[{"date_updated":"2023-09-11T12:44:08Z","department":[{"_id":"EdHa"}],"_id":"288","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","issue":"6","volume":20,"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer."}],"month":"05","intvolume":" 20","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41556-018-0108-1.","ista":"Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687.","mla":"Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:10.1038/s41556-018-0108-1.","ieee":"A. Lilja et al., “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” Nature Cell Biology, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018.","short":"A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687.","ama":"Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 2018;20(6):677-687. doi:10.1038/s41556-018-0108-1","apa":"Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0108-1"},"title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","publist_id":"7594","author":[{"first_name":"Anna","full_name":"Lilja, Anna","last_name":"Lilja"},{"last_name":"Rodilla","full_name":"Rodilla, Veronica","first_name":"Veronica"},{"first_name":"Mathilde","full_name":"Huyghe, Mathilde","last_name":"Huyghe"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Landragin","full_name":"Landragin, Camille","first_name":"Camille"},{"first_name":"Olivier","last_name":"Renaud","full_name":"Renaud, Olivier"},{"last_name":"Leroy","full_name":"Leroy, Olivier","first_name":"Olivier"},{"last_name":"Rulands","full_name":"Rulands, Steffen","first_name":"Steffen"},{"full_name":"Simons, Benjamin","last_name":"Simons","first_name":"Benjamin"},{"first_name":"Silvia","last_name":"Fré","full_name":"Fré, Silvia"}],"external_id":{"isi":["000433237300003"],"pmid":["29784917"]},"article_processing_charge":"No","day":"21","publication":"Nature Cell Biology","isi":1,"year":"2018","date_published":"2018-05-21T00:00:00Z","doi":"10.1038/s41556-018-0108-1","date_created":"2018-12-11T11:45:38Z","page":"677 - 687","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1},{"article_number":"159","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"citation":{"apa":"Auzinger, T., Heidrich, W., & Bickel, B. (2018). Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201376","ama":"Auzinger T, Heidrich W, Bickel B. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201376","short":"T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018).","ieee":"T. Auzinger, W. Heidrich, and B. Bickel, “Computational design of nanostructural color for additive manufacturing,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","mla":"Auzinger, Thomas, et al. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics, vol. 37, no. 4, 159, ACM, 2018, doi:10.1145/3197517.3201376.","ista":"Auzinger T, Heidrich W, Bickel B. 2018. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159.","chicago":"Auzinger, Thomas, Wolfgang Heidrich, and Bernd Bickel. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201376."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Wolfgang","full_name":"Heidrich, Wolfgang","last_name":"Heidrich"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"article_processing_charge":"No","external_id":{"isi":["000448185000120"]},"title":"Computational design of nanostructural color for additive manufacturing","acknowledgement":"This work was in part supported by King Abdullah University of Science and Technology Baseline Funding.","publisher":"ACM","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"ACM Transactions on Graphics","date_published":"2018-08-01T00:00:00Z","doi":"10.1145/3197517.3201376","date_created":"2018-12-11T11:45:43Z","_id":"304","type":"journal_article","status":"public","pubrep_id":"1028","date_updated":"2023-09-11T12:46:13Z","ddc":["000","535","680"],"file_date_updated":"2020-07-14T12:45:59Z","department":[{"_id":"BeBi"}],"abstract":[{"lang":"eng","text":"Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods.\r\nAs a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications.\r\n \r\nIn this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process.\r\nThis requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure.\r\nMany of these components should be re-usable for the design of other optical structures at this scale.\r\n \r\nWe show initial results of material samples fabricated based on our designs.\r\nWhile these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications."}],"oa_version":"Submitted Version","alternative_title":["ACM Transactions on Graphics"],"scopus_import":"1","month":"08","intvolume":" 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on IST Homepage"}]},"issue":"4","ec_funded":1},{"article_number":"135","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"grant_number":"642841","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics, vol. 37, no. 4, 135, ACM, 2018, doi:10.1145/3197517.3201341.","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 2018;37(4). doi:10.1145/3197517.3201341","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., & Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. ACM. https://doi.org/10.1145/3197517.3201341","short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” ACM Transaction on Graphics, vol. 37, no. 4. ACM, 2018.","chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201341.","ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135."},"title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","author":[{"last_name":"Nakashima","full_name":"Nakashima, Kazutaka","first_name":"Kazutaka"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265"},{"first_name":"Emmanuel","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","full_name":"Iarussi, Emmanuel","last_name":"Iarussi"},{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran","orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran","last_name":"Zhang"},{"full_name":"Igarashi, Takeo","last_name":"Igarashi","first_name":"Takeo"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8044","external_id":{"isi":["000448185000096"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"ACM","oa":1,"day":"04","publication":"ACM Transaction on Graphics","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-08-04T00:00:00Z","doi":"10.1145/3197517.3201341","date_created":"2018-12-11T11:44:09Z","_id":"12","status":"public","pubrep_id":"1037","type":"journal_article","ddc":["004","516","670"],"date_updated":"2023-09-11T12:48:09Z","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:44:38Z","oa_version":"Submitted Version","abstract":[{"text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects.","lang":"eng"}],"month":"08","intvolume":" 37","scopus_import":"1","file":[{"file_id":"5360","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:18:38Z","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","creator":"system","date_updated":"2020-07-14T12:44:38Z","file_size":104225664},{"file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","date_created":"2018-12-12T10:18:39Z","file_size":377743553,"date_updated":"2020-07-14T12:44:38Z","creator":"system","file_id":"5361","checksum":"3861e693ba47c51f3ec7b7867d573a61","content_type":"application/zip","relation":"main_file","access_level":"open_access"},{"creator":"system","file_size":162634396,"date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","date_created":"2018-12-12T10:18:41Z","relation":"main_file","access_level":"open_access","content_type":"video/vnd.objectvideo","file_id":"5362","checksum":"490040c685ed869536e2a18f5a906b94"},{"content_type":"image/jpeg","relation":"main_file","access_level":"open_access","checksum":"be7fc8b229adda727419b6504b3b9352","file_id":"5363","file_size":527972,"date_updated":"2020-07-14T12:44:38Z","creator":"system","file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","date_created":"2018-12-12T10:18:42Z"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","relation":"press_release"}]},"volume":37,"issue":"4","ec_funded":1},{"article_number":"555","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"mla":"Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:10.1038/s41467-017-02721-8.","short":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018).","ieee":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","ama":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 2018;9(1). doi:10.1038/s41467-017-02721-8","apa":"Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., & Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02721-8","chicago":"Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-017-02721-8.","ista":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7368","author":[{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"first_name":"David","full_name":"Rand, David","last_name":"Rand"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"isi":["000424318200001"]},"title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","acknowledgement":"This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson.","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"07","publication":"Nature Communications","date_published":"2018-02-07T00:00:00Z","doi":"10.1038/s41467-017-02721-8","date_created":"2018-12-11T11:46:34Z","_id":"454","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"964","date_updated":"2023-09-11T12:51:03Z","ddc":["004"],"file_date_updated":"2020-07-14T12:46:31Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games."}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 9","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"b6b90367545b4c615891c960ab0567f1","file_id":"4741","file_size":843646,"date_updated":"2020-07-14T12:46:31Z","creator":"system","file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","date_created":"2018-12-12T10:09:18Z"}],"language":[{"iso":"eng"}],"volume":9,"issue":"1","ec_funded":1},{"title":"Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000429192100016"]},"publist_id":"7545","author":[{"last_name":"Hu","full_name":"Hu, Hua","first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roth","full_name":"Roth, Fabian","first_name":"Fabian"},{"last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 2018;98(1):156-165. doi:10.1016/j.neuron.2018.02.024","apa":"Hu, H., Roth, F., Vandael, D. H., & Jonas, P. M. (2018). Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.02.024","short":"H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.","ieee":"H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons,” Neuron, vol. 98, no. 1. Elsevier, pp. 156–165, 2018.","mla":"Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:10.1016/j.neuron.2018.02.024.","ista":"Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 98(1), 156–165.","chicago":"Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.02.024."},"project":[{"grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:45:48Z","date_published":"2018-04-04T00:00:00Z","doi":"10.1016/j.neuron.2018.02.024","page":"156 - 165","publication":"Neuron","day":"04","year":"2018","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Elsevier","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:03Z","department":[{"_id":"PeJo"}],"ddc":["570"],"date_updated":"2023-09-11T12:45:10Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"320","ec_funded":1,"volume":98,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/","description":"News on IST Homepage"}]},"issue":"1","language":[{"iso":"eng"}],"file":[{"file_id":"5690","checksum":"76070f3729f9c603e1080d0151aa2b11","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_Neuron_Hu.pdf","date_created":"2018-12-17T10:37:50Z","file_size":3180444,"date_updated":"2020-07-14T12:46:03Z","creator":"dernst"}],"publication_status":"published","intvolume":" 98","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. "}]},{"article_processing_charge":"No","external_id":{"isi":["000431035800001"]},"publist_id":"7400","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","last_name":"Payne"},{"first_name":"Lukas","full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"}],"title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","citation":{"mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"article_number":"e32035","date_created":"2018-12-11T11:46:23Z","date_published":"2018-03-09T00:00:00Z","doi":"10.7554/eLife.32035","year":"2018","has_accepted_license":"1","isi":1,"publication":"eLife","day":"09","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","file_date_updated":"2020-07-14T12:46:25Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_updated":"2023-09-11T12:49:17Z","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"423","ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9840"}]},"volume":7,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-17T10:36:07Z","file_name":"2018_eLife_Payne.pdf","date_updated":"2020-07-14T12:46:25Z","file_size":3533881,"creator":"dernst","file_id":"5689","checksum":"447cf6e680bdc3c01062a8737d876569","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"scopus_import":"1","intvolume":" 7","month":"03","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"oa_version":"Published Version"},{"external_id":{"arxiv":["1808.07608"],"isi":["000672802500016"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tóth, Csaba D.","last_name":"Tóth","first_name":"Csaba D."}],"title":"Crossing minimization in perturbed drawings","citation":{"ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241.","chicago":"Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16.","ieee":"R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241.","short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.","ama":"Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16","apa":"Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization, Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16","mla":"Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings. Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Springer","page":"229-241","date_created":"2018-12-30T22:59:15Z","date_published":"2018-12-18T00:00:00Z","doi":"10.1007/978-3-030-04414-5_16","year":"2018","isi":1,"day":"18","conference":{"name":"Graph Drawing and Network Visualization","location":"Barcelona, Spain","end_date":"2018-09-28","start_date":"2018-09-26"},"type":"conference","status":"public","_id":"5791","department":[{"_id":"UlWa"}],"date_updated":"2023-09-11T12:49:55Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07608"}],"alternative_title":["LNCS"],"scopus_import":"1","month":"12","abstract":[{"text":"Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths.","lang":"eng"}],"oa_version":"Preprint","volume":"11282 ","publication_status":"published","publication_identifier":{"isbn":["9783030044138"]},"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"publication_status":"published","volume":3,"issue":"5","oa_version":"Preprint","abstract":[{"text":"Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions.","lang":"eng"}],"month":"05","intvolume":" 3","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.01918","open_access":"1"}],"date_updated":"2023-09-11T12:45:44Z","department":[{"_id":"BjHo"}],"_id":"291","status":"public","type":"journal_article","day":"30","publication":"Physical Review Fluids","isi":1,"year":"2018","doi":"10.1103/PhysRevFluids.3.054401","date_published":"2018-05-30T00:00:00Z","date_created":"2018-12-11T11:45:39Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in pipe flow,” Physical Review Fluids, vol. 3, no. 5. American Physical Society, 2018.","short":"N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018).","ama":"Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 2018;3(5). doi:10.1103/PhysRevFluids.3.054401","apa":"Budanur, N. B., & Hof, B. (2018). Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.054401","mla":"Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids, vol. 3, no. 5, 054401, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.054401.","ista":"Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 3(5), 054401.","chicago":"Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.054401."},"title":"Complexity of the laminar-turbulent boundary in pipe flow","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"publist_id":"7590","external_id":{"isi":["000433426200001"],"arxiv":["1802.01918"]},"article_processing_charge":"No","article_number":"054401"},{"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"last_name":"Segal Halevi","full_name":"Segal Halevi, Erel","first_name":"Erel"}],"publist_id":"7996","external_id":{"arxiv":["1604.00960"],"isi":["000450810500036"]},"article_processing_charge":"No","title":"Counting blanks in polygonal arrangements","citation":{"ista":"Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 32(3), 2242–2257.","chicago":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X.","ieee":"A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,” SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial and Applied Mathematics , pp. 2242–2257, 2018.","short":"A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018) 2242–2257.","apa":"Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M110407X","ama":"Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X","mla":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"2242 - 2257","doi":"10.1137/16M110407X","date_published":"2018-09-06T00:00:00Z","date_created":"2018-12-11T11:44:24Z","isi":1,"year":"2018","day":"06","publication":"SIAM Journal on Discrete Mathematics","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","oa":1,"department":[{"_id":"HeEd"}],"date_updated":"2023-09-11T12:48:39Z","type":"journal_article","status":"public","_id":"58","issue":"3","volume":32,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1604.00960","open_access":"1"}],"month":"09","intvolume":" 32","abstract":[{"lang":"eng","text":"Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks."}],"oa_version":"Preprint"},{"year":"2018","day":"12","related_material":{"record":[{"relation":"used_in_publication","id":"423","status":"public"}]},"doi":"10.5061/dryad.42n44","date_published":"2018-03-12T00:00:00Z","date_created":"2021-08-09T13:10:02Z","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"oa_version":"Published Version","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.42n44","open_access":"1"}],"oa":1,"month":"03","citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44"},"date_updated":"2023-09-11T12:49:17Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","last_name":"Payne"},{"first_name":"Lukas","full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback"}],"article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","_id":"9840","type":"research_data_reference","status":"public"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 7, e32073.","chicago":"Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse, Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32073.","ieee":"C. Pull et al., “Destructive disinfection of infected brood prevents systemic disease spread in ant colonies,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt, M. Brown, S. Cremer, ELife 7 (2018).","apa":"Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt, T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32073","ama":"Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 2018;7. doi:10.7554/eLife.32073","mla":"Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife, vol. 7, e32073, eLife Sciences Publications, 2018, doi:10.7554/eLife.32073."},"title":"Destructive disinfection of infected brood prevents systemic disease spread in ant colonies","author":[{"last_name":"Pull","full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","last_name":"Ugelvig"},{"last_name":"Wiesenhofer","full_name":"Wiesenhofer, Florian","first_name":"Florian","id":"39523C54-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tragust","full_name":"Tragust, Simon","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmitt","full_name":"Schmitt, Thomas","first_name":"Thomas"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"publist_id":"7188","external_id":{"isi":["000419601300001"]},"article_processing_charge":"Yes","article_number":"e32073","project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"},{"call_identifier":"FP7","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","grant_number":"302004"}],"day":"09","publication":"eLife","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.7554/eLife.32073","date_published":"2018-01-09T00:00:00Z","date_created":"2018-12-11T11:47:31Z","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"ddc":["570","590"],"date_updated":"2023-09-11T12:54:26Z","file_date_updated":"2020-07-14T12:47:20Z","department":[{"_id":"SyCr"}],"_id":"616","status":"public","pubrep_id":"978","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"system","date_updated":"2020-07-14T12:47:20Z","file_size":1435585,"date_created":"2018-12-12T10:10:43Z","file_name":"IST-2018-978-v1+1_elife-32073-v1.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"540f941e8d3530a9441e4affd94f07d7","file_id":"4832"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":7,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"819"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Social insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour − "destructive disinfection" − to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen's non-contagious incubation period, relying on chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation."}],"month":"01","intvolume":" 7","scopus_import":"1"},{"department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:44:43Z","ddc":["570"],"date_updated":"2023-09-11T12:52:41Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"132","volume":46,"issue":"3","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5694","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","creator":"dernst","file_size":8948384,"date_updated":"2020-07-14T12:44:43Z","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","date_created":"2018-12-17T10:49:49Z"}],"publication_status":"published","intvolume":" 46","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments.","lang":"eng"}],"title":"Defining lineage potential and fate behavior of precursors during pancreas development","article_processing_charge":"No","external_id":{"isi":["000441327300012"]},"author":[{"full_name":"Sznurkowska, Magdalena","last_name":"Sznurkowska","first_name":"Magdalena"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Roberta","full_name":"Azzarelli, Roberta","last_name":"Azzarelli"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"},{"first_name":"Sonia","full_name":"Nestorowa, Sonia","last_name":"Nestorowa"},{"first_name":"Christopher","full_name":"Hindley, Christopher","last_name":"Hindley"},{"last_name":"Nichols","full_name":"Nichols, Jennifer","first_name":"Jennifer"},{"first_name":"Berthold","full_name":"Göttgens, Berthold","last_name":"Göttgens"},{"last_name":"Huch","full_name":"Huch, Meritxell","first_name":"Meritxell"},{"first_name":"Anna","full_name":"Philpott, Anna","last_name":"Philpott"},{"full_name":"Simons, Benjamin","last_name":"Simons","first_name":"Benjamin"}],"publist_id":"7791","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028.","ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028.","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.06.028","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","ieee":"M. Sznurkowska et al., “Defining lineage potential and fate behavior of precursors during pancreas development,” Developmental Cell, vol. 46, no. 3. Cell Press, pp. 360–375, 2018."},"date_created":"2018-12-11T11:44:48Z","date_published":"2018-08-06T00:00:00Z","doi":"10.1016/j.devcel.2018.06.028","page":"360 - 375","publication":"Developmental Cell","day":"06","year":"2018","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Cell Press","acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support."},{"abstract":[{"text":"Seeds derive from ovules upon fertilization and therefore the total number of ovules determines the final seed yield, a fundamental trait in crop plants. Among the factors that co-ordinate the process of ovule formation, the transcription factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK) have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2 causes a severe reduction in ovule number, a phenotype that can be rescued by CK treatment. In this study, we combined CK quantification with an integrative genome-wide target identification approach to select Arabidopsis genes regulated by CUCs that are also involved in CK metabolism. We focused our attention on the functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1, which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance of CUCs and CKs in the determination of seed yield.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 69","publication_status":"published","file":[{"date_created":"2018-12-17T10:44:16Z","file_name":"2018_JournalExperimBotany_Cucinotta.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:25Z","file_size":1292128,"file_id":"5691","checksum":"ca3b6711040b1662488aeb3d1f961f13","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":69,"issue":"21","_id":"42","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-11T12:52:03Z","ddc":["575"],"department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:46:25Z","acknowledgement":"This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic through the National Program of Sustainability (grant no. LO1204).","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"26","publication":"Journal of Experimental Botany","page":"5169 - 5176","date_published":"2018-07-26T00:00:00Z","doi":"10.1093/jxb/ery281","date_created":"2018-12-11T11:44:19Z","citation":{"chicago":"Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák, and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281.","ista":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.","mla":"Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281.","short":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal of Experimental Botany 69 (2018) 5169–5176.","ieee":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo, “Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69, no. 21. Oxford University Press, pp. 5169–5176, 2018.","ama":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176. doi:10.1093/jxb/ery281","apa":"Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo, L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery281"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8012","author":[{"first_name":"Mara","last_name":"Cucinotta","full_name":"Cucinotta, Mara"},{"last_name":"Manrique","full_name":"Manrique, Silvia","first_name":"Silvia"},{"first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","last_name":"Cuesta"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"first_name":"Lucia","last_name":"Colombo","full_name":"Colombo, Lucia"}],"article_processing_charge":"No","external_id":{"isi":["000448163900015"]},"title":"Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis"},{"issue":"16","volume":98,"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 98","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.08316","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase.","lang":"eng"}],"department":[{"_id":"MaSe"}],"date_updated":"2023-09-11T12:55:03Z","status":"public","type":"journal_article","article_type":"original","_id":"46","doi":"10.1103/PhysRevB.98.161122","date_published":"2018-10-15T00:00:00Z","date_created":"2018-12-11T11:44:20Z","day":"15","publication":"Physical Review B","isi":1,"year":"2018","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807 through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich (NIM) by the German Excellence Initiative, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award.","title":"Detection and characterization of many-body localization in central spin models","author":[{"first_name":"Daniel","full_name":"Hetterich, Daniel","last_name":"Hetterich"},{"first_name":"Norman","last_name":"Yao","full_name":"Yao, Norman"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"full_name":"Pollmann, Frank","last_name":"Pollmann","first_name":"Frank"},{"last_name":"Trauzettel","full_name":"Trauzettel, Björn","first_name":"Björn"}],"publist_id":"8008","article_processing_charge":"No","external_id":{"arxiv":["1806.08316"],"isi":["000448596500002"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., & Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.161122","ama":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. Physical Review B. 2018;98(16). doi:10.1103/PhysRevB.98.161122","ieee":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” Physical Review B, vol. 98, no. 16. American Physical Society, 2018.","short":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018).","mla":"Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:10.1103/PhysRevB.98.161122.","ista":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122.","chicago":"Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.161122."},"article_number":"161122"},{"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo."}],"acknowledged_ssus":[{"_id":"SSU"}],"month":"05","intvolume":" 45","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2018.04.002"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":45,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/"}]},"ec_funded":1,"_id":"308","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-11T13:22:13Z","department":[{"_id":"DaSi"},{"_id":"CaHe"},{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"MiSi"}],"publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"07","publication":"Developmental Cell","isi":1,"year":"2018","doi":"10.1016/j.devcel.2018.04.002","date_published":"2018-05-07T00:00:00Z","date_created":"2018-12-11T11:45:44Z","page":"331 - 346","project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29638","name":"Drosophila TNFa´s Funktion in Immunzellen"},{"grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2018.04.002","ama":"Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002","ieee":"A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” Developmental Cell, vol. 45, no. 3. Elsevier, pp. 331–346, 2018.","short":"A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346.","mla":"Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002.","ista":"Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346.","chicago":"Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier, 2018. https://doi.org/10.1016/j.devcel.2018.04.002."},"title":"Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration","author":[{"id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","first_name":"Aparna","full_name":"Ratheesh, Aparna","orcid":"0000-0001-7190-0776","last_name":"Ratheesh"},{"full_name":"Biebl, Julia","last_name":"Biebl","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Michael","full_name":"Smutny, Michael","last_name":"Smutny"},{"id":"433253EE-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","full_name":"Veselá, Jana","last_name":"Veselá"},{"full_name":"Papusheva, Ekaterina","last_name":"Papusheva","first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"orcid":"0000-0002-1819-198X","full_name":"György, Attila","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila"},{"id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandra M","last_name":"Casano","full_name":"Casano, Alessandra M","orcid":"0000-0002-6009-6804"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"article_processing_charge":"No","external_id":{"isi":["000432461400009"],"pmid":["29738712"]}},{"citation":{"mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103302.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","apa":"Varshney, A., & Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103302","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103302","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103302.","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000447311500001"]},"author":[{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor","full_name":"Steinberg, Victor","last_name":"Steinberg"}],"publist_id":"8038","title":"Drag enhancement and drag reduction in viscoelastic flow","article_number":"103302 ","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"year":"2018","isi":1,"has_accepted_license":"1","publication":"Physical Review Fluids","day":"15","date_created":"2018-12-11T11:44:11Z","date_published":"2018-10-15T00:00:00Z","doi":"10.1103/PhysRevFluids.3.103302","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_updated":"2023-09-11T12:59:28Z","ddc":["532"],"department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:12Z","_id":"17","type":"journal_article","pubrep_id":"1061","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"e1445be33e8165114e96246275600750","file_id":"4800","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","date_created":"2018-12-12T10:10:14Z","creator":"system","file_size":1409040,"date_updated":"2020-07-14T12:45:12Z"}],"ec_funded":1,"volume":3,"issue":"10","abstract":[{"lang":"eng","text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 3","month":"10"},{"abstract":[{"lang":"eng","text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making."}],"oa_version":"Preprint","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/09/21/192039","open_access":"1"}],"month":"06","intvolume":" 115","publication_status":"published","language":[{"iso":"eng"}],"volume":115,"issue":"23","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6473"}]},"_id":"281","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-11T12:58:24Z","department":[{"_id":"GaTk"}],"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"isi":1,"year":"2018","day":"05","publication":"PNAS","page":"6088 - 6093","date_published":"2018-06-05T00:00:00Z","doi":"10.1073/pnas.1716659115","date_created":"2018-12-11T11:45:35Z","project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1716659115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7618","author":[{"first_name":"Alejandro","full_name":"Granados, Alejandro","last_name":"Granados"},{"full_name":"Pietsch, Julian","last_name":"Pietsch","first_name":"Julian"},{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A"},{"last_name":"Farquhar","full_name":"Farquhar, Isebail","first_name":"Isebail"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Swain","full_name":"Swain, Peter"}],"article_processing_charge":"No","external_id":{"pmid":["29784812"],"isi":["000434114900071"]},"title":"Distributed and dynamic intracellular organization of extracellular information"},{"_id":"620","status":"public","type":"journal_article","date_updated":"2023-09-11T12:57:13Z","department":[{"_id":"DaSi"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis."}],"month":"01","intvolume":" 131","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":131,"issue":"1","article_number":"jcs207696","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.","ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.","mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696"},"title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","author":[{"full_name":"Yamamoto, Wataru","last_name":"Yamamoto","first_name":"Wataru"},{"first_name":"Suguru","last_name":"Wada","full_name":"Wada, Suguru"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"last_name":"Aoshima","full_name":"Aoshima, Kaito","first_name":"Kaito"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"full_name":"Toshima, Junko","last_name":"Toshima","first_name":"Junko"},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"publist_id":"7184","external_id":{"pmid":["29192062"],"isi":["000424786900012"]},"article_processing_charge":"No","publisher":"Company of Biologists","quality_controlled":"1","oa":1,"day":"04","publication":"Journal of Cell Science","isi":1,"year":"2018","date_published":"2018-01-04T00:00:00Z","doi":"10.1242/jcs.207696","date_created":"2018-12-11T11:47:32Z"},{"oa":1,"quality_controlled":"1","publisher":"ACM","page":"177 - 186","date_created":"2018-12-11T11:45:04Z","doi":"10.1145/3178126.3178132","date_published":"2018-04-11T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"publication":"Proceedings of the 21st International Conference on Hybrid Systems","day":"11","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"external_id":{"isi":["000474781600020"]},"article_processing_charge":"No","publist_id":"7739","author":[{"full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin","first_name":"Alexey"},{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere"},{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"}],"title":"Efficient parametric identification for STL","citation":{"ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: Proceedings of the 21st International Conference on Hybrid Systems. ACM; 2018:177-186. doi:10.1145/3178126.3178132","apa":"Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification for STL. In Proceedings of the 21st International Conference on Hybrid Systems (pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186.","ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in Proceedings of the 21st International Conference on Hybrid Systems, Porto, Portugal, 2018, pp. 177–186.","mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86, doi:10.1145/3178126.3178132.","ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In Proceedings of the 21st International Conference on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","alternative_title":["HSCC Proceedings"],"month":"04","abstract":[{"lang":"eng","text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice."}],"oa_version":"Submitted Version","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:45:17Z","file_size":5900421,"date_created":"2020-05-14T12:18:29Z","file_name":"2018_HSCC_Bakhirkin.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7833","checksum":"81eabc96430e84336ea88310ac0a1ad0"}],"conference":{"end_date":"2018-04-13","location":"Porto, Portugal","start_date":"2018-04-11","name":"HSCC: Hybrid Systems: Computation and Control"},"type":"conference","status":"public","_id":"182","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-11T13:30:51Z","ddc":["000"]},{"oa":1,"publisher":"IEEE","quality_controlled":"1","day":"09","year":"2018","isi":1,"date_created":"2018-12-11T11:44:51Z","date_published":"2018-07-09T00:00:00Z","doi":"10.1145/3209108.3209191","page":"185 - 194","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:10.1145/3209108.3209191","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194.","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","mla":"Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191.","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191."},"title":"Efficient algorithms for asymptotic bounds on termination time in VASS","external_id":{"isi":["000545262800020"]},"article_processing_charge":"No","author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Kučera","full_name":"Kučera, Antonín","first_name":"Antonín"},{"last_name":"Novotny","full_name":"Novotny, Petr","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik","last_name":"Velan","full_name":"Velan, Dominik"},{"first_name":"Florian","full_name":"Zuleger, Florian","last_name":"Zuleger"}],"publist_id":"7780","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis."}],"month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10985"}],"scopus_import":"1","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-1-4503-5583-4"]},"ec_funded":1,"volume":"F138033","_id":"143","status":"public","conference":{"start_date":"2018-07-09","location":"Oxford, United Kingdom","end_date":"2018-07-12","name":"LICS: Logic in Computer Science"},"type":"conference","date_updated":"2023-09-11T13:23:42Z","department":[{"_id":"KrCh"}]}]