, Z., & Tancer, M. (2015). Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9720-z chicago: Karasev, Roman, Jan Kynčl, Pavel Paták, Zuzana Patakova, and Martin Tancer. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9720-z. ieee: R. Karasev, J. Kynčl, P. Paták, Z. Patakova, and M. Tancer, “Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex,” Discrete & Computational Geometry, vol. 54, no. 3. Springer, pp. 610–636, 2015. ista: Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. 2015. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 54(3), 610–636. mla: Karasev, Roman, et al. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry, vol. 54, no. 3, Springer, 2015, pp. 610–36, doi:10.1007/s00454-015-9720-z. short: R. Karasev, J. Kynčl, P. Paták, Z. Patakova, M. Tancer, Discrete & Computational Geometry 54 (2015) 610–636. date_created: 2018-12-11T11:53:28Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:52:32Z day: '01' department: - _id: UlWa doi: 10.1007/s00454-015-9720-z intvolume: ' 54' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1403.8147 month: '10' oa: 1 oa_version: Preprint page: 610 - 636 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5457' quality_controlled: '1' scopus_import: 1 status: public title: Bounds for Pach's selection theorem and for the minimum solid angle in a simplex type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2015' ... --- _id: '1680' abstract: - lang: eng text: We consider the satisfiability problem for modal logic over first-order definable classes of frames.We confirm the conjecture from Hemaspaandra and Schnoor [2008] that modal logic is decidable over classes definable by universal Horn formulae. We provide a full classification of Horn formulae with respect to the complexity of the corresponding satisfiability problem. It turns out, that except for the trivial case of inconsistent formulae, local satisfiability is eitherNP-complete or PSPACE-complete, and global satisfiability is NP-complete, PSPACE-complete, or ExpTime-complete. We also show that the finite satisfiability problem for modal logic over Horn definable classes of frames is decidable. On the negative side, we show undecidability of two related problems. First, we exhibit a simple universal three-variable formula defining the class of frames over which modal logic is undecidable. Second, we consider the satisfiability problem of bimodal logic over Horn definable classes of frames, and also present a formula leading to undecidability. article_number: '2' author: - first_name: Jakub full_name: Michaliszyn, Jakub last_name: Michaliszyn - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop - first_name: Emanuel full_name: Kieroňski, Emanuel last_name: Kieroňski citation: ama: Michaliszyn J, Otop J, Kieroňski E. On the decidability of elementary modal logics. ACM Transactions on Computational Logic. 2015;17(1). doi:10.1145/2817825 apa: Michaliszyn, J., Otop, J., & Kieroňski, E. (2015). On the decidability of elementary modal logics. ACM Transactions on Computational Logic. ACM. https://doi.org/10.1145/2817825 chicago: Michaliszyn, Jakub, Jan Otop, and Emanuel Kieroňski. “On the Decidability of Elementary Modal Logics.” ACM Transactions on Computational Logic. ACM, 2015. https://doi.org/10.1145/2817825. ieee: J. Michaliszyn, J. Otop, and E. Kieroňski, “On the decidability of elementary modal logics,” ACM Transactions on Computational Logic, vol. 17, no. 1. ACM, 2015. ista: Michaliszyn J, Otop J, Kieroňski E. 2015. On the decidability of elementary modal logics. ACM Transactions on Computational Logic. 17(1), 2. mla: Michaliszyn, Jakub, et al. “On the Decidability of Elementary Modal Logics.” ACM Transactions on Computational Logic, vol. 17, no. 1, 2, ACM, 2015, doi:10.1145/2817825. short: J. Michaliszyn, J. Otop, E. Kieroňski, ACM Transactions on Computational Logic 17 (2015). date_created: 2018-12-11T11:53:26Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:29Z day: '01' department: - _id: ToHe doi: 10.1145/2817825 ec_funded: 1 intvolume: ' 17' issue: '1' language: - iso: eng month: '09' oa_version: None project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: ACM Transactions on Computational Logic publication_status: published publisher: ACM publist_id: '5468' quality_controlled: '1' status: public title: On the decidability of elementary modal logics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '1682' abstract: - lang: eng text: 'We study the problem of robust satisfiability of systems of nonlinear equations, namely, whether for a given continuous function f:K→ ℝn on a finite simplicial complex K and α > 0, it holds that each function g: K → ℝn such that ||g - f || ∞ < α, has a root in K. Via a reduction to the extension problem of maps into a sphere, we particularly show that this problem is decidable in polynomial time for every fixed n, assuming dimK ≤ 2n - 3. This is a substantial extension of previous computational applications of topological degree and related concepts in numerical and interval analysis. Via a reverse reduction, we prove that the problem is undecidable when dim K > 2n - 2, where the threshold comes from the stable range in homotopy theory. For the lucidity of our exposition, we focus on the setting when f is simplexwise linear. Such functions can approximate general continuous functions, and thus we get approximation schemes and undecidability of the robust satisfiability in other possible settings.' article_number: '26' author: - first_name: Peter full_name: Franek, Peter last_name: Franek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál citation: ama: Franek P, Krcál M. Robust satisfiability of systems of equations. Journal of the ACM. 2015;62(4). doi:10.1145/2751524 apa: Franek, P., & Krcál, M. (2015). Robust satisfiability of systems of equations. Journal of the ACM. ACM. https://doi.org/10.1145/2751524 chicago: Franek, Peter, and Marek Krcál. “Robust Satisfiability of Systems of Equations.” Journal of the ACM. ACM, 2015. https://doi.org/10.1145/2751524. ieee: P. Franek and M. Krcál, “Robust satisfiability of systems of equations,” Journal of the ACM, vol. 62, no. 4. ACM, 2015. ista: Franek P, Krcál M. 2015. Robust satisfiability of systems of equations. Journal of the ACM. 62(4), 26. mla: Franek, Peter, and Marek Krcál. “Robust Satisfiability of Systems of Equations.” Journal of the ACM, vol. 62, no. 4, 26, ACM, 2015, doi:10.1145/2751524. short: P. Franek, M. Krcál, Journal of the ACM 62 (2015). date_created: 2018-12-11T11:53:27Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:30Z day: '01' department: - _id: UlWa - _id: HeEd doi: 10.1145/2751524 intvolume: ' 62' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.0858 month: '08' oa: 1 oa_version: Preprint publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '5466' quality_controlled: '1' scopus_import: 1 status: public title: Robust satisfiability of systems of equations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2015' ... --- _id: '1683' abstract: - lang: eng text: The 1 MDa, 45-subunit proton-pumping NADH-ubiquinone oxidoreductase (complex I) is the largest complex of the mitochondrial electron transport chain. The molecular mechanism of complex I is central to the metabolism of cells, but has yet to be fully characterized. The last two years have seen steady progress towards this goal with the first atomic-resolution structure of the entire bacterial complex I, a 5 Å cryo-electron microscopy map of bovine mitochondrial complex I and a ∼3.8 Å resolution X-ray crystallographic study of mitochondrial complex I from yeast Yarrowia lipotytica. In this review we will discuss what we have learned from these studies and what remains to be elucidated. author: - first_name: Jame A full_name: Letts, Jame A id: 322DA418-F248-11E8-B48F-1D18A9856A87 last_name: Letts orcid: 0000-0002-9864-3586 - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: 'Letts JA, Sazanov LA. Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. 2015;33(8):135-145. doi:10.1016/j.sbi.2015.08.008' apa: 'Letts, J. A., & Sazanov, L. A. (2015). Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2015.08.008' chicago: 'Letts, James A, and Leonid A Sazanov. “Gaining Mass: The Structure of Respiratory Complex I-from Bacterial towards Mitochondrial Versions.” Current Opinion in Structural Biology. Elsevier, 2015. https://doi.org/10.1016/j.sbi.2015.08.008.' ieee: 'J. A. Letts and L. A. Sazanov, “Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions,” Current Opinion in Structural Biology, vol. 33, no. 8. Elsevier, pp. 135–145, 2015.' ista: 'Letts JA, Sazanov LA. 2015. Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. 33(8), 135–145.' mla: 'Letts, James A., and Leonid A. Sazanov. “Gaining Mass: The Structure of Respiratory Complex I-from Bacterial towards Mitochondrial Versions.” Current Opinion in Structural Biology, vol. 33, no. 8, Elsevier, 2015, pp. 135–45, doi:10.1016/j.sbi.2015.08.008.' short: J.A. Letts, L.A. Sazanov, Current Opinion in Structural Biology 33 (2015) 135–145. date_created: 2018-12-11T11:53:27Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:30Z day: '01' department: - _id: LeSa doi: 10.1016/j.sbi.2015.08.008 intvolume: ' 33' issue: '8' language: - iso: eng month: '08' oa_version: None page: 135 - 145 publication: Current Opinion in Structural Biology publication_status: published publisher: Elsevier publist_id: '5465' quality_controlled: '1' scopus_import: 1 status: public title: 'Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2015' ... --- _id: '1686' author: - first_name: Eva full_name: Kiermaier, Eva id: 3EB04B78-F248-11E8-B48F-1D18A9856A87 last_name: Kiermaier orcid: 0000-0001-6165-5738 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Kiermaier E, Sixt MK. Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. 2015;349(6252):1055-1056. doi:10.1126/science.aad0867' apa: 'Kiermaier, E., & Sixt, M. K. (2015). Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aad0867' chicago: 'Kiermaier, Eva, and Michael K Sixt. “Fragmented Communication between Immune Cells: Neutrophils Blaze a Trail with Migratory Cues for T Cells to Follow to Sites of Infection.” Science. American Association for the Advancement of Science, 2015. https://doi.org/10.1126/science.aad0867.' ieee: 'E. Kiermaier and M. K. Sixt, “Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection,” Science, vol. 349, no. 6252. American Association for the Advancement of Science, pp. 1055–1056, 2015.' ista: 'Kiermaier E, Sixt MK. 2015. Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. 349(6252), 1055–1056.' mla: 'Kiermaier, Eva, and Michael K. Sixt. “Fragmented Communication between Immune Cells: Neutrophils Blaze a Trail with Migratory Cues for T Cells to Follow to Sites of Infection.” Science, vol. 349, no. 6252, American Association for the Advancement of Science, 2015, pp. 1055–56, doi:10.1126/science.aad0867.' short: E. Kiermaier, M.K. Sixt, Science 349 (2015) 1055–1056. date_created: 2018-12-11T11:53:28Z date_published: 2015-09-04T00:00:00Z date_updated: 2021-01-12T06:52:31Z day: '04' department: - _id: MiSi doi: 10.1126/science.aad0867 intvolume: ' 349' issue: '6252' language: - iso: eng month: '09' oa_version: None page: 1055 - 1056 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5459' quality_controlled: '1' scopus_import: 1 status: public title: 'Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 349 year: '2015' ... --- _id: '1692' abstract: - lang: eng text: Computing an approximation of the reachable states of a hybrid system is a challenge, mainly because overapproximating the solutions of ODEs with a finite number of sets does not scale well. Using template polyhedra can greatly reduce the computational complexity, since it replaces complex operations on sets with a small number of optimization problems. However, the use of templates may make the over-approximation too conservative. Spurious transitions, which are falsely considered reachable, are particularly detrimental to performance and accuracy, and may exacerbate the state explosion problem. In this paper, we examine how spurious transitions can be avoided with minimal computational effort. To this end, detecting spurious transitions is reduced to the well-known problem of showing that two convex sets are disjoint by finding a hyperplane that separates them. We generalize this to owpipes by considering hyperplanes that evolve with time in correspondence to the dynamics of the system. The approach is implemented in the model checker SpaceEx and demonstrated on examples. author: - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Marius full_name: Greitschus, Marius last_name: Greitschus - first_name: Thomas full_name: Strump, Thomas last_name: Strump - first_name: Andreas full_name: Podelski, Andreas last_name: Podelski citation: ama: 'Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. Eliminating spurious transitions in reachability with support functions. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:149-158. doi:10.1145/2728606.2728622' apa: 'Frehse, G., Bogomolov, S., Greitschus, M., Strump, T., & Podelski, A. (2015). Eliminating spurious transitions in reachability with support functions. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 149–158). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728622' chicago: 'Frehse, Goran, Sergiy Bogomolov, Marius Greitschus, Thomas Strump, and Andreas Podelski. “Eliminating Spurious Transitions in Reachability with Support Functions.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 149–58. ACM, 2015. https://doi.org/10.1145/2728606.2728622.' ieee: 'G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, and A. Podelski, “Eliminating spurious transitions in reachability with support functions,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 149–158.' ista: 'Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. 2015. Eliminating spurious transitions in reachability with support functions. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 149–158.' mla: 'Frehse, Goran, et al. “Eliminating Spurious Transitions in Reachability with Support Functions.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 149–58, doi:10.1145/2728606.2728622.' short: 'G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, A. Podelski, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 149–158.' conference: end_date: 2015-04-16 location: Seattle, WA, United States name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2015-04-14 date_created: 2018-12-11T11:53:30Z date_published: 2015-04-14T00:00:00Z date_updated: 2021-01-12T06:52:33Z day: '14' department: - _id: ToHe doi: 10.1145/2728606.2728622 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 149 - 158 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 'Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control' publication_identifier: isbn: - 978-1-4503-3433-4 publication_status: published publisher: ACM publist_id: '5452' quality_controlled: '1' scopus_import: 1 status: public title: Eliminating spurious transitions in reachability with support functions type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1693' abstract: - lang: eng text: Quantum interference between energetically close states is theoretically investigated, with the state structure being observed via laser spectroscopy. In this work, we focus on hyperfine states of selected hydrogenic muonic isotopes, and on how quantum interference affects the measured Lamb shift. The process of photon excitation and subsequent photon decay is implemented within the framework of nonrelativistic second-order perturbation theory. Due to its experimental interest, calculations are performed for muonic hydrogen, deuterium, and helium-3. We restrict our analysis to the case of photon scattering by incident linear polarized photons and the polarization of the scattered photons not being observed. We conclude that while quantum interference effects can be safely neglected in muonic hydrogen and helium-3, in the case of muonic deuterium there are resonances with close proximity, where quantum interference effects can induce shifts up to a few percent of the linewidth, assuming a pointlike detector. However, by taking into account the geometry of the setup used by the CREMA collaboration, this effect is reduced to less than 0.2% of the linewidth in all possible cases, which makes it irrelevant at the present level of accuracy. © 2015 American Physical Society. article_number: '022514' author: - first_name: Pedro full_name: Amaro, Pedro last_name: Amaro - first_name: Beatrice full_name: Franke, Beatrice last_name: Franke - first_name: Julian full_name: Krauth, Julian last_name: Krauth - first_name: Marc full_name: Diepold, Marc last_name: Diepold - first_name: Filippo full_name: Fratini, Filippo last_name: Fratini - first_name: Laleh full_name: Safari, Laleh id: 3C325E5E-F248-11E8-B48F-1D18A9856A87 last_name: Safari - first_name: Jorge full_name: Machado, Jorge last_name: Machado - first_name: Aldo full_name: Antognini, Aldo last_name: Antognini - first_name: Franz full_name: Kottmann, Franz last_name: Kottmann - first_name: Paul full_name: Indelicato, Paul last_name: Indelicato - first_name: Randolf full_name: Pohl, Randolf last_name: Pohl - first_name: José full_name: Santos, José last_name: Santos citation: ama: Amaro P, Franke B, Krauth J, et al. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. 2015;92(2). doi:10.1103/PhysRevA.92.022514 apa: Amaro, P., Franke, B., Krauth, J., Diepold, M., Fratini, F., Safari, L., … Santos, J. (2015). Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.92.022514 chicago: Amaro, Pedro, Beatrice Franke, Julian Krauth, Marc Diepold, Filippo Fratini, Laleh Safari, Jorge Machado, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.022514. ieee: P. Amaro et al., “Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3,” Physical Review A, vol. 92, no. 2. American Physical Society, 2015. ista: Amaro P, Franke B, Krauth J, Diepold M, Fratini F, Safari L, Machado J, Antognini A, Kottmann F, Indelicato P, Pohl R, Santos J. 2015. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. 92(2), 022514. mla: Amaro, Pedro, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” Physical Review A, vol. 92, no. 2, 022514, American Physical Society, 2015, doi:10.1103/PhysRevA.92.022514. short: P. Amaro, B. Franke, J. Krauth, M. Diepold, F. Fratini, L. Safari, J. Machado, A. Antognini, F. Kottmann, P. Indelicato, R. Pohl, J. Santos, Physical Review A 92 (2015). date_created: 2018-12-11T11:53:30Z date_published: 2015-08-28T00:00:00Z date_updated: 2021-01-12T06:52:34Z day: '28' department: - _id: MiLe doi: 10.1103/PhysRevA.92.022514 ec_funded: 1 intvolume: ' 92' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1506.02734 month: '08' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review A publication_status: published publisher: American Physical Society publist_id: '5451' quality_controlled: '1' scopus_import: 1 status: public title: Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '1690' abstract: - lang: eng text: A number of powerful and scalable hybrid systems model checkers have recently emerged. Although all of them honor roughly the same hybrid systems semantics, they have drastically different model description languages. This situation (a) makes it difficult to quickly evaluate a specific hybrid automaton model using the different tools, (b) obstructs comparisons of reachability approaches, and (c) impedes the widespread application of research results that perform model modification and could benefit many of the tools. In this paper, we present Hyst, a Hybrid Source Transformer. Hyst is a source-to-source translation tool, currently taking input in the SpaceEx model format, and translating to the formats of HyCreate, Flow∗, or dReach. Internally, the tool supports generic model-to-model transformation passes that serve to both ease the translation and potentially improve reachability results for the supported tools. Although these model transformation passes could be implemented within each tool, the Hyst approach provides a single place for model modification, generating modified input sources for the unmodified target tools. Our evaluation demonstrates Hyst is capable of automatically translating benchmarks in several classes (including affine and nonlinear hybrid automata) to the input formats of several tools. Additionally, we illustrate a general model transformation pass based on pseudo-invariants implemented in Hyst that illustrates the reachability improvement. acknowledgement: The material presented in this paper is based upon work sup-ported by the Air Force Research Laboratory’s Information Directorate (AFRL/RI) through the Visiting Faculty Research Program (VFRP) under contract number FA8750-13-2-0115 and the Air Force Office of Scientific Research (AFOSR). Any opinions,findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the AFRL/RI or AFOSR. This work was also partly supported in part by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR14 AVACS, http://www.avacs.org/), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). author: - first_name: Stanley full_name: Bak, Stanley last_name: Bak - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Taylor full_name: Johnson, Taylor last_name: Johnson citation: ama: 'Bak S, Bogomolov S, Johnson T. HYST: A source transformation and translation tool for hybrid automaton models. In: Springer; 2015:128-133. doi:10.1145/2728606.2728630' apa: 'Bak, S., Bogomolov, S., & Johnson, T. (2015). HYST: A source transformation and translation tool for hybrid automaton models (pp. 128–133). Presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States: Springer. https://doi.org/10.1145/2728606.2728630' chicago: 'Bak, Stanley, Sergiy Bogomolov, and Taylor Johnson. “HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models,” 128–33. Springer, 2015. https://doi.org/10.1145/2728606.2728630.' ieee: 'S. Bak, S. Bogomolov, and T. Johnson, “HYST: A source transformation and translation tool for hybrid automaton models,” presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States, 2015, pp. 128–133.' ista: 'Bak S, Bogomolov S, Johnson T. 2015. HYST: A source transformation and translation tool for hybrid automaton models. HSCC: Hybrid Systems - Computation and Control, 128–133.' mla: 'Bak, Stanley, et al. HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models. Springer, 2015, pp. 128–33, doi:10.1145/2728606.2728630.' short: S. Bak, S. Bogomolov, T. Johnson, in:, Springer, 2015, pp. 128–133. conference: end_date: 2015-04-16 location: Seattle, WA, United States name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2015-04-14 date_created: 2018-12-11T11:53:29Z date_published: 2015-04-14T00:00:00Z date_updated: 2021-01-12T06:52:33Z day: '14' department: - _id: ToHe doi: 10.1145/2728606.2728630 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 128 - 133 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5454' quality_controlled: '1' status: public title: 'HYST: A source transformation and translation tool for hybrid automaton models' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ...