[{"type":"journal_article","issue":"26","abstract":[{"lang":"eng","text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses."}],"intvolume":" 115","title":"Auxin methylation is required for differential growth in Arabidopsis","status":"public","_id":"203","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"26","page":"6864-6869","citation":{"apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115","ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115."},"publication":"PNAS","date_published":"2018-06-26T00:00:00Z","ec_funded":1,"publist_id":"7710","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","year":"2018","volume":115,"date_created":"2018-12-11T11:45:11Z","date_updated":"2023-09-08T13:24:40Z","author":[{"full_name":"Abbas, Mohamad","last_name":"Abbas","first_name":"Mohamad","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hernández","first_name":"García J","full_name":"Hernández, García J"},{"first_name":"Stephan","last_name":"Pollmann","full_name":"Pollmann, Stephan"},{"full_name":"Samodelov, Sophia L","last_name":"Samodelov","first_name":"Sophia L"},{"first_name":"Martina","last_name":"Kolb","full_name":"Kolb, Martina"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Hammes, Ulrich Z","first_name":"Ulrich Z","last_name":"Hammes"},{"first_name":"Matias D","last_name":"Zurbriggen","full_name":"Zurbriggen, Matias D"},{"full_name":"Blázquez, Miguel","first_name":"Miguel","last_name":"Blázquez"},{"last_name":"Alabadí","first_name":"David","full_name":"Alabadí, David"}],"month":"06","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000436245000096"]},"oa":1,"main_file_link":[{"url":"http://eprints.nottingham.ac.uk/52388/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1806565115"},{"publication":"EPL","citation":{"mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no. 1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007.","ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1). doi:10.1209/0295-5075/121/10007","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL, vol. 121, no. 1. IOP Publishing Ltd., 2018."},"article_type":"original","date_published":"2018-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","_id":"399","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","intvolume":" 121","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm."}],"issue":"1","main_file_link":[{"url":"https://arxiv.org/abs/1706.01822","open_access":"1"}],"oa":1,"external_id":{"isi":["000460003000003"],"arxiv":["1706.01822"]},"isi":1,"quality_controlled":"1","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"doi":"10.1209/0295-5075/121/10007","language":[{"iso":"eng"}],"month":"01","year":"2018","acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","publication_status":"published","publisher":"IOP Publishing Ltd.","department":[{"_id":"RoSe"}],"author":[{"full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","last_name":"Napiórkowski","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reuvers, Robin","first_name":"Robin","last_name":"Reuvers"},{"full_name":"Solovej, Jan","first_name":"Jan","last_name":"Solovej"}],"date_updated":"2023-09-08T13:30:51Z","date_created":"2018-12-11T11:46:15Z","volume":121,"article_number":"10007","publist_id":"7432"},{"author":[{"last_name":"Zhang","first_name":"Luosha","full_name":"Zhang, Luosha"},{"last_name":"Shi","first_name":"Xiong","full_name":"Shi, Xiong"},{"full_name":"Zhang, Yutao","first_name":"Yutao","last_name":"Zhang"},{"full_name":"Wang, Jiajing","first_name":"Jiajing","last_name":"Wang"},{"full_name":"Yang, Jingwei","first_name":"Jingwei","last_name":"Yang"},{"full_name":"Ishida, Takashi","first_name":"Takashi","last_name":"Ishida"},{"full_name":"Jiang, Wenqian","first_name":"Wenqian","last_name":"Jiang"},{"full_name":"Han, Xiangyu","last_name":"Han","first_name":"Xiangyu"},{"first_name":"Jingke","last_name":"Kang","full_name":"Kang, Jingke"},{"first_name":"Xuening","last_name":"Wang","full_name":"Wang, Xuening"},{"full_name":"Pan, Lixia","first_name":"Lixia","last_name":"Pan"},{"full_name":"Lv, Shuo","first_name":"Shuo","last_name":"Lv"},{"last_name":"Cao","first_name":"Bing","full_name":"Cao, Bing"},{"first_name":"Yonghong","last_name":"Zhang","full_name":"Zhang, Yonghong"},{"first_name":"Jinbin","last_name":"Wu","full_name":"Wu, Jinbin"},{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zhubing","last_name":"Hu","full_name":"Hu, Zhubing"},{"full_name":"Cui, Langjun","last_name":"Cui","first_name":"Langjun"},{"first_name":"Shinichiro","last_name":"Sawa","full_name":"Sawa, Shinichiro"},{"full_name":"He, Junmin","last_name":"He","first_name":"Junmin"},{"last_name":"Wang","first_name":"Guodong","full_name":"Wang, Guodong"}],"oa_version":"Published Version","date_created":"2019-01-13T22:59:11Z","date_updated":"2023-09-11T12:43:31Z","pmid":1,"_id":"5830","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","department":[{"_id":"JiFr"}],"publisher":"Wiley","publication_status":"epub_ahead","title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","status":"public","abstract":[{"text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.","lang":"eng"}],"type":"journal_article","doi":"10.1111/pce.13475","date_published":"2018-10-31T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140","open_access":"1"}],"external_id":{"pmid":["30378140"],"isi":["000459014800021"]},"oa":1,"citation":{"ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2018. doi:10.1111/pce.13475","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475","ieee":"L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment. Wiley, 2018.","ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment.","short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018).","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475.","chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475."},"publication":"Plant Cell and Environment","quality_controlled":"1","isi":1,"article_processing_charge":"No","publication_identifier":{"issn":["01407791"]},"day":"31","month":"10","scopus_import":"1"},{"abstract":[{"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.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Submitted Version","title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","status":"public","intvolume":" 20","_id":"288","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"21","article_processing_charge":"No","scopus_import":"1","date_published":"2018-05-21T00:00:00Z","article_type":"original","page":"677 - 687","publication":"Nature Cell Biology","citation":{"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","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.","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.","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.","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.","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."},"publist_id":"7594","date_updated":"2023-09-11T12:44:08Z","date_created":"2018-12-11T11:45:38Z","volume":20,"author":[{"full_name":"Lilja, Anna","first_name":"Anna","last_name":"Lilja"},{"last_name":"Rodilla","first_name":"Veronica","full_name":"Rodilla, Veronica"},{"last_name":"Huyghe","first_name":"Mathilde","full_name":"Huyghe, Mathilde"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Camille","last_name":"Landragin","full_name":"Landragin, Camille"},{"first_name":"Olivier","last_name":"Renaud","full_name":"Renaud, Olivier"},{"first_name":"Olivier","last_name":"Leroy","full_name":"Leroy, Olivier"},{"full_name":"Rulands, Steffen","first_name":"Steffen","last_name":"Rulands"},{"full_name":"Simons, Benjamin","first_name":"Benjamin","last_name":"Simons"},{"full_name":"Fré, Silvia","first_name":"Silvia","last_name":"Fré"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"EdHa"}],"year":"2018","pmid":1,"month":"05","language":[{"iso":"eng"}],"doi":"10.1038/s41556-018-0108-1","isi":1,"quality_controlled":"1","external_id":{"isi":["000433237300003"],"pmid":["29784917"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964"}]},{"doi":"10.1145/3197517.3201376","language":[{"iso":"eng"}],"external_id":{"isi":["000448185000120"]},"oa":1,"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","month":"08","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/color-effects-from-transparent-3d-printed-nanostructures/"}]},"author":[{"full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265","first_name":"Thomas","last_name":"Auzinger"},{"full_name":"Heidrich, Wolfgang","last_name":"Heidrich","first_name":"Wolfgang"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"}],"volume":37,"date_updated":"2023-09-11T12:46:13Z","date_created":"2018-12-11T11:45:43Z","year":"2018","acknowledgement":"This work was in part supported by King Abdullah University of Science and Technology Baseline Funding.","department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:45:59Z","article_number":"159","date_published":"2018-08-01T00:00:00Z","citation":{"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","ista":"Auzinger T, Heidrich W, Bickel B. 2018. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159.","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.","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","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.","short":"T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018).","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."},"publication":"ACM Transactions on 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Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"304","intvolume":" 37","status":"public","title":"Computational design of nanostructural color for additive manufacturing","ddc":["000","535","680"],"issue":"4","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."}],"type":"journal_article","alternative_title":["ACM Transactions on 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Version","pubrep_id":"1037","intvolume":" 37","title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","status":"public","ddc":["004","516","670"],"_id":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2018-08-04T00:00:00Z","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.","short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (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.","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","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.","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","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."},"publication":"ACM Transaction on Graphics","has_accepted_license":"1","article_processing_charge":"No","day":"04","scopus_import":"1","volume":37,"date_created":"2018-12-11T11:44:09Z","date_updated":"2023-09-11T12:48:09Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"first_name":"Kazutaka","last_name":"Nakashima","full_name":"Nakashima, Kazutaka"},{"first_name":"Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas"},{"last_name":"Iarussi","first_name":"Emmanuel","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","full_name":"Iarussi, Emmanuel"},{"orcid":"0000-0002-3808-281X","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Ran","full_name":"Zhang, Ran"},{"full_name":"Igarashi, Takeo","last_name":"Igarashi","first_name":"Takeo"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"}],"department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published","year":"2018","ec_funded":1,"publist_id":"8044","file_date_updated":"2020-07-14T12:44:38Z","article_number":"135","language":[{"iso":"eng"}],"doi":"10.1145/3197517.3201341","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000448185000096"]},"oa":1,"month":"08"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41467-017-02721-8","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000424318200001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"02","volume":9,"date_created":"2018-12-11T11:46:34Z","date_updated":"2023-09-11T12:51:03Z","author":[{"first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rand, David","last_name":"Rand","first_name":"David"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","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.","year":"2018","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"publist_id":"7368","file_date_updated":"2020-07-14T12:46:31Z","article_number":"555","date_published":"2018-02-07T00:00:00Z","citation":{"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","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.","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.","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","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).","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."},"publication":"Nature Communications","has_accepted_license":"1","article_processing_charge":"No","day":"07","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":843646,"file_id":"4741","relation":"main_file","date_created":"2018-12-12T10:09:18Z","date_updated":"2020-07-14T12:46:31Z","checksum":"b6b90367545b4c615891c960ab0567f1"}],"pubrep_id":"964","intvolume":" 9","title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","ddc":["004"],"status":"public","_id":"454","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","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."}],"type":"journal_article"},{"oa_version":"Published Version","file":[{"creator":"dernst","file_size":3180444,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_Neuron_Hu.pdf","checksum":"76070f3729f9c603e1080d0151aa2b11","date_created":"2018-12-17T10:37:50Z","date_updated":"2020-07-14T12:46:03Z","file_id":"5690","relation":"main_file"}],"_id":"320","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 98","ddc":["570"],"title":"Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons","status":"public","issue":"1","abstract":[{"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. ","lang":"eng"}],"type":"journal_article","date_published":"2018-04-04T00:00:00Z","citation":{"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.","short":"H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.","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.","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","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.","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.","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"},"publication":"Neuron","page":"156 - 165","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"04","scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"full_name":"Hu, Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","last_name":"Hu","first_name":"Hua"},{"first_name":"Fabian","last_name":"Roth","full_name":"Roth, Fabian"},{"first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"volume":98,"date_updated":"2023-09-11T12:45:10Z","date_created":"2018-12-11T11:45:48Z","year":"2018","publisher":"Elsevier","department":[{"_id":"PeJo"}],"publication_status":"published","publist_id":"7545","ec_funded":1,"file_date_updated":"2020-07-14T12:46:03Z","doi":"10.1016/j.neuron.2018.02.024","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000429192100016"]},"project":[{"grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"},{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","month":"04"},{"project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000431035800001"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.32035","month":"03","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"eLife Sciences Publications","publication_status":"published","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.","year":"2018","volume":7,"date_created":"2018-12-11T11:46:23Z","date_updated":"2023-09-11T12:49:17Z","related_material":{"record":[{"id":"9840","status":"public","relation":"research_data"}]},"author":[{"full_name":"Payne, Pavel","first_name":"Pavel","last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453"},{"first_name":"Lukas","last_name":"Geyrhofer","full_name":"Geyrhofer, Lukas"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"article_number":"e32035","publist_id":"7400","ec_funded":1,"file_date_updated":"2020-07-14T12:46:25Z","citation":{"short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","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.","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.","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","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.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035."},"publication":"eLife","date_published":"2018-03-09T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"09","intvolume":" 7","status":"public","ddc":["576"],"title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"423","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_eLife_Payne.pdf","content_type":"application/pdf","file_size":3533881,"creator":"dernst","relation":"main_file","file_id":"5689","checksum":"447cf6e680bdc3c01062a8737d876569","date_created":"2018-12-17T10:36:07Z","date_updated":"2020-07-14T12:46:25Z"}],"type":"journal_article","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."}]},{"date_created":"2018-12-30T22:59:15Z","date_updated":"2023-09-11T12:49:55Z","volume":"11282 ","author":[{"first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"last_name":"Tóth","first_name":"Csaba D.","full_name":"Tóth, Csaba D."}],"publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"year":"2018","month":"12","publication_identifier":{"isbn":["9783030044138"]},"language":[{"iso":"eng"}],"conference":{"name":"Graph Drawing and Network Visualization","location":"Barcelona, Spain","start_date":"2018-09-26","end_date":"2018-09-28"},"doi":"10.1007/978-3-030-04414-5_16","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07608"}],"external_id":{"arxiv":["1808.07608"],"isi":["000672802500016"]},"oa":1,"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"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"Crossing minimization in perturbed drawings","_id":"5791","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"18","article_processing_charge":"No","scopus_import":"1","date_published":"2018-12-18T00:00:00Z","page":"229-241","citation":{"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","ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241.","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.","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.","short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 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."}}]