--- _id: '659' abstract: - lang: eng text: Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching. article_number: '14832' article_processing_charge: No author: - first_name: Frieda full_name: Kage, Frieda last_name: Kage - first_name: Moritz full_name: Winterhoff, Moritz last_name: Winterhoff - first_name: Vanessa full_name: Dimchev, Vanessa last_name: Dimchev - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Tobias full_name: Thalheim, Tobias last_name: Thalheim - first_name: Anika full_name: Freise, Anika last_name: Freise - first_name: Stefan full_name: Brühmann, Stefan last_name: Brühmann - first_name: Jana full_name: Kollasser, Jana last_name: Kollasser - first_name: Jennifer full_name: Block, Jennifer last_name: Block - first_name: Georgi A full_name: Dimchev, Georgi A last_name: Dimchev - first_name: Matthias full_name: Geyer, Matthias last_name: Geyer - first_name: Hams full_name: Schnittler, Hams last_name: Schnittler - first_name: Cord full_name: Brakebusch, Cord last_name: Brakebusch - first_name: Theresia full_name: Stradal, Theresia last_name: Stradal - first_name: Marie full_name: Carlier, Marie last_name: Carlier - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Josef full_name: Käs, Josef last_name: Käs - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832 apa: Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14832 chicago: Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14832. ieee: F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832. mla: Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832. short: F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017). date_created: 2018-12-11T11:47:46Z date_published: 2017-03-22T00:00:00Z date_updated: 2021-01-12T08:08:06Z day: '22' ddc: - '570' department: - _id: MiSi doi: 10.1038/ncomms14832 file: - access_level: open_access checksum: dae30190291c3630e8102d8714a8d23e content_type: application/pdf creator: system date_created: 2018-12-12T10:14:21Z date_updated: 2020-07-14T12:47:34Z file_id: '5072' file_name: IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf file_size: 9523746 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7075' pubrep_id: '902' quality_controlled: '1' scopus_import: 1 status: public title: FMNL formins boost lamellipodial force generation 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: '2017' ... --- _id: '660' abstract: - lang: eng text: Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth. acknowledgement: We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.). author: - first_name: Jamie full_name: Rickman, Jamie last_name: Rickman - first_name: Christian F full_name: Düllberg, Christian F id: 459064DC-F248-11E8-B48F-1D18A9856A87 last_name: Düllberg orcid: 0000-0001-6335-9748 - first_name: Nicholas full_name: Cade, Nicholas last_name: Cade - first_name: Lewis full_name: Griffin, Lewis last_name: Griffin - first_name: Thomas full_name: Surrey, Thomas last_name: Surrey citation: ama: Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 2017;114(13):3427-3432. doi:10.1073/pnas.1620274114 apa: Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., & Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1620274114 chicago: Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1620274114. ieee: J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” PNAS, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017. ista: Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432. mla: Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:10.1073/pnas.1620274114. short: J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432. date_created: 2018-12-11T11:47:46Z date_published: 2017-03-28T00:00:00Z date_updated: 2021-01-12T08:08:09Z day: '28' department: - _id: MaLo doi: 10.1073/pnas.1620274114 external_id: pmid: - '28280102' intvolume: ' 114' issue: '13' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/ month: '03' oa: 1 oa_version: Submitted Version page: 3427 - 3432 pmid: 1 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7073' quality_controlled: '1' scopus_import: 1 status: public title: Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '662' abstract: - lang: eng text: 'We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays.' article_number: '044107' author: - first_name: Liang full_name: Shi, Liang last_name: Shi - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Markus full_name: Rampp, Markus last_name: Rampp - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 2017;29(4). doi:10.1063/1.4981525 apa: Shi, L., Hof, B., Rampp, M., & Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4981525 chicago: Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids. American Institute of Physics, 2017. https://doi.org/10.1063/1.4981525. ieee: L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi Keplerian rotating flows,” Physics of Fluids, vol. 29, no. 4. American Institute of Physics, 2017. ista: Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107. mla: Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids, vol. 29, no. 4, 044107, American Institute of Physics, 2017, doi:10.1063/1.4981525. short: L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017). date_created: 2018-12-11T11:47:47Z date_published: 2017-04-01T00:00:00Z date_updated: 2021-01-12T08:08:15Z day: '01' department: - _id: BjHo doi: 10.1063/1.4981525 intvolume: ' 29' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.01714 month: '04' oa: 1 oa_version: Submitted Version project: - _id: 2511D90C-B435-11E9-9278-68D0E5697425 grant_number: SFB 963 TP A8 name: Astrophysical instability of currents and turbulences publication: Physics of Fluids publication_identifier: issn: - '10706631' publication_status: published publisher: American Institute of Physics publist_id: '7072' quality_controlled: '1' scopus_import: 1 status: public title: Hydrodynamic turbulence in quasi Keplerian rotating flows type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2017' ... --- _id: '663' abstract: - lang: eng text: 'In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. ' author: - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 - first_name: Sergiy full_name: Bogomolov, Sergiy last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Christian full_name: Schilling, Christian last_name: Schilling - first_name: Yu full_name: Jiang, Yu last_name: Jiang - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification of nonlinear hybrid systems based on invariant clusters. In: Proceedings of the 20th International Conference on Hybrid Systems. ACM; 2017:163-172. doi:10.1145/3049797.3049814' apa: 'Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., & Henzinger, T. A. (2017). Safety verification of nonlinear hybrid systems based on invariant clusters. In Proceedings of the 20th International Conference on Hybrid Systems (pp. 163–172). Pittsburgh, PA, United States: ACM. https://doi.org/10.1145/3049797.3049814' chicago: Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” In Proceedings of the 20th International Conference on Hybrid Systems, 163–72. ACM, 2017. https://doi.org/10.1145/3049797.3049814. ieee: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety verification of nonlinear hybrid systems based on invariant clusters,” in Proceedings of the 20th International Conference on Hybrid Systems, Pittsburgh, PA, United States, 2017, pp. 163–172. ista: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and Control , 163–172.' mla: Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–72, doi:10.1145/3049797.3049814. short: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172. conference: end_date: 2017-04-20 location: Pittsburgh, PA, United States name: 'HSCC: Hybrid Systems Computation and Control ' start_date: 2017-04-18 date_created: 2018-12-11T11:47:47Z date_published: 2017-04-01T00:00:00Z date_updated: 2021-01-12T08:08:17Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1145/3049797.3049814 file: - access_level: open_access checksum: b7667434cbf5b5f0ade3bea1dbe5bf63 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:20Z date_updated: 2020-07-14T12:47:34Z file_id: '4873' file_name: IST-2017-817-v1+1_p163-kong.pdf file_size: 1650530 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 163 - 172 publication: Proceedings of the 20th International Conference on Hybrid Systems publication_identifier: isbn: - 978-145034590-3 publication_status: published publisher: ACM publist_id: '7067' pubrep_id: '817' quality_controlled: '1' scopus_import: 1 status: public title: Safety verification of nonlinear hybrid systems based on invariant clusters type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '667' abstract: - lang: eng text: Perinatal exposure to penicillin may result in longlasting gut and behavioral changes. article_number: '2786' author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Novarino G. The antisocial side of antibiotics. Science Translational Medicine. 2017;9(387). doi:10.1126/scitranslmed.aan2786 apa: Novarino, G. (2017). The antisocial side of antibiotics. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan2786 chicago: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan2786. ieee: G. Novarino, “The antisocial side of antibiotics,” Science Translational Medicine, vol. 9, no. 387. American Association for the Advancement of Science, 2017. ista: Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786. mla: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine, vol. 9, no. 387, 2786, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan2786. short: G. Novarino, Science Translational Medicine 9 (2017). date_created: 2018-12-11T11:47:48Z date_published: 2017-04-26T00:00:00Z date_updated: 2021-01-12T08:08:30Z day: '26' department: - _id: GaNo doi: 10.1126/scitranslmed.aan2786 intvolume: ' 9' issue: '387' language: - iso: eng month: '04' oa_version: None publication: Science Translational Medicine publication_identifier: issn: - '19466234' publication_status: published publisher: American Association for the Advancement of Science publist_id: '7060' quality_controlled: '1' scopus_import: 1 status: public title: The antisocial side of antibiotics type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '668' abstract: - lang: eng text: Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading. article_type: original author: - first_name: Markus full_name: Horsthemke, Markus last_name: Horsthemke - first_name: Anne full_name: Bachg, Anne last_name: Bachg - first_name: Katharina full_name: Groll, Katharina last_name: Groll - first_name: Sven full_name: Moyzio, Sven last_name: Moyzio - first_name: Barbara full_name: Müther, Barbara last_name: Müther - first_name: Sandra full_name: Hemkemeyer, Sandra last_name: Hemkemeyer - first_name: Roland full_name: Wedlich Söldner, Roland last_name: Wedlich Söldner - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Sebastian full_name: Tacke, Sebastian last_name: Tacke - first_name: Martin full_name: Bähler, Martin last_name: Bähler - first_name: Peter full_name: Hanley, Peter last_name: Hanley citation: ama: Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 2017;292(17):7258-7273. doi:10.1074/jbc.M116.766923 apa: Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S., … Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.766923 chicago: Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther, Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2017. https://doi.org/10.1074/jbc.M116.766923. ieee: M. Horsthemke et al., “Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” Journal of Biological Chemistry, vol. 292, no. 17. American Society for Biochemistry and Molecular Biology, pp. 7258–7273, 2017. ista: Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 292(17), 7258–7273. mla: Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry, vol. 292, no. 17, American Society for Biochemistry and Molecular Biology, 2017, pp. 7258–73, doi:10.1074/jbc.M116.766923. short: M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R. Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological Chemistry 292 (2017) 7258–7273. date_created: 2018-12-11T11:47:49Z date_published: 2017-04-28T00:00:00Z date_updated: 2021-01-12T08:08:34Z day: '28' ddc: - '570' department: - _id: MiSi doi: 10.1074/jbc.M116.766923 file: - access_level: open_access checksum: d488162874326a4bb056065fa549dc4a content_type: application/pdf creator: dernst date_created: 2019-10-24T15:25:42Z date_updated: 2020-07-14T12:47:37Z file_id: '6971' file_name: 2017_JBC_Horsthemke.pdf file_size: 5647880 relation: main_file file_date_updated: 2020-07-14T12:47:37Z has_accepted_license: '1' intvolume: ' 292' issue: '17' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 7258 - 7273 publication: Journal of Biological Chemistry publication_identifier: issn: - '00219258' publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '7059' quality_controlled: '1' scopus_import: 1 status: public title: Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 292 year: '2017' ... --- _id: '669' abstract: - lang: eng text: 'The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. ' article_processing_charge: No article_type: original author: - first_name: Lukáš full_name: Synek, Lukáš last_name: Synek - first_name: Nemanja full_name: Vukašinović, Nemanja last_name: Vukašinović - first_name: Ivan full_name: Kulich, Ivan last_name: Kulich - first_name: Michal full_name: Hála, Michal last_name: Hála - first_name: Klára full_name: Aldorfová, Klára last_name: Aldorfová - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Viktor full_name: Žárský, Viktor last_name: Žárský citation: ama: Synek L, Vukašinović N, Kulich I, et al. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 2017;174(1):223-240. doi:10.1104/pp.16.01282 apa: Synek, L., Vukašinović, N., Kulich, I., Hála, M., Aldorfová, K., Fendrych, M., & Žárský, V. (2017). EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01282 chicago: Synek, Lukáš, Nemanja Vukašinović, Ivan Kulich, Michal Hála, Klára Aldorfová, Matyas Fendrych, and Viktor Žárský. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01282. ieee: L. Synek et al., “EXO70C2 is a key regulatory factor for optimal tip growth of pollen,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 223–240, 2017. ista: Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský V. 2017. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 174(1), 223–240. mla: Synek, Lukáš, et al. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 223–40, doi:10.1104/pp.16.01282. short: L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240. date_created: 2018-12-11T11:47:49Z date_published: 2017-05-01T00:00:00Z date_updated: 2021-01-12T08:08:35Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1104/pp.16.01282 external_id: pmid: - '28356503' file: - access_level: open_access checksum: 97155acc6aa5f0d0a78e0589a932fe02 content_type: application/pdf creator: dernst date_created: 2019-11-18T16:16:18Z date_updated: 2020-07-14T12:47:37Z file_id: '7041' file_name: 2017_PlantPhysio_Synek.pdf file_size: 2176903 relation: main_file file_date_updated: 2020-07-14T12:47:37Z has_accepted_license: '1' intvolume: ' 174' issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 223 - 240 pmid: 1 publication: Plant Physiology publication_identifier: issn: - '00320889' publication_status: published publisher: American Society of Plant Biologists publist_id: '7058' quality_controlled: '1' scopus_import: 1 status: public title: EXO70C2 is a key regulatory factor for optimal tip growth of pollen type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 174 year: '2017' ... --- _id: '671' abstract: - lang: eng text: Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation. article_processing_charge: Yes (in subscription journal) author: - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Vaquero full_name: Martinez, Vaquero last_name: Martinez - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Hilbe C, Martinez V, Chatterjee K, Nowak M. Memory-n strategies of direct reciprocity. PNAS. 2017;114(18):4715-4720. doi:10.1073/pnas.1621239114 apa: Hilbe, C., Martinez, V., Chatterjee, K., & Nowak, M. (2017). Memory-n strategies of direct reciprocity. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1621239114 chicago: Hilbe, Christian, Vaquero Martinez, Krishnendu Chatterjee, and Martin Nowak. “Memory-n Strategies of Direct Reciprocity.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621239114. ieee: C. Hilbe, V. Martinez, K. Chatterjee, and M. Nowak, “Memory-n strategies of direct reciprocity,” PNAS, vol. 114, no. 18. National Academy of Sciences, pp. 4715–4720, 2017. ista: Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720. mla: Hilbe, Christian, et al. “Memory-n Strategies of Direct Reciprocity.” PNAS, vol. 114, no. 18, National Academy of Sciences, 2017, pp. 4715–20, doi:10.1073/pnas.1621239114. short: C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720. date_created: 2018-12-11T11:47:50Z date_published: 2017-05-02T00:00:00Z date_updated: 2021-01-12T08:08:37Z day: '02' department: - _id: KrCh doi: 10.1073/pnas.1621239114 ec_funded: 1 external_id: pmid: - '28420786' intvolume: ' 114' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/ month: '05' oa: 1 oa_version: Published Version page: 4715 - 4720 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _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 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7053' quality_controlled: '1' scopus_import: 1 status: public title: Memory-n strategies of direct reciprocity type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '670' abstract: - lang: eng text: We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical-based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears. article_processing_charge: No article_type: original author: - first_name: Camille full_name: Schreck, Camille id: 2B14B676-F248-11E8-B48F-1D18A9856A87 last_name: Schreck - first_name: Damien full_name: Rohmer, Damien last_name: Rohmer - first_name: Stefanie full_name: Hahmann, Stefanie last_name: Hahmann citation: ama: Schreck C, Rohmer D, Hahmann S. Interactive paper tearing. Computer Graphics Forum. 2017;36(2):95-106. doi:10.1111/cgf.13110 apa: Schreck, C., Rohmer, D., & Hahmann, S. (2017). Interactive paper tearing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13110 chicago: Schreck, Camille, Damien Rohmer, and Stefanie Hahmann. “Interactive Paper Tearing.” Computer Graphics Forum. Wiley, 2017. https://doi.org/10.1111/cgf.13110. ieee: C. Schreck, D. Rohmer, and S. Hahmann, “Interactive paper tearing,” Computer Graphics Forum, vol. 36, no. 2. Wiley, pp. 95–106, 2017. ista: Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106. mla: Schreck, Camille, et al. “Interactive Paper Tearing.” Computer Graphics Forum, vol. 36, no. 2, Wiley, 2017, pp. 95–106, doi:10.1111/cgf.13110. short: C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106. date_created: 2018-12-11T11:47:49Z date_published: 2017-05-01T00:00:00Z date_updated: 2021-01-12T08:08:37Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.13110 intvolume: ' 36' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf month: '05' oa: 1 oa_version: Published Version page: 95 - 106 project: - _id: 25357BD2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 24352-N23 name: 'Deep Pictures: Creating Visual and Haptic Vector Images' publication: Computer Graphics Forum publication_identifier: issn: - '01677055' publication_status: published publisher: Wiley publist_id: '7056' quality_controlled: '1' scopus_import: 1 status: public title: Interactive paper tearing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2017' ... --- _id: '672' abstract: - lang: eng text: Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration. article_processing_charge: Yes author: - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner - first_name: Matthias full_name: Mehling, Matthias id: 3C23B994-F248-11E8-B48F-1D18A9856A87 last_name: Mehling orcid: 0000-0001-8599-1226 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - 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: Vaahtomeri K, Brown M, Hauschild R, et al. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 2017;19(5):902-909. doi:10.1016/j.celrep.2017.04.027 apa: Vaahtomeri, K., Brown, M., Hauschild, R., de Vries, I., Leithner, A. F., Mehling, M., … Sixt, M. K. (2017). Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.027 chicago: Vaahtomeri, Kari, Markus Brown, Robert Hauschild, Ingrid de Vries, Alexander F Leithner, Matthias Mehling, Walter Kaufmann, and Michael K Sixt. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.027. ieee: K. Vaahtomeri et al., “Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia,” Cell Reports, vol. 19, no. 5. Cell Press, pp. 902–909, 2017. ista: Vaahtomeri K, Brown M, Hauschild R, de Vries I, Leithner AF, Mehling M, Kaufmann W, Sixt MK. 2017. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 19(5), 902–909. mla: Vaahtomeri, Kari, et al. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports, vol. 19, no. 5, Cell Press, 2017, pp. 902–09, doi:10.1016/j.celrep.2017.04.027. short: K. Vaahtomeri, M. Brown, R. Hauschild, I. de Vries, A.F. Leithner, M. Mehling, W. Kaufmann, M.K. Sixt, Cell Reports 19 (2017) 902–909. date_created: 2018-12-11T11:47:50Z date_published: 2017-05-02T00:00:00Z date_updated: 2023-02-23T12:50:09Z day: '02' ddc: - '570' department: - _id: MiSi - _id: Bio - _id: EM-Fac doi: 10.1016/j.celrep.2017.04.027 ec_funded: 1 file: - access_level: open_access checksum: 8fdddaab1f1d76a6ec9ca94dcb6b07a2 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:54Z date_updated: 2020-07-14T12:47:38Z file_id: '5109' file_name: IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf file_size: 2248814 relation: main_file file_date_updated: 2020-07-14T12:47:38Z has_accepted_license: '1' intvolume: ' 19' issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: 902 - 909 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: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and transduction of leukocytes (FWF) publication: Cell Reports publication_identifier: issn: - '22111247' publication_status: published publisher: Cell Press publist_id: '7052' pubrep_id: '900' quality_controlled: '1' scopus_import: 1 status: public title: Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2017' ... --- _id: '674' abstract: - lang: eng text: Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo. author: - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Veronika full_name: Bierbaum, Veronika id: 3FD04378-F248-11E8-B48F-1D18A9856A87 last_name: Bierbaum - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner - first_name: Anne full_name: Reversat, Anne id: 35B76592-F248-11E8-B48F-1D18A9856A87 last_name: Reversat orcid: 0000-0003-0666-8928 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Teresa full_name: Tarrant, Teresa last_name: Tarrant - first_name: Tobias full_name: Bollenbach, 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: Schwarz J, Bierbaum V, Vaahtomeri K, et al. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 2017;27(9):1314-1325. doi:10.1016/j.cub.2017.04.004 apa: Schwarz, J., Bierbaum, V., Vaahtomeri, K., Hauschild, R., Brown, M., de Vries, I., … Sixt, M. K. (2017). Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.04.004 chicago: Schwarz, Jan, Veronika Bierbaum, Kari Vaahtomeri, Robert Hauschild, Markus Brown, Ingrid de Vries, Alexander F Leithner, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.04.004. ieee: J. Schwarz et al., “Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6,” Current Biology, vol. 27, no. 9. Cell Press, pp. 1314–1325, 2017. ista: Schwarz J, Bierbaum V, Vaahtomeri K, Hauschild R, Brown M, de Vries I, Leithner AF, Reversat A, Merrin J, Tarrant T, Bollenbach MT, Sixt MK. 2017. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 27(9), 1314–1325. mla: Schwarz, Jan, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology, vol. 27, no. 9, Cell Press, 2017, pp. 1314–25, doi:10.1016/j.cub.2017.04.004. short: J. Schwarz, V. Bierbaum, K. Vaahtomeri, R. Hauschild, M. Brown, I. de Vries, A.F. Leithner, A. Reversat, J. Merrin, T. Tarrant, M.T. Bollenbach, M.K. Sixt, Current Biology 27 (2017) 1314–1325. date_created: 2018-12-11T11:47:51Z date_published: 2017-05-09T00:00:00Z date_updated: 2023-02-23T12:50:44Z day: '09' department: - _id: MiSi - _id: Bio - _id: NanoFab doi: 10.1016/j.cub.2017.04.004 ec_funded: 1 intvolume: ' 27' issue: '9' language: - iso: eng month: '05' oa_version: None page: 1314 - 1325 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and transduction of leukocytes (FWF) publication: Current Biology publication_identifier: issn: - '09609822' publication_status: published publisher: Cell Press publist_id: '7050' quality_controlled: '1' scopus_import: 1 status: public title: Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6 type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2017' ... --- _id: '677' abstract: - lang: eng text: The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR. author: - first_name: Claudio full_name: Lademann, Claudio last_name: Lademann - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Boris full_name: Pfander, Boris last_name: Pfander - first_name: Stefan full_name: Jentsch, Stefan last_name: Jentsch citation: ama: Lademann C, Renkawitz J, Pfander B, Jentsch S. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 2017;19(7):1294-1303. doi:10.1016/j.celrep.2017.04.051 apa: Lademann, C., Renkawitz, J., Pfander, B., & Jentsch, S. (2017). The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.051 chicago: Lademann, Claudio, Jörg Renkawitz, Boris Pfander, and Stefan Jentsch. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.051. ieee: C. Lademann, J. Renkawitz, B. Pfander, and S. Jentsch, “The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination,” Cell Reports, vol. 19, no. 7. Cell Press, pp. 1294–1303, 2017. ista: Lademann C, Renkawitz J, Pfander B, Jentsch S. 2017. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 19(7), 1294–1303. mla: Lademann, Claudio, et al. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports, vol. 19, no. 7, Cell Press, 2017, pp. 1294–303, doi:10.1016/j.celrep.2017.04.051. short: C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303. date_created: 2018-12-11T11:47:52Z date_published: 2017-05-16T00:00:00Z date_updated: 2021-01-12T08:08:57Z day: '16' ddc: - '570' department: - _id: MiSi doi: 10.1016/j.celrep.2017.04.051 file: - access_level: open_access checksum: efc7287d9c6354983cb151880e9ad72a content_type: application/pdf creator: system date_created: 2018-12-12T10:15:48Z date_updated: 2020-07-14T12:47:40Z file_id: '5171' file_name: IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf file_size: 3005610 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 19' issue: '7' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1294 - 1303 publication: Cell Reports publication_identifier: issn: - '22111247' publication_status: published publisher: Cell Press publist_id: '7046' pubrep_id: '899' quality_controlled: '1' scopus_import: 1 status: public title: The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2017' ... --- _id: '678' abstract: - lang: eng text: The seminal observation that mechanical signals can elicit changes in biochemical signalling within cells, a process commonly termed mechanosensation and mechanotransduction, has revolutionized our understanding of the role of cell mechanics in various fundamental biological processes, such as cell motility, adhesion, proliferation and differentiation. In this Review, we will discuss how the interplay and feedback between mechanical and biochemical signals control tissue morphogenesis and cell fate specification in embryonic development. author: - first_name: Nicoletta full_name: Petridou, Nicoletta id: 2A003F6C-F248-11E8-B48F-1D18A9856A87 last_name: Petridou orcid: 0000-0002-8451-1195 - first_name: Zoltan P full_name: Spiro, Zoltan P id: 426AD026-F248-11E8-B48F-1D18A9856A87 last_name: Spiro - 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: Petridou N, Spiro ZP, Heisenberg C-PJ. Multiscale force sensing in development. Nature Cell Biology. 2017;19(6):581-588. doi:10.1038/ncb3524 apa: Petridou, N., Spiro, Z. P., & Heisenberg, C.-P. J. (2017). Multiscale force sensing in development. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3524 chicago: Petridou, Nicoletta, Zoltan P Spiro, and Carl-Philipp J Heisenberg. “Multiscale Force Sensing in Development.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3524. ieee: N. Petridou, Z. P. Spiro, and C.-P. J. Heisenberg, “Multiscale force sensing in development,” Nature Cell Biology, vol. 19, no. 6. Nature Publishing Group, pp. 581–588, 2017. ista: Petridou N, Spiro ZP, Heisenberg C-PJ. 2017. Multiscale force sensing in development. Nature Cell Biology. 19(6), 581–588. mla: Petridou, Nicoletta, et al. “Multiscale Force Sensing in Development.” Nature Cell Biology, vol. 19, no. 6, Nature Publishing Group, 2017, pp. 581–88, doi:10.1038/ncb3524. short: N. Petridou, Z.P. Spiro, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 581–588. date_created: 2018-12-11T11:47:53Z date_published: 2017-05-31T00:00:00Z date_updated: 2021-01-12T08:08:59Z day: '31' department: - _id: CaHe doi: 10.1038/ncb3524 intvolume: ' 19' issue: '6' language: - iso: eng month: '05' oa_version: None page: 581 - 588 project: - _id: 25236028-B435-11E9-9278-68D0E5697425 grant_number: ALTF534-2016 name: The generation and function of anisotropic tissue tension in zebrafish epiboly (EMBO Fellowship) publication: Nature Cell Biology publication_identifier: issn: - '14657392' publication_status: published publisher: Nature Publishing Group publist_id: '7040' quality_controlled: '1' scopus_import: 1 status: public title: Multiscale force sensing in development type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2017' ... --- _id: '681' abstract: - lang: eng text: Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information. In this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile where all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players' objective, then the objective of every player is violated. We present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games. We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games. article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu 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: Emmanuel full_name: Filiot, Emmanuel last_name: Filiot - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: ama: Chatterjee K, Doyen L, Filiot E, Raskin J. Doomsday equilibria for omega-regular games. Information and Computation. 2017;254:296-315. doi:10.1016/j.ic.2016.10.012 apa: Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J. (2017). Doomsday equilibria for omega-regular games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.012 chicago: Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean Raskin. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.012. ieee: K. Chatterjee, L. Doyen, E. Filiot, and J. Raskin, “Doomsday equilibria for omega-regular games,” Information and Computation, vol. 254. Elsevier, pp. 296–315, 2017. ista: Chatterjee K, Doyen L, Filiot E, Raskin J. 2017. Doomsday equilibria for omega-regular games. Information and Computation. 254, 296–315. mla: Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation, vol. 254, Elsevier, 2017, pp. 296–315, doi:10.1016/j.ic.2016.10.012. short: K. Chatterjee, L. Doyen, E. Filiot, J. Raskin, Information and Computation 254 (2017) 296–315. date_created: 2018-12-11T11:47:53Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-21T16:06:02Z day: '01' department: - _id: KrCh doi: 10.1016/j.ic.2016.10.012 ec_funded: 1 external_id: arxiv: - '1311.3238' intvolume: ' 254' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.3238 month: '06' oa: 1 oa_version: Submitted Version page: 296 - 315 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: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Information and Computation publication_identifier: issn: - '08905401' publication_status: published publisher: Elsevier publist_id: '7036' quality_controlled: '1' related_material: record: - id: '10885' relation: earlier_version status: public scopus_import: '1' status: public title: Doomsday equilibria for omega-regular games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 254 year: '2017' ... --- _id: '6841' abstract: - lang: eng text: In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified. author: - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Martius GS, Lampert C. Extrapolation and learning equations. In: 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations; 2017.' apa: 'Martius, G. S., & Lampert, C. (2017). Extrapolation and learning equations. In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. Toulon, France: International Conference on Learning Representations.' chicago: Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations, 2017. ieee: G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, Toulon, France, 2017. ista: 'Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations.' mla: Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017. short: G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017. conference: end_date: 2017-04-26 location: Toulon, France name: 'ICLR: International Conference on Learning Representations' start_date: 2017-04-24 date_created: 2019-09-01T22:01:00Z date_published: 2017-02-21T00:00:00Z date_updated: 2021-01-12T08:09:17Z day: '21' department: - _id: ChLa ec_funded: 1 external_id: arxiv: - '1610.02995' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.02995 month: '02' oa: 1 oa_version: Preprint project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings publication_status: published publisher: International Conference on Learning Representations quality_controlled: '1' scopus_import: 1 status: public title: Extrapolation and learning equations type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '684' abstract: - lang: eng text: We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic. article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: Chatterjee K, Piterman N. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 2017;82(2):420-452. doi:10.1017/jsl.2016.71 apa: Chatterjee, K., & Piterman, N. (2017). Obligation blackwell games and p-automata. Journal of Symbolic Logic. Cambridge University Press. https://doi.org/10.1017/jsl.2016.71 chicago: Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic. Cambridge University Press, 2017. https://doi.org/10.1017/jsl.2016.71. ieee: K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” Journal of Symbolic Logic, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017. ista: Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452. mla: Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:10.1017/jsl.2016.71. short: K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452. date_created: 2018-12-11T11:47:54Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-04-16T12:10:53Z day: '01' department: - _id: KrCh doi: 10.1017/jsl.2016.71 intvolume: ' 82' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1206.5174 month: '06' oa: 1 oa_version: Submitted Version page: 420 - 452 publication: Journal of Symbolic Logic publication_identifier: eissn: - 1943-5886 issn: - 0022-4812 publication_status: published publisher: Cambridge University Press publist_id: '7026' quality_controlled: '1' scopus_import: '1' status: public title: Obligation blackwell games and p-automata type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2017' ... --- _id: '685' abstract: - lang: eng text: By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube. author: - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. 2017;145:26-31. doi:10.1016/j.mod.2017.03.005 apa: Briscoe, J., & Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.005 chicago: Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.005. ieee: J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” Mechanisms of Development, vol. 145. Elsevier, pp. 26–31, 2017. ista: Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31. mla: Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 26–31, doi:10.1016/j.mod.2017.03.005. short: J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31. date_created: 2018-12-11T11:47:55Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:20Z day: '01' ddc: - '571' department: - _id: AnKi doi: 10.1016/j.mod.2017.03.005 ec_funded: 1 external_id: pmid: - '28366718' file: - access_level: open_access checksum: 727043d2e4199fbef6b3704e6d1ac105 content_type: application/pdf creator: dernst date_created: 2019-04-17T07:58:48Z date_updated: 2020-07-14T12:47:42Z file_id: '6335' file_name: 2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf file_size: 652313 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 145' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 26 - 31 pmid: 1 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord publication: Mechanisms of Development publication_identifier: issn: - '09254773' publication_status: published publisher: Elsevier publist_id: '7025' pubrep_id: '985' quality_controlled: '1' scopus_import: 1 status: public title: The physics of development 100 years after D'Arcy Thompson's “on growth and form” type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 145 year: '2017' ... --- _id: '688' abstract: - lang: eng text: 'We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. ' alternative_title: - LIPIcs author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: 'Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:10.4230/LIPIcs.SoCG.2017.39' apa: 'Edelsbrunner, H., & Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.39' chicago: Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.39. ieee: H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916. ista: Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916. mla: Edelsbrunner, Herbert, and Hubert Wagner. Topological Data Analysis with Bregman Divergences. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:10.4230/LIPIcs.SoCG.2017.39. short: H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916. conference: end_date: 2017-07-07 location: Brisbane, Australia name: Symposium on Computational Geometry, SoCG start_date: 2017-07-04 date_created: 2018-12-11T11:47:56Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:26Z day: '01' ddc: - '514' - '516' department: - _id: HeEd - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2017.39 file: - access_level: open_access checksum: 067ab0cb3f962bae6c3af6bf0094e0f3 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:03Z date_updated: 2020-07-14T12:47:42Z file_id: '4856' file_name: IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf file_size: 990546 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 77' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 391-3916 publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7021' pubrep_id: '895' quality_controlled: '1' scopus_import: 1 status: public title: Topological data analysis with Bregman divergences 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2017' ... --- _id: '687' abstract: - lang: eng text: Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs. author: - first_name: Ben full_name: Davison, Ben id: 4634AB1E-F248-11E8-B48F-1D18A9856A87 last_name: Davison orcid: 0000-0002-8944-4390 citation: ama: Davison B. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 2017;68(2):635-703. doi:10.1093/qmath/haw053 apa: Davison, B. (2017). The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haw053 chicago: Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics. Oxford University Press, 2017. https://doi.org/10.1093/qmath/haw053. ieee: B. Davison, “The critical CoHA of a quiver with potential,” Quarterly Journal of Mathematics, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017. ista: Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703. mla: Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:10.1093/qmath/haw053. short: B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703. date_created: 2018-12-11T11:47:55Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:24Z day: '01' department: - _id: TaHa doi: 10.1093/qmath/haw053 ec_funded: 1 intvolume: ' 68' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.7172 month: '06' oa: 1 oa_version: Submitted Version page: 635 - 703 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Quarterly Journal of Mathematics publication_identifier: issn: - '00335606' publication_status: published publisher: Oxford University Press publist_id: '7022' quality_controlled: '1' scopus_import: 1 status: public title: The critical CoHA of a quiver with potential type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2017' ... --- _id: '686' abstract: - lang: eng text: Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology. 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 citation: ama: 'Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 2017;145:32-37. doi:10.1016/j.mod.2017.03.006' apa: 'Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.006' chicago: 'Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.006.' ieee: 'C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” Mechanisms of Development, vol. 145. Elsevier, pp. 32–37, 2017.' ista: 'Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.' mla: 'Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 32–37, doi:10.1016/j.mod.2017.03.006.' short: C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37. date_created: 2018-12-11T11:47:55Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:23Z day: '01' department: - _id: CaHe doi: 10.1016/j.mod.2017.03.006 intvolume: ' 145' language: - iso: eng month: '06' oa_version: None page: 32 - 37 publication: Mechanisms of Development publication_identifier: issn: - '09254773' publication_status: published publisher: Elsevier publist_id: '7024' quality_controlled: '1' scopus_import: 1 status: public title: 'D''Arcy Thompson''s ‘on growth and form’: From soap bubbles to tissue self organization' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 145 year: '2017' ...