--- _id: '2824' abstract: - lang: eng text: We study synthesis of controllers for real-time systems, where the objective is to stay in a given safe set. The problem is solved by obtaining winning strategies in the setting of concurrent two player timed automaton games with safety objectives. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a Zeno run. We construct winning strategies for the controller which require access only to (1) the system clocks (thus, controllers which require their own internal infinitely precise clocks are not necessary), and (2) a logarithmic (in the number of clocks) number of memory bits (i.e. a linear number of memory states). Precisely, we show that for safety objectives, a memory of size (3 + lg (| C | + 1)) bits suffices for winning controller strategies, where C is the set of clocks of the timed automaton game, significantly improving the previous known exponential memory states bound. We also settle the open question of whether winning region-based strategies require memory for safety objectives by showing with an example the necessity of memory for such strategies to win for safety objectives. Finally, we show that the decision problem of determining if there exists a receptive player-1 winning strategy for safety objectives is EXPTIME-complete over timed automaton games. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vinayak full_name: Prabhu, Vinayak last_name: Prabhu citation: ama: Chatterjee K, Prabhu V. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. 2013;228-229:83-119. doi:10.1016/j.ic.2013.04.003 apa: Chatterjee, K., & Prabhu, V. (2013). Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2013.04.003 chicago: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information and Computation. Elsevier, 2013. https://doi.org/10.1016/j.ic.2013.04.003. ieee: K. Chatterjee and V. Prabhu, “Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems,” Information and Computation, vol. 228–229. Elsevier, pp. 83–119, 2013. ista: Chatterjee K, Prabhu V. 2013. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. 228–229, 83–119. mla: Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information and Computation, vol. 228–229, Elsevier, 2013, pp. 83–119, doi:10.1016/j.ic.2013.04.003. short: K. Chatterjee, V. Prabhu, Information and Computation 228–229 (2013) 83–119. date_created: 2018-12-11T11:59:47Z date_published: 2013-04-24T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '24' department: - _id: KrCh doi: 10.1016/j.ic.2013.04.003 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 83-119 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '3977' quality_controlled: '1' scopus_import: 1 status: public title: Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 228-229 year: '2013' ... --- _id: '2832' abstract: - lang: eng text: PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and mediate intercellular polar transport of the plant hormone auxin that is crucial for a multitude of developmental processes in plants. PIN localization is under extensive control by environmental or developmental cues, but mechanisms regulating PIN localization are not fully understood. Here we show that early endosomal components ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively required for polar PIN localization, for their dynamic repolarization, and consequently for auxin activity gradient formation and auxin-related developmental processes including embryonic patterning, organogenesis, and vasculature venation patterning. These results show that early endosomal trafficking is crucial for cell polarity and auxin-dependent regulation of plant architecture. article_number: e1003540 author: - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová - first_name: Tomohiro full_name: Uemura, Tomohiro last_name: Uemura - first_name: Mugurel full_name: Feraru, Mugurel last_name: Feraru - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Tatsuo full_name: Kakimoto, Tatsuo last_name: Kakimoto - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Tanaka H, Kitakura S, Rakusová H, et al. Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 2013;9(5). doi:10.1371/journal.pgen.1003540 apa: Tanaka, H., Kitakura, S., Rakusová, H., Uemura, T., Feraru, M., De Rycke, R., … Friml, J. (2013). Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003540 chicago: Tanaka, Hirokazu, Saeko Kitakura, Hana Rakusová, Tomohiro Uemura, Mugurel Feraru, Riet De Rycke, Stéphanie Robert, Tatsuo Kakimoto, and Jiří Friml. “Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003540. ieee: H. Tanaka et al., “Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana,” PLoS Genetics, vol. 9, no. 5. Public Library of Science, 2013. ista: Tanaka H, Kitakura S, Rakusová H, Uemura T, Feraru M, De Rycke R, Robert S, Kakimoto T, Friml J. 2013. Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 9(5), e1003540. mla: Tanaka, Hirokazu, et al. “Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics, vol. 9, no. 5, e1003540, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003540. short: H. Tanaka, S. Kitakura, H. Rakusová, T. Uemura, M. Feraru, R. De Rycke, S. Robert, T. Kakimoto, J. Friml, PLoS Genetics 9 (2013). date_created: 2018-12-11T11:59:50Z date_published: 2013-05-05T00:00:00Z date_updated: 2021-01-12T07:00:03Z day: '05' ddc: - '570' department: - _id: JiFr doi: 10.1371/journal.pgen.1003540 ec_funded: 1 file: - access_level: open_access checksum: 050237d6c53e8d1601b26808ee1dd6d8 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:39Z date_updated: 2020-07-14T12:45:50Z file_id: '4957' file_name: IST-2016-411-v1+1_journal.pgen.1003540.pdf file_size: 3813091 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 9' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '3967' pubrep_id: '411' quality_controlled: '1' scopus_import: 1 status: public title: Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana 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: 9 year: '2013' ... --- _id: '2828' abstract: - lang: eng text: 'We study the complexity of valued constraint satisfaction problems (VCSPs) parametrized by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimize the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well understood, see Raghavendra [2008]. However, there is no characterization of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimization perspective. We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e., relations), such languages have been called conservative and studied by Bulatov [2003, 2011] and recently by Barto [2011]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [2006] for languages over Boolean domains, by Deineko et al. [2008] for {0, 1}-valued languages (a.k.a Max-CSP), and by Takhanov [2010a] for {0, ∞}-valued languages containing all finite-valued unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimor-phisms), then any instance can be solved in polynomial time (via a new algorithm developed in this article), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains are significantly harder than the Boolean cases. The polynomial-time algorithm we present for the tractable cases is a generalization of the submodular minimization problem and a result of Cohen et al. [2008]. Our results generalize previous results by Takhanov [2010a] and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [2008], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.' article_number: '10' author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Stanislav full_name: Živný, Stanislav last_name: Živný citation: ama: Kolmogorov V, Živný S. The complexity of conservative valued CSPs. Journal of the ACM. 2013;60(2). doi:10.1145/2450142.2450146 apa: Kolmogorov, V., & Živný, S. (2013). The complexity of conservative valued CSPs. Journal of the ACM. ACM. https://doi.org/10.1145/2450142.2450146 chicago: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” Journal of the ACM. ACM, 2013. https://doi.org/10.1145/2450142.2450146. ieee: V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,” Journal of the ACM, vol. 60, no. 2. ACM, 2013. ista: Kolmogorov V, Živný S. 2013. The complexity of conservative valued CSPs. Journal of the ACM. 60(2), 10. mla: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” Journal of the ACM, vol. 60, no. 2, 10, ACM, 2013, doi:10.1145/2450142.2450146. short: V. Kolmogorov, S. Živný, Journal of the ACM 60 (2013). date_created: 2018-12-11T11:59:48Z date_published: 2013-04-02T00:00:00Z date_updated: 2021-01-12T07:00:00Z day: '02' department: - _id: VlKo doi: 10.1145/2450142.2450146 external_id: arxiv: - '1110.2809' intvolume: ' 60' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1110.2809 month: '04' oa: 1 oa_version: Preprint publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '3971' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of conservative valued CSPs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2013' ... --- _id: '2829' abstract: - lang: eng text: Laminar-turbulent intermittency is intrinsic to the transitional regime of a wide range of fluid flows including pipe, channel, boundary layer, and Couette flow. In the latter turbulent spots can grow and form continuous stripes, yet in the stripe-normal direction they remain interspersed by laminar fluid. We carry out direct numerical simulations in a long narrow domain and observe that individual turbulent stripes are transient. In agreement with recent observations in pipe flow, we find that turbulence becomes sustained at a distinct critical point once the spatial proliferation outweighs the inherent decaying process. By resolving the asymptotic size distributions close to criticality we can for the first time demonstrate scale invariance at the onset of turbulence. article_number: '204502' author: - first_name: Liang full_name: Shi, Liang id: 374A3F1A-F248-11E8-B48F-1D18A9856A87 last_name: Shi - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Shi L, Avila M, Hof B. Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.204502 apa: Shi, L., Avila, M., & Hof, B. (2013). Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.204502 chicago: Shi, Liang, Marc Avila, and Björn Hof. “Scale Invariance at the Onset of Turbulence in Couette Flow.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.204502. ieee: L. Shi, M. Avila, and B. Hof, “Scale invariance at the onset of turbulence in couette flow,” Physical Review Letters, vol. 110, no. 20. American Physical Society, 2013. ista: Shi L, Avila M, Hof B. 2013. Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. 110(20), 204502. mla: Shi, Liang, et al. “Scale Invariance at the Onset of Turbulence in Couette Flow.” Physical Review Letters, vol. 110, no. 20, 204502, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.204502. short: L. Shi, M. Avila, B. Hof, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:59:49Z date_published: 2013-05-13T00:00:00Z date_updated: 2021-01-12T07:00:00Z day: '13' department: - _id: BjHo doi: 10.1103/PhysRevLett.110.204502 ec_funded: 1 external_id: arxiv: - '1304.5446' intvolume: ' 110' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.5446 month: '05' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin - _id: 2511D90C-B435-11E9-9278-68D0E5697425 grant_number: SFB 963 TP A8 name: Astrophysical instability of currents and turbulences publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '3970' quality_controlled: '1' scopus_import: 1 status: public title: Scale invariance at the onset of turbulence in couette flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2834' abstract: - lang: eng text: Although the equations governing fluid flow are well known, there are no analytical expressions that describe the complexity of turbulent motion. A recent proposition is that in analogy to low dimensional chaotic systems, turbulence is organized around unstable solutions of the governing equations which provide the building blocks of the disordered dynamics. We report the discovery of periodic solutions which just like intermittent turbulence are spatially localized and show that turbulent transients arise from one such solution branch. article_number: '224502' author: - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Fernando full_name: Mellibovsky, Fernando last_name: Mellibovsky - first_name: Nicolas full_name: Roland, Nicolas last_name: Roland - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Avila M, Mellibovsky F, Roland N, Hof B. Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. 2013;110(22). doi:10.1103/PhysRevLett.110.224502 apa: Avila, M., Mellibovsky, F., Roland, N., & Hof, B. (2013). Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.224502 chicago: Avila, Marc, Fernando Mellibovsky, Nicolas Roland, and Björn Hof. “Streamwise-Localized Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.224502. ieee: M. Avila, F. Mellibovsky, N. Roland, and B. Hof, “Streamwise-localized solutions at the onset of turbulence in pipe flow,” Physical Review Letters, vol. 110, no. 22. American Physical Society, 2013. ista: Avila M, Mellibovsky F, Roland N, Hof B. 2013. Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. 110(22), 224502. mla: Avila, Marc, et al. “Streamwise-Localized Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters, vol. 110, no. 22, 224502, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.224502. short: M. Avila, F. Mellibovsky, N. Roland, B. Hof, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:59:50Z date_published: 2013-05-29T00:00:00Z date_updated: 2021-01-12T07:00:05Z day: '29' department: - _id: BjHo doi: 10.1103/PhysRevLett.110.224502 ec_funded: 1 external_id: arxiv: - '1212.0230' intvolume: ' 110' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1212.0230 month: '05' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '3965' quality_controlled: '1' scopus_import: 1 status: public title: Streamwise-localized solutions at the onset of turbulence in pipe flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2833' abstract: - lang: eng text: During development, mechanical forces cause changes in size, shape, number, position, and gene expression of cells. They are therefore integral to any morphogenetic processes. Force generation by actin-myosin networks and force transmission through adhesive complexes are two self-organizing phenomena driving tissue morphogenesis. Coordination and integration of forces by long-range force transmission and mechanosensing of cells within tissues produce large-scale tissue shape changes. Extrinsic mechanical forces also control tissue patterning by modulating cell fate specification and differentiation. Thus, the interplay between tissue mechanics and biochemical signaling orchestrates tissue morphogenesis and patterning in development. acknowledgement: C.-P.H. is supported by the Institute of Science and Technology Austria and grants from the Deutsche Forschungsgemeinschaft (DFG) and Fonds zur Förderung der wissenschaftlichen Forschung (FWF). author: - 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: Yohanns full_name: Bellaïche, Yohanns last_name: Bellaïche citation: ama: Heisenberg C-PJ, Bellaïche Y. Forces in tissue morphogenesis and patterning. Cell. 2013;153(5):948-962. doi:10.1016/j.cell.2013.05.008 apa: Heisenberg, C.-P. J., & Bellaïche, Y. (2013). Forces in tissue morphogenesis and patterning. Cell. Cell Press. https://doi.org/10.1016/j.cell.2013.05.008 chicago: Heisenberg, Carl-Philipp J, and Yohanns Bellaïche. “Forces in Tissue Morphogenesis and Patterning.” Cell. Cell Press, 2013. https://doi.org/10.1016/j.cell.2013.05.008. ieee: C.-P. J. Heisenberg and Y. Bellaïche, “Forces in tissue morphogenesis and patterning,” Cell, vol. 153, no. 5. Cell Press, pp. 948–962, 2013. ista: Heisenberg C-PJ, Bellaïche Y. 2013. Forces in tissue morphogenesis and patterning. Cell. 153(5), 948–962. mla: Heisenberg, Carl-Philipp J., and Yohanns Bellaïche. “Forces in Tissue Morphogenesis and Patterning.” Cell, vol. 153, no. 5, Cell Press, 2013, pp. 948–62, doi:10.1016/j.cell.2013.05.008. short: C.-P.J. Heisenberg, Y. Bellaïche, Cell 153 (2013) 948–962. date_created: 2018-12-11T11:59:50Z date_published: 2013-05-23T00:00:00Z date_updated: 2021-01-12T07:00:04Z day: '23' department: - _id: CaHe doi: 10.1016/j.cell.2013.05.008 intvolume: ' 153' issue: '5' language: - iso: eng month: '05' oa_version: None page: 948 - 962 publication: Cell publication_status: published publisher: Cell Press publist_id: '3966' quality_controlled: '1' scopus_import: 1 status: public title: Forces in tissue morphogenesis and patterning type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 153 year: '2013' ... --- _id: '2830' author: - first_name: Christine full_name: Moussion, Christine id: 3356F664-F248-11E8-B48F-1D18A9856A87 last_name: Moussion - 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: Moussion C, Sixt MK. A conduit to amplify innate immunity. Immunity. 2013;38(5):853-854. doi:10.1016/j.immuni.2013.05.005 apa: Moussion, C., & Sixt, M. K. (2013). A conduit to amplify innate immunity. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2013.05.005 chicago: Moussion, Christine, and Michael K Sixt. “A Conduit to Amplify Innate Immunity.” Immunity. Cell Press, 2013. https://doi.org/10.1016/j.immuni.2013.05.005. ieee: C. Moussion and M. K. Sixt, “A conduit to amplify innate immunity,” Immunity, vol. 38, no. 5. Cell Press, pp. 853–854, 2013. ista: Moussion C, Sixt MK. 2013. A conduit to amplify innate immunity. Immunity. 38(5), 853–854. mla: Moussion, Christine, and Michael K. Sixt. “A Conduit to Amplify Innate Immunity.” Immunity, vol. 38, no. 5, Cell Press, 2013, pp. 853–54, doi:10.1016/j.immuni.2013.05.005. short: C. Moussion, M.K. Sixt, Immunity 38 (2013) 853–854. date_created: 2018-12-11T11:59:49Z date_published: 2013-05-23T00:00:00Z date_updated: 2021-01-12T07:00:01Z day: '23' department: - _id: MiSi doi: 10.1016/j.immuni.2013.05.005 intvolume: ' 38' issue: '5' language: - iso: eng month: '05' oa_version: None page: 853 - 854 publication: Immunity publication_status: published publisher: Cell Press publist_id: '3969' quality_controlled: '1' scopus_import: 1 status: public title: A conduit to amplify innate immunity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2013' ... --- _id: '2842' abstract: - lang: eng text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: 'Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001' apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001' chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.' ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.' ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 87(1), 105–119.' mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.' short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119. date_created: 2018-12-11T11:59:53Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T07:00:09Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1016/j.tpb.2013.03.001 ec_funded: 1 file: - access_level: open_access checksum: 9bf9d9a6fd03dd9df50906891f393bf8 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:33Z date_updated: 2020-07-14T12:45:50Z file_id: '5288' file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf file_size: 1554712 relation: main_file - access_level: open_access checksum: 2bceddb76edacd0cd5fad73051e2a928 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:34Z date_updated: 2020-07-14T12:45:50Z file_id: '5289' file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf file_size: 822964 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 87' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 105 - 119 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_status: published publisher: Elsevier publist_id: '3953' pubrep_id: '558' quality_controlled: '1' scopus_import: 1 status: public title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2013' ... --- _id: '2838' abstract: - lang: eng text: Individuals with Down syndrome (DS) present important motor deficits that derive from altered motor development of infants and young children. DYRK1A, a candidate gene for DS abnormalities has been implicated in motor function due to its expression in motor nuclei in the adult brain, and its overexpression in DS mouse models leads to hyperactivity and altered motor learning. However, its precise role in the adult motor system, or its possible involvement in postnatal locomotor development has not yet been clarified. During the postnatal period we observed time-specific expression of Dyrk1A in discrete subsets of brainstem nuclei and spinal cord motor neurons. Interestingly, we describe for the first time the presence of Dyrk1A in the presynaptic terminal of the neuromuscular junctions and its axonal transport from the facial nucleus, suggesting a function for Dyrk1A in these structures. Relevant to DS, Dyrk1A overexpression in transgenic mice (TgDyrk1A) produces motor developmental alterations possibly contributing to DS motor phenotypes and modifies the numbers of motor cholinergic neurons, suggesting that the kinase may have a role in the development of the brainstem and spinal cord motor system. article_number: e54285 author: - first_name: Gloria full_name: Arquè Fuste, Gloria id: 3CF33908-F248-11E8-B48F-1D18A9856A87 last_name: Arquè Fuste - first_name: Anna full_name: Casanovas, Anna last_name: Casanovas - first_name: Mara full_name: Dierssen, Mara last_name: Dierssen citation: ama: 'Arquè Fuste G, Casanovas A, Dierssen M. Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. 2013;8(1). doi:10.1371/journal.pone.0054285' apa: 'Arquè Fuste, G., Casanovas, A., & Dierssen, M. (2013). Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0054285' chicago: 'Arquè Fuste, Gloria, Anna Casanovas, and Mara Dierssen. “Dyrk1A Is Dynamically Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0054285.' ieee: 'G. Arquè Fuste, A. Casanovas, and M. Dierssen, “Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome,” PLoS One, vol. 8, no. 1. Public Library of Science, 2013.' ista: 'Arquè Fuste G, Casanovas A, Dierssen M. 2013. Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. 8(1), e54285.' mla: 'Arquè Fuste, Gloria, et al. “Dyrk1A Is Dynamically Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.” PLoS One, vol. 8, no. 1, e54285, Public Library of Science, 2013, doi:10.1371/journal.pone.0054285.' short: G. Arquè Fuste, A. Casanovas, M. Dierssen, PLoS One 8 (2013). date_created: 2018-12-11T11:59:52Z date_published: 2013-01-16T00:00:00Z date_updated: 2021-01-12T07:00:07Z day: '16' ddc: - '570' department: - _id: SiHi doi: 10.1371/journal.pone.0054285 file: - access_level: open_access checksum: 512733b21419574a45f10cabef3d7f81 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:38Z date_updated: 2020-07-14T12:45:50Z file_id: '5160' file_name: IST-2016-407-v1+1_journal.pone.0054285.pdf file_size: 4795977 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '3960' pubrep_id: '407' quality_controlled: '1' scopus_import: 1 status: public title: 'Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2839' abstract: - lang: eng text: Directional guidance of cells via gradients of chemokines is considered crucial for embryonic development, cancer dissemination, and immune responses. Nevertheless, the concept still lacks direct experimental confirmation in vivo. Here, we identify endogenous gradients of the chemokine CCL21 within mouse skin and show that they guide dendritic cells toward lymphatic vessels. Quantitative imaging reveals depots of CCL21 within lymphatic endothelial cells and steeply decaying gradients within the perilymphatic interstitium. These gradients match the migratory patterns of the dendritic cells, which directionally approach vessels from a distance of up to 90-micrometers. Interstitial CCL21 is immobilized to heparan sulfates, and its experimental delocalization or swamping the endogenous gradients abolishes directed migration. These findings functionally establish the concept of haptotaxis, directed migration along immobilized gradients, in tissues. acknowledgement: We thank M. Frank for technical assistance and S. Cremer, P. Schmalhorst, and E. Kiermaier for critical reading of the manuscript. This work was supported by a Humboldt Foundation postdoctoral fellowship (to M.W.), the German Research Foundation (Si1323 1,2 to M.S.), the Human Frontier Science Program (HFSP RGP0058/2011 to M.S.), the European Research Council (ERC StG 281556 to M.S.), and the Swiss National Science Foundation (31003A 127474 to D.F.L., 130488 to S.A.L.). article_processing_charge: No article_type: original author: - first_name: Michele full_name: Weber, Michele id: 3A3FC708-F248-11E8-B48F-1D18A9856A87 last_name: Weber - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Christine full_name: Moussion, Christine id: 3356F664-F248-11E8-B48F-1D18A9856A87 last_name: Moussion - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Daniel full_name: Legler, Daniel last_name: Legler - first_name: Sanjiv full_name: Luther, Sanjiv last_name: Luther - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Weber M, Hauschild R, Schwarz J, et al. Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. 2013;339(6117):328-332. doi:10.1126/science.1228456 apa: Weber, M., Hauschild, R., Schwarz, J., Moussion, C., de Vries, I., Legler, D., … Sixt, M. K. (2013). Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1228456 chicago: Weber, Michele, Robert Hauschild, Jan Schwarz, Christine Moussion, Ingrid de Vries, Daniel Legler, Sanjiv Luther, Mark Tobias Bollenbach, and Michael K Sixt. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1228456. ieee: M. Weber et al., “Interstitial dendritic cell guidance by haptotactic chemokine gradients,” Science, vol. 339, no. 6117. American Association for the Advancement of Science, pp. 328–332, 2013. ista: Weber M, Hauschild R, Schwarz J, Moussion C, de Vries I, Legler D, Luther S, Bollenbach MT, Sixt MK. 2013. Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. 339(6117), 328–332. mla: Weber, Michele, et al. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.” Science, vol. 339, no. 6117, American Association for the Advancement of Science, 2013, pp. 328–32, doi:10.1126/science.1228456. short: M. Weber, R. Hauschild, J. Schwarz, C. Moussion, I. de Vries, D. Legler, S. Luther, M.T. Bollenbach, M.K. Sixt, Science 339 (2013) 328–332. date_created: 2018-12-11T11:59:52Z date_published: 2013-01-18T00:00:00Z date_updated: 2022-06-10T10:21:40Z day: '18' department: - _id: MiSi - _id: Bio doi: 10.1126/science.1228456 ec_funded: 1 intvolume: ' 339' issue: '6117' language: - iso: eng main_file_link: - open_access: '1' url: https://kops.uni-konstanz.de/bitstream/123456789/26341/2/Weber_263418.pdf month: '01' oa: 1 oa_version: Published Version page: 328 - 332 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) - _id: 25ABD200-B435-11E9-9278-68D0E5697425 grant_number: RGP0058/2011 name: 'Cell migration in complex environments: from in vivo experiments to theoretical models' publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '3959' quality_controlled: '1' scopus_import: '1' status: public title: Interstitial dendritic cell guidance by haptotactic chemokine gradients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 339 year: '2013' ...