[{"publisher":"The Company of Biologists","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported in part by the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by the National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF P28844). Deposited in PMC for release after 12 months.","doi":"10.1242/dev.176065","date_published":"2021-02-01T00:00:00Z","date_created":"2021-03-07T23:01:25Z","day":"01","publication":"Development","isi":1,"year":"2021","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"article_number":"dev176065","title":"The many bits of positional information","author":[{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"}],"external_id":{"pmid":["33526425"],"isi":["000613906000007"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"G. Tkačik and T. Gregor, “The many bits of positional information,” Development, vol. 148, no. 2. The Company of Biologists, 2021.","short":"G. Tkačik, T. Gregor, Development 148 (2021).","ama":"Tkačik G, Gregor T. The many bits of positional information. Development. 2021;148(2). doi:10.1242/dev.176065","apa":"Tkačik, G., & Gregor, T. (2021). The many bits of positional information. Development. The Company of Biologists. https://doi.org/10.1242/dev.176065","mla":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development, vol. 148, no. 2, dev176065, The Company of Biologists, 2021, doi:10.1242/dev.176065.","ista":"Tkačik G, Gregor T. 2021. The many bits of positional information. Development. 148(2), dev176065.","chicago":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development. The Company of Biologists, 2021. https://doi.org/10.1242/dev.176065."},"month":"02","intvolume":" 148","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1242/dev.176065","open_access":"1"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?","lang":"eng"}],"issue":"2","volume":148,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1477-9129"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"9226","department":[{"_id":"GaTk"}],"date_updated":"2023-08-07T13:57:30Z"},{"issue":"5","volume":284,"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"c630b691fb9e716b02aa6103a9794ec8","file_id":"9267","creator":"dernst","file_size":473310,"date_updated":"2021-03-22T07:18:01Z","file_name":"2021_JourDiffEquations_Cornalba.pdf","date_created":"2021-03-22T07:18:01Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-0396"],"eissn":["1090-2732"]},"publication_status":"published","month":"05","intvolume":" 284","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A stochastic PDE, describing mesoscopic fluctuations in systems of weakly interacting inertial particles of finite volume, is proposed and analysed in any finite dimension . It is a regularised and inertial version of the Dean–Kawasaki model. A high-probability well-posedness theory for this model is developed. This theory improves significantly on the spatial scaling restrictions imposed in an earlier work of the same authors, which applied only to significantly larger particles in one dimension. The well-posedness theory now applies in d-dimensions when the particle-width ϵ is proportional to for and N is the number of particles. This scaling is optimal in a certain Sobolev norm. Key tools of the analysis are fractional Sobolev spaces, sharp bounds on Bessel functions, separability of the regularisation in the d-spatial dimensions, and use of the Faà di Bruno's formula."}],"file_date_updated":"2021-03-22T07:18:01Z","department":[{"_id":"JuFi"}],"ddc":["510"],"date_updated":"2023-08-07T14:08:05Z","status":"public","type":"journal_article","article_type":"original","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)"},"_id":"9240","doi":"10.1016/j.jde.2021.02.048","date_published":"2021-05-25T00:00:00Z","date_created":"2021-03-14T23:01:32Z","page":"253-283","day":"25","publication":"Journal of Differential Equations","has_accepted_license":"1","isi":1,"year":"2021","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"All authors thank the anonymous referee for his/her careful reading of the manuscript and valuable suggestions. This paper was motivated by stimulating discussions at the First Berlin–Leipzig Workshop on Fluctuating Hydrodynamics in August 2019 with Ana Djurdjevac, Rupert Klein and Ralf Kornhuber. JZ gratefully acknowledges funding by a Royal Society Wolfson Research Merit Award. FC gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","title":"Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions","author":[{"full_name":"Cornalba, Federico","last_name":"Cornalba","id":"2CEB641C-A400-11E9-A717-D712E6697425","first_name":"Federico"},{"first_name":"Tony","full_name":"Shardlow, Tony","last_name":"Shardlow"},{"last_name":"Zimmer","full_name":"Zimmer, Johannes","first_name":"Johannes"}],"external_id":{"isi":["000634823300010"]},"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Cornalba F, Shardlow T, Zimmer J. 2021. Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. Journal of Differential Equations. 284(5), 253–283.","chicago":"Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “Well-Posedness for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several Space Dimensions.” Journal of Differential Equations. Elsevier, 2021. https://doi.org/10.1016/j.jde.2021.02.048.","short":"F. Cornalba, T. Shardlow, J. Zimmer, Journal of Differential Equations 284 (2021) 253–283.","ieee":"F. Cornalba, T. Shardlow, and J. Zimmer, “Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions,” Journal of Differential Equations, vol. 284, no. 5. Elsevier, pp. 253–283, 2021.","apa":"Cornalba, F., Shardlow, T., & Zimmer, J. (2021). Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2021.02.048","ama":"Cornalba F, Shardlow T, Zimmer J. Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. Journal of Differential Equations. 2021;284(5):253-283. doi:10.1016/j.jde.2021.02.048","mla":"Cornalba, Federico, et al. “Well-Posedness for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several Space Dimensions.” Journal of Differential Equations, vol. 284, no. 5, Elsevier, 2021, pp. 253–83, doi:10.1016/j.jde.2021.02.048."},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}]},{"title":"Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic","author":[{"full_name":"Heiler, Georg","last_name":"Heiler","first_name":"Georg"},{"first_name":"Tobias","last_name":"Reisch","full_name":"Reisch, Tobias"},{"last_name":"Hurt","full_name":"Hurt, Jan","first_name":"Jan"},{"first_name":"Mohammad","full_name":"Forghani, Mohammad","last_name":"Forghani"},{"first_name":"Aida","full_name":"Omani, Aida","last_name":"Omani"},{"last_name":"Hanbury","full_name":"Hanbury, Allan","first_name":"Allan"},{"id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","first_name":"Farid","last_name":"Karimipour","full_name":"Karimipour, Farid","orcid":"0000-0001-6746-4174"}],"external_id":{"arxiv":["2008.10064"],"isi":["000662554703032"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"G. Heiler, T. Reisch, J. Hurt, M. Forghani, A. Omani, A. Hanbury, F. Karimipour, in:, 2020 IEEE International Conference on Big Data, IEEE, 2021, pp. 3123–3132.","ieee":"G. Heiler et al., “Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic,” in 2020 IEEE International Conference on Big Data, Atlanta, GA, United States, 2021, pp. 3123–3132.","ama":"Heiler G, Reisch T, Hurt J, et al. Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. In: 2020 IEEE International Conference on Big Data. IEEE; 2021:3123-3132. doi:10.1109/bigdata50022.2020.9378374","apa":"Heiler, G., Reisch, T., Hurt, J., Forghani, M., Omani, A., Hanbury, A., & Karimipour, F. (2021). Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. In 2020 IEEE International Conference on Big Data (pp. 3123–3132). Atlanta, GA, United States: IEEE. https://doi.org/10.1109/bigdata50022.2020.9378374","mla":"Heiler, Georg, et al. “Country-Wide Mobility Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2020 IEEE International Conference on Big Data, IEEE, 2021, pp. 3123–32, doi:10.1109/bigdata50022.2020.9378374.","ista":"Heiler G, Reisch T, Hurt J, Forghani M, Omani A, Hanbury A, Karimipour F. 2021. Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. 2020 IEEE International Conference on Big Data. Big Data: International Conference on Big Data, 3123–3132.","chicago":"Heiler, Georg, Tobias Reisch, Jan Hurt, Mohammad Forghani, Aida Omani, Allan Hanbury, and Farid Karimipour. “Country-Wide Mobility Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2020 IEEE International Conference on Big Data, 3123–32. IEEE, 2021. https://doi.org/10.1109/bigdata50022.2020.9378374."},"publisher":"IEEE","quality_controlled":"1","oa":1,"doi":"10.1109/bigdata50022.2020.9378374","date_published":"2021-03-19T00:00:00Z","date_created":"2021-03-21T11:34:07Z","page":"3123-3132","day":"19","publication":"2020 IEEE International Conference on Big Data","isi":1,"year":"2021","status":"public","type":"conference","conference":{"start_date":"2020-12-10","end_date":"2020-12-13","location":"Atlanta, GA, United States","name":"Big Data: International Conference on Big Data"},"_id":"9253","department":[{"_id":"HeEd"}],"date_updated":"2023-08-07T14:00:13Z","month":"03","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.10064"}],"oa_version":"Preprint","abstract":[{"text":"In March 2020, the Austrian government introduced a widespread lock-down in response to the COVID-19 pandemic. Based on subjective impressions and anecdotal evidence, Austrian public and private life came to a sudden halt. Here we assess the effect of the lock-down quantitatively for all regions in Austria and present an analysis of daily changes of human mobility throughout Austria using near-real-time anonymized mobile phone data. We describe an efficient data aggregation pipeline and analyze the mobility by quantifying mobile-phone traffic at specific point of interests (POIs), analyzing individual trajectories and investigating the cluster structure of the origin-destination graph. We found a reduction of commuters at Viennese metro stations of over 80% and the number of devices with a radius of gyration of less than 500 m almost doubled. The results of studying crowd-movement behavior highlight considerable changes in the structure of mobility networks, revealed by a higher modularity and an increase from 12 to 20 detected communities. We demonstrate the relevance of mobility data for epidemiological studies by showing a significant correlation of the outflow from the town of Ischgl (an early COVID-19 hotspot) and the reported COVID-19 cases with an 8-day time lag. This research indicates that mobile phone usage data permits the moment-by-moment quantification of mobility behavior for a whole country. We emphasize the need to improve the availability of such data in anonymized form to empower rapid response to combat COVID-19 and future pandemics.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781728162515"]},"publication_status":"published"},{"year":"2021","has_accepted_license":"1","isi":1,"publication":"Trends in Cognitive Sciences","day":"01","page":"265-268","date_created":"2021-03-07T23:01:25Z","date_published":"2021-04-01T00:00:00Z","doi":"10.1016/j.tics.2021.01.007","acknowledgement":"We thank all of our volunteers from the NMC conferences (list of names in the appendix). We also thank the NSF for support from 1734220 to B.W., and DARPA for support to T.A.","oa":1,"publisher":"Elsevier","quality_controlled":"1","citation":{"ista":"Achakulvisut T, Ruangrong T, Mineault P, Vogels TP, Peters MAK, Poirazi P, Rozell C, Wyble B, Goodman DFM, Kording KP. 2021. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. 25(4), 265–268.","chicago":"Achakulvisut, Titipat, Tulakan Ruangrong, Patrick Mineault, Tim P Vogels, Megan A.K. Peters, Panayiota Poirazi, Christopher Rozell, Brad Wyble, Dan F.M. Goodman, and Konrad Paul Kording. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” Trends in Cognitive Sciences. Elsevier, 2021. https://doi.org/10.1016/j.tics.2021.01.007.","ieee":"T. Achakulvisut et al., “Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences,” Trends in Cognitive Sciences, vol. 25, no. 4. Elsevier, pp. 265–268, 2021.","short":"T. Achakulvisut, T. Ruangrong, P. Mineault, T.P. Vogels, M.A.K. Peters, P. Poirazi, C. Rozell, B. Wyble, D.F.M. Goodman, K.P. Kording, Trends in Cognitive Sciences 25 (2021) 265–268.","ama":"Achakulvisut T, Ruangrong T, Mineault P, et al. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. 2021;25(4):265-268. doi:10.1016/j.tics.2021.01.007","apa":"Achakulvisut, T., Ruangrong, T., Mineault, P., Vogels, T. P., Peters, M. A. K., Poirazi, P., … Kording, K. P. (2021). Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. Elsevier. https://doi.org/10.1016/j.tics.2021.01.007","mla":"Achakulvisut, Titipat, et al. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” Trends in Cognitive Sciences, vol. 25, no. 4, Elsevier, 2021, pp. 265–68, doi:10.1016/j.tics.2021.01.007."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000627418000001"],"pmid":["33608214"]},"author":[{"full_name":"Achakulvisut, Titipat","last_name":"Achakulvisut","first_name":"Titipat"},{"last_name":"Ruangrong","full_name":"Ruangrong, Tulakan","first_name":"Tulakan"},{"last_name":"Mineault","full_name":"Mineault, Patrick","first_name":"Patrick"},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"},{"last_name":"Peters","full_name":"Peters, Megan A.K.","first_name":"Megan A.K."},{"first_name":"Panayiota","full_name":"Poirazi, Panayiota","last_name":"Poirazi"},{"first_name":"Christopher","full_name":"Rozell, Christopher","last_name":"Rozell"},{"full_name":"Wyble, Brad","last_name":"Wyble","first_name":"Brad"},{"first_name":"Dan F.M.","full_name":"Goodman, Dan F.M.","last_name":"Goodman"},{"first_name":"Konrad Paul","full_name":"Kording, Konrad Paul","last_name":"Kording"}],"title":"Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences","publication_status":"published","publication_identifier":{"eissn":["1879-307X"],"issn":["1364-6613"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"11415","checksum":"87e39ea7bd266b976e8631b66979214d","creator":"dernst","file_size":380720,"date_updated":"2022-05-27T07:31:24Z","file_name":"2021_TrendsCognitiveSciences_Achakulvisut.pdf","date_created":"2022-05-27T07:31:24Z"}],"volume":25,"issue":"4","abstract":[{"lang":"eng","text":"Legacy conferences are costly and time consuming, and exclude scientists lacking various resources or abilities. During the 2020 pandemic, we created an online conference platform, Neuromatch Conferences (NMC), aimed at developing technological and cultural changes to make conferences more democratic, scalable, and accessible. We discuss the lessons we learned."}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","intvolume":" 25","month":"04","date_updated":"2023-08-07T13:59:07Z","ddc":["570"],"department":[{"_id":"TiVo"}],"file_date_updated":"2022-05-27T07:31:24Z","_id":"9228","article_type":"original","type":"journal_article","status":"public"},{"publication_identifier":{"eissn":["1096035X"],"issn":["00034916"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":427,"issue":"4","abstract":[{"lang":"eng","text":"We re-examine attempts to study the many-body localization transition using measures that are physically natural on the ergodic/quantum chaotic regime of the phase diagram. Using simple scaling arguments and an analysis of various models for which rigorous results are available, we find that these measures can be particularly adversely affected by the strong finite-size effects observed in nearly all numerical studies of many-body localization. This severely impacts their utility in probing the transition and the localized phase. In light of this analysis, we discuss a recent study (Šuntajs et al., 2020) of the behaviour of the Thouless energy and level repulsion in disordered spin chains, and its implications for the question of whether MBL is a true phase of matter."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.04501"}],"month":"04","intvolume":" 427","date_updated":"2023-08-07T13:58:30Z","department":[{"_id":"MaSe"}],"_id":"9224","type":"journal_article","article_type":"original","status":"public","isi":1,"year":"2021","day":"01","publication":"Annals of Physics","date_published":"2021-04-01T00:00:00Z","doi":"10.1016/j.aop.2021.168415","date_created":"2021-03-07T23:01:25Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"citation":{"chicago":"Abanin, D. A., J. H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani, S. A. Parameswaran, F. Pollmann, A. C. Potter, Maksym Serbyn, and R. Vasseur. “Distinguishing Localization from Chaos: Challenges in Finite-Size Systems.” Annals of Physics. Elsevier, 2021. https://doi.org/10.1016/j.aop.2021.168415.","ista":"Abanin DA, Bardarson JH, De Tomasi G, Gopalakrishnan S, Khemani V, Parameswaran SA, Pollmann F, Potter AC, Serbyn M, Vasseur R. 2021. Distinguishing localization from chaos: Challenges in finite-size systems. Annals of Physics. 427(4), 168415.","mla":"Abanin, D. A., et al. “Distinguishing Localization from Chaos: Challenges in Finite-Size Systems.” Annals of Physics, vol. 427, no. 4, 168415, Elsevier, 2021, doi:10.1016/j.aop.2021.168415.","apa":"Abanin, D. A., Bardarson, J. H., De Tomasi, G., Gopalakrishnan, S., Khemani, V., Parameswaran, S. A., … Vasseur, R. (2021). Distinguishing localization from chaos: Challenges in finite-size systems. Annals of Physics. Elsevier. https://doi.org/10.1016/j.aop.2021.168415","ama":"Abanin DA, Bardarson JH, De Tomasi G, et al. Distinguishing localization from chaos: Challenges in finite-size systems. Annals of Physics. 2021;427(4). doi:10.1016/j.aop.2021.168415","ieee":"D. A. Abanin et al., “Distinguishing localization from chaos: Challenges in finite-size systems,” Annals of Physics, vol. 427, no. 4. Elsevier, 2021.","short":"D.A. Abanin, J.H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani, S.A. Parameswaran, F. Pollmann, A.C. Potter, M. Serbyn, R. Vasseur, Annals of Physics 427 (2021)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Abanin, D. A.","last_name":"Abanin","first_name":"D. A."},{"full_name":"Bardarson, J. H.","last_name":"Bardarson","first_name":"J. H."},{"last_name":"De Tomasi","full_name":"De Tomasi, G.","first_name":"G."},{"first_name":"S.","last_name":"Gopalakrishnan","full_name":"Gopalakrishnan, S."},{"last_name":"Khemani","full_name":"Khemani, V.","first_name":"V."},{"full_name":"Parameswaran, S. A.","last_name":"Parameswaran","first_name":"S. A."},{"full_name":"Pollmann, F.","last_name":"Pollmann","first_name":"F."},{"first_name":"A. C.","last_name":"Potter","full_name":"Potter, A. C."},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"R.","full_name":"Vasseur, R.","last_name":"Vasseur"}],"article_processing_charge":"No","external_id":{"arxiv":["1911.04501"],"isi":["000634879800007"]},"title":"Distinguishing localization from chaos: Challenges in finite-size systems","article_number":"168415"},{"external_id":{"arxiv":["1905.03835"],"isi":["000634149800009"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Žikelić","full_name":"Žikelić, Đorđe","first_name":"Đorđe"}],"title":"Bidding mechanisms in graph games","citation":{"ista":"Avni G, Henzinger TA, Žikelić Đ. 2021. Bidding mechanisms in graph games. Journal of Computer and System Sciences. 119(8), 133–144.","chicago":"Avni, Guy, Thomas A Henzinger, and Đorđe Žikelić. “Bidding Mechanisms in Graph Games.” Journal of Computer and System Sciences. Elsevier, 2021. https://doi.org/10.1016/j.jcss.2021.02.008.","ama":"Avni G, Henzinger TA, Žikelić Đ. Bidding mechanisms in graph games. Journal of Computer and System Sciences. 2021;119(8):133-144. doi:10.1016/j.jcss.2021.02.008","apa":"Avni, G., Henzinger, T. A., & Žikelić, Đ. (2021). Bidding mechanisms in graph games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2021.02.008","short":"G. Avni, T.A. Henzinger, Đ. Žikelić, Journal of Computer and System Sciences 119 (2021) 133–144.","ieee":"G. Avni, T. A. Henzinger, and Đ. Žikelić, “Bidding mechanisms in graph games,” Journal of Computer and System Sciences, vol. 119, no. 8. Elsevier, pp. 133–144, 2021.","mla":"Avni, Guy, et al. “Bidding Mechanisms in Graph Games.” Journal of Computer and System Sciences, vol. 119, no. 8, Elsevier, 2021, pp. 133–44, doi:10.1016/j.jcss.2021.02.008."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Elsevier","quality_controlled":"1","page":"133-144","date_created":"2021-03-14T23:01:32Z","date_published":"2021-03-03T00:00:00Z","doi":"10.1016/j.jcss.2021.02.008","year":"2021","isi":1,"publication":"Journal of Computer and System Sciences","day":"03","article_type":"original","type":"journal_article","status":"public","_id":"9239","department":[{"_id":"ToHe"}],"date_updated":"2023-08-07T14:08:34Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1905.03835"}],"scopus_import":"1","intvolume":" 119","month":"03","abstract":[{"text":"A graph game proceeds as follows: two players move a token through a graph to produce a finite or infinite path, which determines the payoff of the game. We study bidding games in which in each turn, an auction determines which player moves the token. Bidding games were largely studied in combination with two variants of first-price auctions called “Richman” and “poorman” bidding. We study taxman bidding, which span the spectrum between the two. The game is parameterized by a constant : portion τ of the winning bid is paid to the other player, and portion to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games: we unify, generalize, and simplify previous equivalences between bidding games and a class of stochastic games called random-turn games.","lang":"eng"}],"oa_version":"Preprint","related_material":{"record":[{"status":"public","id":"6884","relation":"earlier_version"}]},"volume":119,"issue":"8","publication_status":"published","publication_identifier":{"eissn":["1090-2724"],"issn":["0022-0000"]},"language":[{"iso":"eng"}]},{"date_updated":"2023-08-07T14:12:54Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2021-03-22T08:50:33Z","_id":"9244","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","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"20ccf4dfe46c48cf986794c8bf4fd1cb","file_id":"9271","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-03-22T08:50:33Z","file_name":"2021_eLife_Hankeova.pdf","date_updated":"2021-03-22T08:50:33Z","file_size":9259690,"creator":"dernst"}],"ec_funded":1,"volume":10,"abstract":[{"lang":"eng","text":"Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"02","citation":{"ieee":"S. Hankeova et al., “DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek, V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis, A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021).","apa":"Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek, A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.60916","ama":"Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 2021;10. doi:10.7554/eLife.60916","mla":"Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife, vol. 10, e60916, eLife Sciences Publications, 2021, doi:10.7554/eLife.60916.","ista":"Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 10, e60916.","chicago":"Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.60916."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000625357100001"],"pmid":["33635272"]},"article_processing_charge":"No","author":[{"last_name":"Hankeova","full_name":"Hankeova, Simona","first_name":"Simona"},{"full_name":"Salplachta, Jakub","last_name":"Salplachta","first_name":"Jakub"},{"first_name":"Tomas","full_name":"Zikmund, Tomas","last_name":"Zikmund"},{"last_name":"Kavkova","full_name":"Kavkova, Michaela","first_name":"Michaela"},{"last_name":"Van Hul","full_name":"Van Hul, Noémi","first_name":"Noémi"},{"first_name":"Adam","full_name":"Brinek, Adam","last_name":"Brinek"},{"full_name":"Smekalova, Veronika","last_name":"Smekalova","first_name":"Veronika"},{"full_name":"Laznovsky, Jakub","last_name":"Laznovsky","first_name":"Jakub"},{"first_name":"Feven","full_name":"Dawit, Feven","last_name":"Dawit"},{"full_name":"Jaros, Josef","last_name":"Jaros","first_name":"Josef"},{"first_name":"Vítězslav","last_name":"Bryja","full_name":"Bryja, Vítězslav"},{"full_name":"Lendahl, Urban","last_name":"Lendahl","first_name":"Urban"},{"full_name":"Ellis, Ewa","last_name":"Ellis","first_name":"Ewa"},{"first_name":"Antal","full_name":"Nemeth, Antal","last_name":"Nemeth"},{"last_name":"Fischler","full_name":"Fischler, Björn","first_name":"Björn"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaiser, Jozef","last_name":"Kaiser","first_name":"Jozef"},{"last_name":"Andersson","full_name":"Andersson, Emma Rachel","first_name":"Emma Rachel"}],"title":"DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome","article_number":"e60916","project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"year":"2021","isi":1,"has_accepted_license":"1","publication":"eLife","day":"26","date_created":"2021-03-14T23:01:34Z","date_published":"2021-02-26T00:00:00Z","doi":"10.7554/eLife.60916","acknowledgement":"Work in ERA lab is supported by the Swedish Research Council, the Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated to this project. The funders have no role in the design or interpretation of the work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m Foundation Scholarship. We are grateful for support from Tornspiran foundation to NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II and CzechNanoLab Research Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged. JJ: The work was supported by the Grant Agency of Masaryk University (project no. MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise and help regarding bile duct cannulation and their laboratory hospitality. We also thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion. We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics (SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242. We thank Goncalo M Brito for all illustrations. This work was supported by the European Union (European Research Council Starting grant 851288 to E.H.).","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1"},{"status":"public","article_type":"original","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)"},"_id":"9241","department":[{"_id":"BeBi"}],"file_date_updated":"2021-03-22T08:15:28Z","ddc":["000"],"date_updated":"2023-08-07T14:11:57Z","month":"03","intvolume":" 29","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Volumetric light transport is a pervasive physical phenomenon, and therefore its accurate simulation is important for a broad array of disciplines. While suitable mathematical models for computing the transport are now available, obtaining the necessary material parameters needed to drive such simulations is a challenging task: direct measurements of these parameters from material samples are seldom possible. Building on the inverse scattering paradigm, we present a novel measurement approach which indirectly infers the transport parameters from extrinsic observations of multiple-scattered radiance. The novelty of the proposed approach lies in replacing structured illumination with a structured reflector bonded to the sample, and a robust fitting procedure that largely compensates for potential systematic errors in the calibration of the setup. We show the feasibility of our approach by validating simulations of complex 3D compositions of the measured materials against physical prints, using photo-polymer resins. As presented in this paper, our technique yields colorspace data suitable for accurate appearance reproduction in the area of 3D printing. Beyond that, and without fundamental changes to the basic measurement methodology, it could equally well be used to obtain spectral measurements that are useful for other application areas."}],"issue":"5","volume":29,"ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9269","checksum":"a9697ad83136c19ad87e46aa2db63cfd","success":1,"creator":"dernst","date_updated":"2021-03-22T08:15:28Z","file_size":10873700,"date_created":"2021-03-22T08:15:28Z","file_name":"2021_OpticsExpress_Elek.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1094-4087"]},"publication_status":"published","project":[{"name":"Distributed 3D Object Design","grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing","author":[{"first_name":"Oskar","full_name":"Elek, Oskar","last_name":"Elek"},{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran","last_name":"Zhang","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X"},{"last_name":"Sumin","full_name":"Sumin, Denis","first_name":"Denis"},{"last_name":"Myszkowski","full_name":"Myszkowski, Karol","first_name":"Karol"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"full_name":"Wilkie, Alexander","last_name":"Wilkie","first_name":"Alexander"},{"first_name":"Jaroslav","full_name":"Křivánek, Jaroslav","last_name":"Křivánek"},{"first_name":"Tim","last_name":"Weyrich","full_name":"Weyrich, Tim"}],"external_id":{"isi":["000624968100103"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Elek O, Zhang R, Sumin D, Myszkowski K, Bickel B, Wilkie A, Křivánek J, Weyrich T. 2021. Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing. Optics Express. 29(5), 7568–7588.","chicago":"Elek, Oskar, Ran Zhang, Denis Sumin, Karol Myszkowski, Bernd Bickel, Alexander Wilkie, Jaroslav Křivánek, and Tim Weyrich. “Robust and Practical Measurement of Volume Transport Parameters in Solid Photo-Polymer Materials for 3D Printing.” Optics Express. The Optical Society, 2021. https://doi.org/10.1364/OE.406095.","short":"O. Elek, R. Zhang, D. Sumin, K. Myszkowski, B. Bickel, A. Wilkie, J. Křivánek, T. Weyrich, Optics Express 29 (2021) 7568–7588.","ieee":"O. Elek et al., “Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing,” Optics Express, vol. 29, no. 5. The Optical Society, pp. 7568–7588, 2021.","apa":"Elek, O., Zhang, R., Sumin, D., Myszkowski, K., Bickel, B., Wilkie, A., … Weyrich, T. (2021). Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing. Optics Express. The Optical Society. https://doi.org/10.1364/OE.406095","ama":"Elek O, Zhang R, Sumin D, et al. Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing. Optics Express. 2021;29(5):7568-7588. doi:10.1364/OE.406095","mla":"Elek, Oskar, et al. “Robust and Practical Measurement of Volume Transport Parameters in Solid Photo-Polymer Materials for 3D Printing.” Optics Express, vol. 29, no. 5, The Optical Society, 2021, pp. 7568–88, doi:10.1364/OE.406095."},"quality_controlled":"1","publisher":"The Optical Society","oa":1,"acknowledgement":"H2020 Marie Skłodowska-Curie Actions (642841); European Research Council (715767); Grantová Agentura České Republiky (16-08111S, 16-18964S); Univerzita Karlova v Praze (SVV-2017-260452); Engineering and Physical Sciences Research Council (EP/K023578/1).\r\nWe are grateful to Stratasys Ltd. for access to the voxel-level print interface of the J750\r\nmachine.","date_published":"2021-03-01T00:00:00Z","doi":"10.1364/OE.406095","date_created":"2021-03-14T23:01:33Z","page":"7568-7588","day":"01","publication":"Optics Express","has_accepted_license":"1","isi":1,"year":"2021"},{"article_number":"1-32","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall sythesis"}],"citation":{"ista":"Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. 2021. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. eLife. 10, 1–32.","chicago":"Hernández-Rocamora, Víctor M., Natalia S. Baranova, Katharina Peters, Eefjan Breukink, Martin Loose, and Waldemar Vollmer. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.61525.","ieee":"V. M. Hernández-Rocamora, N. S. Baranova, K. Peters, E. Breukink, M. Loose, and W. Vollmer, “Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"V.M. Hernández-Rocamora, N.S. Baranova, K. Peters, E. Breukink, M. Loose, W. Vollmer, ELife 10 (2021).","ama":"Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. eLife. 2021;10. doi:10.7554/eLife.61525","apa":"Hernández-Rocamora, V. M., Baranova, N. S., Peters, K., Breukink, E., Loose, M., & Vollmer, W. (2021). Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.61525","mla":"Hernández-Rocamora, Víctor M., et al. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” ELife, vol. 10, 1–32, eLife Sciences Publications, 2021, doi:10.7554/eLife.61525."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000627596400001"]},"article_processing_charge":"No","author":[{"full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora","first_name":"Víctor M."},{"last_name":"Baranova","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S."},{"last_name":"Peters","full_name":"Peters, Katharina","first_name":"Katharina"},{"last_name":"Breukink","full_name":"Breukink, Eefjan","first_name":"Eefjan"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Vollmer, Waldemar","last_name":"Vollmer","first_name":"Waldemar"}],"title":"Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins","acknowledgement":"We thank Alexander Egan (Newcastle University) for purified proteins LpoB(sol) and LpoPPa(sol), Federico Corona (Newcastle University) for purified MepM, and Oliver Birkholz and Jacob Piehler (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for their help with PBP1B reconstitution into polymer-SLBs and initial guidance on single particle tracking. We also acknowledge Christian P Richter and Changjiang You (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for providing SLIMfast software and tris-DODA-NTA reagent, respectively. This work was funded by the BBSRC grant BB/R017409/1 (to WV), the European Research Council through grant ERC-2015-StG-679239 (to ML), and long-term fellowships HFSP LT 000824/2016-L4 and EMBO ALTF 1163–2015 (to NB). ","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","year":"2021","isi":1,"has_accepted_license":"1","publication":"eLife","day":"24","date_created":"2021-03-14T23:01:33Z","doi":"10.7554/eLife.61525","date_published":"2021-02-24T00:00:00Z","_id":"9243","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","article_type":"original","status":"public","date_updated":"2023-08-07T14:10:50Z","ddc":["570"],"department":[{"_id":"MaLo"}],"file_date_updated":"2021-03-22T07:36:08Z","abstract":[{"text":"Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"02","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2021-03-22T07:36:08Z","file_size":2314698,"date_created":"2021-03-22T07:36:08Z","file_name":"2021_eLife_HernandezRocamora.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"79897a09bfecd9914d39c4aea2841855","file_id":"9268","success":1}],"ec_funded":1,"volume":10},{"file":[{"success":1,"file_id":"9270","checksum":"23449e44dc5132501a5c86e70638800f","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_ArchRationalMechAnal_Leopold.pdf","date_created":"2021-03-22T08:31:29Z","creator":"dernst","file_size":558006,"date_updated":"2021-03-22T08:31:29Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00039527"],"eissn":["14320673"]},"publication_status":"published","volume":240,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"We consider the Fröhlich Hamiltonian in a mean-field limit where many bosonic particles weakly couple to the quantized phonon field. For large particle numbers and a suitably small coupling, we show that the dynamics of the system is approximately described by the Landau–Pekar equations. These describe a Bose–Einstein condensate interacting with a classical polarization field, whose dynamics is effected by the condensate, i.e., the back-reaction of the phonons that are created by the particles during the time evolution is of leading order.","lang":"eng"}],"month":"02","intvolume":" 240","scopus_import":"1","ddc":["510"],"date_updated":"2023-08-07T14:12:27Z","department":[{"_id":"RoSe"}],"file_date_updated":"2021-03-22T08:31:29Z","_id":"9246","status":"public","type":"journal_article","article_type":"original","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)"},"day":"26","publication":"Archive for Rational Mechanics and Analysis","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1007/s00205-021-01616-9","date_published":"2021-02-26T00:00:00Z","date_created":"2021-03-14T23:01:34Z","page":"383-417","acknowledgement":"Financial support by the European Research Council (ERC) under the\r\nEuropean Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo 694227; N.L and R.S.), the SNSF Eccellenza Project PCEFP2 181153 (N.L) and the\r\nDeutsche Forschungsgemeinschaft (DFG) through the Research TrainingGroup 1838: Spectral\r\nTheory and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. N.L.\r\ngratefully acknowledges support from the NCCRSwissMAP and would like to thank Simone\r\nRademacher and Benjamin Schlein for interesting discussions about the time-evolution of\r\nthe polaron at strong coupling. D.M. thanks Marcel Griesemer and Andreas Wünsch for\r\nextensive discussions about the Fröhlich polaron.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Leopold, Nikolai K., et al. “Derivation of the Landau–Pekar Equations in a Many-Body Mean-Field Limit.” Archive for Rational Mechanics and Analysis, vol. 240, Springer Nature, 2021, pp. 383–417, doi:10.1007/s00205-021-01616-9.","ieee":"N. K. Leopold, D. J. Mitrouskas, and R. Seiringer, “Derivation of the Landau–Pekar equations in a many-body mean-field limit,” Archive for Rational Mechanics and Analysis, vol. 240. Springer Nature, pp. 383–417, 2021.","short":"N.K. Leopold, D.J. Mitrouskas, R. Seiringer, Archive for Rational Mechanics and Analysis 240 (2021) 383–417.","apa":"Leopold, N. K., Mitrouskas, D. J., & Seiringer, R. (2021). Derivation of the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01616-9","ama":"Leopold NK, Mitrouskas DJ, Seiringer R. Derivation of the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational Mechanics and Analysis. 2021;240:383-417. doi:10.1007/s00205-021-01616-9","chicago":"Leopold, Nikolai K, David Johannes Mitrouskas, and Robert Seiringer. “Derivation of the Landau–Pekar Equations in a Many-Body Mean-Field Limit.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01616-9.","ista":"Leopold NK, Mitrouskas DJ, Seiringer R. 2021. Derivation of the Landau–Pekar equations in a many-body mean-field limit. Archive for Rational Mechanics and Analysis. 240, 383–417."},"title":"Derivation of the Landau–Pekar equations in a many-body mean-field limit","author":[{"orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K"},{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000622226200001"],"arxiv":["2001.03993"]},"article_processing_charge":"No","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider the ferromagnetic quantum Heisenberg model in one dimension, for any spin S≥1/2. We give upper and lower bounds on the free energy, proving that at low temperature it is asymptotically equal to the one of an ideal Bose gas of magnons, as predicted by the spin-wave approximation. The trial state used in the upper bound yields an analogous estimate also in the case of two spatial dimensions, which is believed to be sharp at low temperature."}],"intvolume":" 111","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2021-03-22T11:01:09Z","file_name":"2021_LettersMathPhysics_Napiorkowski.pdf","date_updated":"2021-03-22T11:01:09Z","file_size":397962,"creator":"dernst","file_id":"9273","checksum":"687fef1525789c0950de90468dd81604","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["15730530"],"issn":["03779017"]},"issue":"2","volume":111,"_id":"9256","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","article_type":"original","ddc":["510"],"date_updated":"2023-08-07T14:17:00Z","file_date_updated":"2021-03-22T11:01:09Z","department":[{"_id":"RoSe"}],"acknowledgement":"The work of MN was supported by the National Science Centre (NCN) Project Nr. 2016/21/D/ST1/02430. The work of RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227).\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Letters in Mathematical Physics","day":"09","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-03-21T23:01:19Z","doi":"10.1007/s11005-021-01375-4","date_published":"2021-03-09T00:00:00Z","article_number":"31","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Napiórkowski MM, Seiringer R. 2021. Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. 111(2), 31.","chicago":"Napiórkowski, Marcin M, and Robert Seiringer. “Free Energy Asymptotics of the Quantum Heisenberg Spin Chain.” Letters in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s11005-021-01375-4.","short":"M.M. Napiórkowski, R. Seiringer, Letters in Mathematical Physics 111 (2021).","ieee":"M. M. Napiórkowski and R. Seiringer, “Free energy asymptotics of the quantum Heisenberg spin chain,” Letters in Mathematical Physics, vol. 111, no. 2. Springer Nature, 2021.","apa":"Napiórkowski, M. M., & Seiringer, R. (2021). Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-021-01375-4","ama":"Napiórkowski MM, Seiringer R. Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. 2021;111(2). doi:10.1007/s11005-021-01375-4","mla":"Napiórkowski, Marcin M., and Robert Seiringer. “Free Energy Asymptotics of the Quantum Heisenberg Spin Chain.” Letters in Mathematical Physics, vol. 111, no. 2, 31, Springer Nature, 2021, doi:10.1007/s11005-021-01375-4."},"title":"Free energy asymptotics of the quantum Heisenberg spin chain","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000626837400001"]},"author":[{"last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}]},{"department":[{"_id":"JoFi"}],"date_updated":"2023-08-07T14:11:18Z","type":"journal_article","article_type":"original","status":"public","_id":"9242","issue":"2","volume":103,"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2010.05356","open_access":"1"}],"month":"02","intvolume":" 103","abstract":[{"lang":"eng","text":"In the recent years important experimental advances in resonant electro-optic modulators as high-efficiency sources for coherent frequency combs and as devices for quantum information transfer have been realized, where strong optical and microwave mode coupling were achieved. These features suggest electro-optic-based devices as candidates for entangled optical frequency comb sources. In the present work, I study the generation of entangled optical frequency combs in millimeter-sized resonant electro-optic modulators. These devices profit from the experimentally proven advantages such as nearly constant optical free spectral ranges over several gigahertz, and high optical and microwave quality factors. The generation of frequency multiplexed quantum channels with spectral bandwidth in the MHz range for conservative parameter values paves the way towards novel uses in long-distance hybrid quantum networks, quantum key distribution, enhanced optical metrology, and quantum computing."}],"oa_version":"Preprint","author":[{"last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R"}],"article_processing_charge":"No","external_id":{"isi":["000617037900013"],"arxiv":["2010.05356"]},"title":"Frequency-multiplexed hybrid optical entangled source based on the Pockels effect","citation":{"apa":"Rueda Sanchez, A. R. (2021). Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.023708","ama":"Rueda Sanchez AR. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. 2021;103(2). doi:10.1103/PhysRevA.103.023708","ieee":"A. R. Rueda Sanchez, “Frequency-multiplexed hybrid optical entangled source based on the Pockels effect,” Physical Review A, vol. 103, no. 2. American Physical Society, 2021.","short":"A.R. Rueda Sanchez, Physical Review A 103 (2021).","mla":"Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” Physical Review A, vol. 103, no. 2, 023708, American Physical Society, 2021, doi:10.1103/PhysRevA.103.023708.","ista":"Rueda Sanchez AR. 2021. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. 103(2), 023708.","chicago":"Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.023708."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"023708","date_published":"2021-02-11T00:00:00Z","doi":"10.1103/PhysRevA.103.023708","date_created":"2021-03-14T23:01:33Z","isi":1,"year":"2021","day":"11","publication":"Physical Review A","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"I thank Prof. Shabir Barzanjeh and Dr. Ulrich Vogl for the fruitful discussions.\r\n"},{"date_created":"2021-03-21T23:01:20Z","doi":"10.1073/pnas.2024083118","date_published":"2021-03-09T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","day":"09","year":"2021","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","acknowledgement":"We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng, and Roy Frostig for helpful discussions. This material is based on work supported by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator of the Simons Foundation.","title":"Designing self-assembling kinetics with differentiable statistical physics models","external_id":{"pmid":["33653960"],"isi":["000627429100097"]},"article_processing_charge":"No","author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"full_name":"King, Ella M.","last_name":"King","first_name":"Ella M."},{"last_name":"Schoenholz","full_name":"Schoenholz, Samuel S.","first_name":"Samuel S."},{"full_name":"Cubuk, Ekin D.","last_name":"Cubuk","first_name":"Ekin D."},{"last_name":"Brenner","full_name":"Brenner, Michael P.","first_name":"Michael P."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences 118 (2021).","ieee":"C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” Proceedings of the National Academy of Sciences, vol. 118, no. 10. National Academy of Sciences, 2021.","apa":"Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., & Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2024083118","ama":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. 2021;118(10). doi:10.1073/pnas.2024083118","mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:10.1073/pnas.2024083118.","ista":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences. 118(10), e2024083118.","chicago":"Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118."},"article_number":"e2024083118","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":118,"issue":"10","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"5be8da2b1c0757feb1057f1a515cf9e0","file_id":"9278","file_size":1047954,"date_updated":"2021-03-22T12:23:54Z","creator":"dernst","file_name":"2021_PNAS_Goodrich.pdf","date_created":"2021-03-22T12:23:54Z"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"intvolume":" 118","month":"03","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems."}],"file_date_updated":"2021-03-22T12:23:54Z","department":[{"_id":"CaGo"}],"ddc":["530"],"date_updated":"2023-08-07T14:19:34Z","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","_id":"9257"},{"citation":{"ista":"Mbianda J, Bakail MM, André C, Moal G, Perrin ME, Pinna G, Guerois R, Becher F, Legrand P, Traoré S, Douat C, Guichard G, Ochsenbein F. 2021. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. 7(12), eabd9153.","chicago":"Mbianda, Johanne, May M Bakail, Christophe André, Gwenaëlle Moal, Marie E. Perrin, Guillaume Pinna, Raphaël Guerois, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abd9153.","short":"J. Mbianda, M.M. Bakail, C. André, G. Moal, M.E. Perrin, G. Pinna, R. Guerois, F. Becher, P. Legrand, S. Traoré, C. Douat, G. Guichard, F. Ochsenbein, Science Advances 7 (2021).","ieee":"J. Mbianda et al., “Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity,” Science Advances, vol. 7, no. 12. American Association for the Advancement of Science, 2021.","apa":"Mbianda, J., Bakail, M. M., André, C., Moal, G., Perrin, M. E., Pinna, G., … Ochsenbein, F. (2021). Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abd9153","ama":"Mbianda J, Bakail MM, André C, et al. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. Science Advances. 2021;7(12). doi:10.1126/sciadv.abd9153","mla":"Mbianda, Johanne, et al. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances, vol. 7, no. 12, eabd9153, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abd9153."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000633443000011"],"pmid":["33741589"]},"author":[{"first_name":"Johanne","last_name":"Mbianda","full_name":"Mbianda, Johanne"},{"last_name":"Bakail","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E"},{"full_name":"André, Christophe","last_name":"André","first_name":"Christophe"},{"first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle","last_name":"Moal"},{"first_name":"Marie E.","full_name":"Perrin, Marie E.","last_name":"Perrin"},{"full_name":"Pinna, Guillaume","last_name":"Pinna","first_name":"Guillaume"},{"last_name":"Guerois","full_name":"Guerois, Raphaël","first_name":"Raphaël"},{"last_name":"Becher","full_name":"Becher, Francois","first_name":"Francois"},{"full_name":"Legrand, Pierre","last_name":"Legrand","first_name":"Pierre"},{"first_name":"Seydou","full_name":"Traoré, Seydou","last_name":"Traoré"},{"first_name":"Céline","full_name":"Douat, Céline","last_name":"Douat"},{"full_name":"Guichard, Gilles","last_name":"Guichard","first_name":"Gilles"},{"first_name":"Françoise","full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein"}],"title":"Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity","article_number":"eabd9153","year":"2021","isi":1,"has_accepted_license":"1","publication":"Science Advances","day":"19","date_created":"2021-03-22T07:14:03Z","doi":"10.1126/sciadv.abd9153","date_published":"2021-03-19T00:00:00Z","acknowledgement":"We thank the Synchrotron SOLEIL, the European Synchrotron Radiation Facility (ESRF), and the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INBS-05. We are particularly grateful to A. Clavier and A. Campalans for help in setting up and performing the cell penetration assays. Funding: Research was funded by the French Centre National de Recherche Scientifique (CNRS), the Commissariat à l’Energie Atomique (CEA), University of Bordeaux, University Paris-Saclay, and the Synchrotron Soleil. The project was supported by the ANR 2007 BREAKABOUND (JC-07-216078), 2011 BIPBIP (ANR-10-BINF-0003), 2012 CHAPINHIB (ANR-12-BSV5-0022-01), 2015 CHIPSET (ANR-15-CE11-008-01), 2015 HIMPP2I (ANR-15-CE07-0010), and the program labeled by the ARC foundation 2016 PGA1*20160203953). M.B. was supported by Canceropole (Paris, France) and a grant for young researchers from La Ligue contre le Cancer. J.M. was supported by La Ligue contre le Cancer.","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","date_updated":"2023-08-07T14:20:26Z","ddc":["570"],"department":[{"_id":"CampIT"}],"file_date_updated":"2021-03-22T12:49:00Z","_id":"9262","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["2375-2548"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"737624cd0e630ffa7c52797a690500e3","file_id":"9280","creator":"dernst","file_size":837156,"date_updated":"2021-03-22T12:49:00Z","file_name":"2021_ScienceAdv_Mbianda.pdf","date_created":"2021-03-22T12:49:00Z"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":7,"issue":"12","abstract":[{"lang":"eng","text":"Sequence-specific oligomers with predictable folding patterns, i.e., foldamers, provide new opportunities to mimic α-helical peptides and design inhibitors of protein-protein interactions. One major hurdle of this strategy is to retain the correct orientation of key side chains involved in protein surface recognition. Here, we show that the structural plasticity of a foldamer backbone may notably contribute to the required spatial adjustment for optimal interaction with the protein surface. By using oligoureas as α helix mimics, we designed a foldamer/peptide hybrid inhibitor of histone chaperone ASF1, a key regulator of chromatin dynamics. The crystal structure of its complex with ASF1 reveals a notable plasticity of the urea backbone, which adapts to the ASF1 surface to maintain the same binding interface. One additional benefit of generating ASF1 ligands with nonpeptide oligourea segments is the resistance to proteolysis in human plasma, which was highly improved compared to the cognate α-helical peptide."}],"oa_version":"Published Version","pmid":1,"intvolume":" 7","month":"03"},{"oa":1,"quality_controlled":"1","publisher":"Frontiers","acknowledgement":"This work was supported by Sigrid Juselius fellowship (KV), University of Helsinki 3-year research grant (KV), Academy of Finland Research fellow funding (315710, to KV), the European Research Council (ERC CoG 724373 to MS), and by the Austrian Science foundation (FWF) (Y564-B12 START award to MS).\r\nTaija Mäkinen is acknowledged for providing Prox1CreERT2 transgenic mice and Yu Yamaguchi for providing the conditional Ext1 mouse strain.","date_created":"2021-03-21T23:01:20Z","date_published":"2021-02-25T00:00:00Z","doi":"10.3389/fimmu.2021.630002","publication":"Frontiers in Immunology","day":"25","year":"2021","isi":1,"has_accepted_license":"1","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"Y 564-B12"}],"article_number":"630002","title":"Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium","external_id":{"pmid":["33717158"],"isi":["000627134400001"]},"article_processing_charge":"No","author":[{"last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Moussion, Christine","last_name":"Moussion","id":"3356F664-F248-11E8-B48F-1D18A9856A87","first_name":"Christine"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Vaahtomeri, Kari, et al. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology, vol. 12, 630002, Frontiers, 2021, doi:10.3389/fimmu.2021.630002.","ama":"Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. 2021;12. doi:10.3389/fimmu.2021.630002","apa":"Vaahtomeri, K., Moussion, C., Hauschild, R., & Sixt, M. K. (2021). Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2021.630002","short":"K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology 12 (2021).","ieee":"K. Vaahtomeri, C. Moussion, R. Hauschild, and M. K. Sixt, “Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium,” Frontiers in Immunology, vol. 12. Frontiers, 2021.","chicago":"Vaahtomeri, Kari, Christine Moussion, Robert Hauschild, and Michael K Sixt. “Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium.” Frontiers in Immunology. Frontiers, 2021. https://doi.org/10.3389/fimmu.2021.630002.","ista":"Vaahtomeri K, Moussion C, Hauschild R, Sixt MK. 2021. Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium. Frontiers in Immunology. 12, 630002."},"intvolume":" 12","month":"02","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Gradients of chemokines and growth factors guide migrating cells and morphogenetic processes. Migration of antigen-presenting dendritic cells from the interstitium into the lymphatic system is dependent on chemokine CCL21, which is secreted by endothelial cells of the lymphatic capillary, binds heparan sulfates and forms gradients decaying into the interstitium. Despite the importance of CCL21 gradients, and chemokine gradients in general, the mechanisms of gradient formation are unclear. Studies on fibroblast growth factors have shown that limited diffusion is crucial for gradient formation. Here, we used the mouse dermis as a model tissue to address the necessity of CCL21 anchoring to lymphatic capillary heparan sulfates in the formation of interstitial CCL21 gradients. Surprisingly, the absence of lymphatic endothelial heparan sulfates resulted only in a modest decrease of CCL21 levels at the lymphatic capillaries and did neither affect interstitial CCL21 gradient shape nor dendritic cell migration toward lymphatic capillaries. Thus, heparan sulfates at the level of the lymphatic endothelium are dispensable for the formation of a functional CCL21 gradient."}],"ec_funded":1,"volume":12,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9277","checksum":"663f5a48375e42afa4bfef58d42ec186","file_size":3740146,"date_updated":"2021-03-22T12:08:26Z","creator":"dernst","file_name":"2021_FrontiersImmumo_Vaahtomeri.pdf","date_created":"2021-03-22T12:08:26Z"}],"publication_status":"published","publication_identifier":{"eissn":["1664-3224"]},"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":"9259","file_date_updated":"2021-03-22T12:08:26Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"ddc":["570"],"date_updated":"2023-08-07T14:18:26Z"},{"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms.","lang":"eng"}],"intvolume":" 12","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e1022f3aee349853ded2b2b3e092362d","file_id":"9275","success":1,"date_updated":"2021-03-22T11:18:58Z","file_size":8602096,"creator":"dernst","date_created":"2021-03-22T11:18:58Z","file_name":"2021_NatureComm_Hu.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"volume":12,"_id":"9254","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","ddc":["580"],"date_updated":"2023-08-07T14:17:55Z","department":[{"_id":"JiFr"}],"file_date_updated":"2021-03-22T11:18:58Z","acknowledgement":"This work was supported by grants from the Israel Science Foundation (2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.), the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships (to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF to I.T.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature Communications","day":"12","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-03-21T23:01:19Z","doi":"10.1038/s41467-021-21802-3","date_published":"2021-03-12T00:00:00Z","article_number":"1657","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli, Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021).","ieee":"Y. Hu et al., “Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing,” Nature Communications, vol. 12. Springer Nature, 2021.","ama":"Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 2021;12. doi:10.1038/s41467-021-21802-3","apa":"Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021). Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-21802-3","mla":"Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” Nature Communications, vol. 12, 1657, Springer Nature, 2021, doi:10.1038/s41467-021-21802-3.","ista":"Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 12, 1657.","chicago":"Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-21802-3."},"title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","article_processing_charge":"No","external_id":{"isi":["000630419400048"],"pmid":["33712581"]},"author":[{"first_name":"Yangjie","last_name":"Hu","full_name":"Hu, Yangjie"},{"full_name":"Omary, Moutasem","last_name":"Omary","first_name":"Moutasem"},{"last_name":"Hu","full_name":"Hu, Yun","first_name":"Yun"},{"first_name":"Ohad","full_name":"Doron, Ohad","last_name":"Doron"},{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"},{"full_name":"Chen, Qingguo","last_name":"Chen","first_name":"Qingguo"},{"first_name":"Or","full_name":"Megides, Or","last_name":"Megides"},{"last_name":"Chekli","full_name":"Chekli, Ori","first_name":"Ori"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Zhao","full_name":"Zhao, Yunde","first_name":"Yunde"},{"full_name":"Tsarfaty, Ilan","last_name":"Tsarfaty","first_name":"Ilan"},{"first_name":"Eilon","last_name":"Shani","full_name":"Shani, Eilon"}]},{"article_number":"50","title":"Semi-device-independent random number generation with flexible assumptions","author":[{"first_name":"Matej","full_name":"Pivoluska, Matej","last_name":"Pivoluska"},{"last_name":"Plesch","full_name":"Plesch, Martin","first_name":"Martin"},{"full_name":"Farkas, Máté","last_name":"Farkas","first_name":"Máté"},{"last_name":"Ruzickova","full_name":"Ruzickova, Natalia","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"},{"last_name":"Flegel","full_name":"Flegel, Clara","first_name":"Clara"},{"first_name":"Natalia Herrera","last_name":"Valencia","full_name":"Valencia, Natalia Herrera"},{"full_name":"Mccutcheon, Will","last_name":"Mccutcheon","first_name":"Will"},{"first_name":"Mehul","last_name":"Malik","full_name":"Malik, Mehul"},{"last_name":"Aguilar","full_name":"Aguilar, Edgar A.","first_name":"Edgar A."}],"article_processing_charge":"No","external_id":{"isi":["000629173100001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Pivoluska, Matej, Martin Plesch, Máté Farkas, Natalia Ruzickova, Clara Flegel, Natalia Herrera Valencia, Will Mccutcheon, Mehul Malik, and Edgar A. Aguilar. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” Npj Quantum Information. Springer Nature, 2021. https://doi.org/10.1038/s41534-021-00387-1.","ista":"Pivoluska M, Plesch M, Farkas M, Ruzickova N, Flegel C, Valencia NH, Mccutcheon W, Malik M, Aguilar EA. 2021. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 7, 50.","mla":"Pivoluska, Matej, et al. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” Npj Quantum Information, vol. 7, 50, Springer Nature, 2021, doi:10.1038/s41534-021-00387-1.","short":"M. Pivoluska, M. Plesch, M. Farkas, N. Ruzickova, C. Flegel, N.H. Valencia, W. Mccutcheon, M. Malik, E.A. Aguilar, Npj Quantum Information 7 (2021).","ieee":"M. Pivoluska et al., “Semi-device-independent random number generation with flexible assumptions,” npj Quantum Information, vol. 7. Springer Nature, 2021.","ama":"Pivoluska M, Plesch M, Farkas M, et al. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 2021;7. doi:10.1038/s41534-021-00387-1","apa":"Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia, N. H., … Aguilar, E. A. (2021). Semi-device-independent random number generation with flexible assumptions. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-021-00387-1"},"publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank Robert Fickler for discussions about the experimental realization and Marek Sýs for running the NIST randomness test on the data we acquired in the experiment. We would like to thank Ugo Zanforlin, Gerald Buller, Daniel White, and Cristian Bonato for their help with the experiment. M. Pivoluska, M. Plesch, and M.M. acknowledge Czech-Austrian project MultiQUEST (I3053-N27 and GF17-33780L). M. Pivoluska and M. Plesch additionally acknowledge the support of VEGA project 2/0136/19. M.F. acknowledges support from the Polish NCN grant Sonata UMO-2014/14/E/ST2/00020, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program ERC AdG CERQUTE (grant agreement No 834266), the State Research Agency (AEI) TRANQI (PID2019-106888GB-I00/10.13039/501100011033), the Government of Spain (FIS2020-TRANQI; Severo Ochoa CEX2019-000910-S), Fundació Cellex, Fundació Mir-Puig, and Generalitat de Catalunya (CERCA, AGAUR). M.M., W.M., N.H.V., and C.F. acknowledge support from the QuantERA ERA-NET Co-fund (FWF Project I3773-N36) and the UK Engineering and Physical Sciences Research Council (EPSRC) (EP/P024114/1).","date_published":"2021-03-15T00:00:00Z","doi":"10.1038/s41534-021-00387-1","date_created":"2021-03-21T23:01:19Z","day":"15","publication":"npj Quantum Information","has_accepted_license":"1","isi":1,"year":"2021","status":"public","type":"journal_article","article_type":"original","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)"},"_id":"9255","department":[{"_id":"FyKo"}],"file_date_updated":"2021-03-22T11:09:34Z","ddc":["530"],"date_updated":"2023-08-07T14:17:26Z","month":"03","intvolume":" 7","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Our ability to trust that a random number is truly random is essential for fields as diverse as cryptography and fundamental tests of quantum mechanics. Existing solutions both come with drawbacks—device-independent quantum random number generators (QRNGs) are highly impractical and standard semi-device-independent QRNGs are limited to a specific physical implementation and level of trust. Here we propose a framework for semi-device-independent randomness certification, using a source of trusted vacuum in the form of a signal shutter. It employs a flexible set of assumptions and levels of trust, allowing it to be applied in a wide range of physical scenarios involving both quantum and classical entropy sources. We experimentally demonstrate our protocol with a photonic setup and generate secure random bits under three different assumptions with varying degrees of security and resulting data rates."}],"volume":7,"file":[{"creator":"dernst","date_updated":"2021-03-22T11:09:34Z","file_size":1360271,"date_created":"2021-03-22T11:09:34Z","file_name":"2021_NPJQuantumInformation_Pivoluska.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"26d3f2a2c8c8fa8c1002028326b45f64","file_id":"9274","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2056-6387"]},"publication_status":"published"},{"type":"journal_article","article_type":"original","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","_id":"9260","file_date_updated":"2021-03-22T12:41:26Z","department":[{"_id":"TiBr"}],"date_updated":"2023-08-07T14:20:00Z","ddc":["510"],"scopus_import":"1","month":"03","intvolume":" 299","abstract":[{"lang":"eng","text":"We study the density of rational points on a higher-dimensional orbifold (Pn−1,Δ) when Δ is a Q-divisor involving hyperplanes. This allows us to address a question of Tanimoto about whether the set of rational points on such an orbifold constitutes a thin set. Our approach relies on the Hardy–Littlewood circle method to first study an asymptotic version of Waring’s problem for mixed powers. In doing so we make crucial use of the recent resolution of the main conjecture in Vinogradov’s mean value theorem, due to Bourgain–Demeter–Guth and Wooley."}],"oa_version":"Published Version","volume":299,"publication_identifier":{"issn":["0025-5874"],"eissn":["1432-1823"]},"publication_status":"published","file":[{"date_created":"2021-03-22T12:41:26Z","file_name":"2021_MathZeitschrift_Browning.pdf","creator":"dernst","date_updated":"2021-03-22T12:41:26Z","file_size":492685,"file_id":"9279","checksum":"8ed9f49568806894744096dbbca0ad7b","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"EP-P026710-2","name":"Between rational and integral points","_id":"26A8D266-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yamagishi, Shuntaro","last_name":"Yamagishi","first_name":"Shuntaro"}],"external_id":{"isi":["000625573800002"]},"article_processing_charge":"No","title":"Arithmetic of higher-dimensional orbifolds and a mixed Waring problem","citation":{"ista":"Browning TD, Yamagishi S. 2021. Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. Mathematische Zeitschrift. 299, 1071–1101.","chicago":"Browning, Timothy D, and Shuntaro Yamagishi. “Arithmetic of Higher-Dimensional Orbifolds and a Mixed Waring Problem.” Mathematische Zeitschrift. Springer Nature, 2021. https://doi.org/10.1007/s00209-021-02695-w.","apa":"Browning, T. D., & Yamagishi, S. (2021). Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. Mathematische Zeitschrift. Springer Nature. https://doi.org/10.1007/s00209-021-02695-w","ama":"Browning TD, Yamagishi S. Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. Mathematische Zeitschrift. 2021;299:1071–1101. doi:10.1007/s00209-021-02695-w","ieee":"T. D. Browning and S. Yamagishi, “Arithmetic of higher-dimensional orbifolds and a mixed Waring problem,” Mathematische Zeitschrift, vol. 299. Springer Nature, pp. 1071–1101, 2021.","short":"T.D. Browning, S. Yamagishi, Mathematische Zeitschrift 299 (2021) 1071–1101.","mla":"Browning, Timothy D., and Shuntaro Yamagishi. “Arithmetic of Higher-Dimensional Orbifolds and a Mixed Waring Problem.” Mathematische Zeitschrift, vol. 299, Springer Nature, 2021, pp. 1071–1101, doi:10.1007/s00209-021-02695-w."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"While working on this paper the authors were both supported by EPSRC grant EP/P026710/1, and the second author received additional support from the NWO Veni Grant 016.Veni.192.047. Thanks are due to Marta Pieropan, Arne Smeets and Sho Tanimoto for useful conversations related to this topic, and to the anonymous referee for numerous helpful suggestions.","page":"1071–1101","date_published":"2021-03-05T00:00:00Z","doi":"10.1007/s00209-021-02695-w","date_created":"2021-03-21T23:01:21Z","isi":1,"has_accepted_license":"1","year":"2021","day":"05","publication":"Mathematische Zeitschrift"},{"status":"public","type":"journal_article","article_type":"letter_note","_id":"9258","department":[{"_id":"JoDa"}],"date_updated":"2023-08-07T14:19:08Z","intvolume":" 18","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-021-01087-6"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"issue":"3","volume":18,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"title":"Pycro-Manager: Open-source software for customized and reproducible microscope control","external_id":{"pmid":["33674797"],"isi":["000625600600007"]},"article_processing_charge":"No","author":[{"full_name":"Pinkard, Henry","last_name":"Pinkard","first_name":"Henry"},{"last_name":"Stuurman","full_name":"Stuurman, Nico","first_name":"Nico"},{"first_name":"Ivan E.","last_name":"Ivanov","full_name":"Ivanov, Ivan E."},{"full_name":"Anthony, Nicholas M.","last_name":"Anthony","first_name":"Nicholas M."},{"full_name":"Ouyang, Wei","last_name":"Ouyang","first_name":"Wei"},{"last_name":"Li","full_name":"Li, Bin","first_name":"Bin"},{"first_name":"Bin","last_name":"Yang","full_name":"Yang, Bin"},{"first_name":"Mark A.","last_name":"Tsuchida","full_name":"Tsuchida, Mark A."},{"full_name":"Chhun, Bryant","last_name":"Chhun","first_name":"Bryant"},{"last_name":"Zhang","full_name":"Zhang, Grace","first_name":"Grace"},{"first_name":"Ryan","full_name":"Mei, Ryan","last_name":"Mei"},{"first_name":"Michael","full_name":"Anderson, Michael","last_name":"Anderson"},{"first_name":"Douglas P.","last_name":"Shepherd","full_name":"Shepherd, Douglas P."},{"last_name":"Hunt-Isaak","full_name":"Hunt-Isaak, Ian","first_name":"Ian"},{"full_name":"Dunn, Raymond L.","last_name":"Dunn","first_name":"Raymond L."},{"full_name":"Jahr, Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke"},{"first_name":"Saul","last_name":"Kato","full_name":"Kato, Saul"},{"last_name":"Royer","full_name":"Royer, Loïc A.","first_name":"Loïc A."},{"last_name":"Thiagarajah","full_name":"Thiagarajah, Jay R.","first_name":"Jay R."},{"first_name":"Kevin W.","full_name":"Eliceiri, Kevin W.","last_name":"Eliceiri"},{"last_name":"Lundberg","full_name":"Lundberg, Emma","first_name":"Emma"},{"full_name":"Mehta, Shalin B.","last_name":"Mehta","first_name":"Shalin B."},{"first_name":"Laura","full_name":"Waller, Laura","last_name":"Waller"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Pinkard, Henry, et al. “Pycro-Manager: Open-Source Software for Customized and Reproducible Microscope Control.” Nature Methods, vol. 18, no. 3, Springer Nature, 2021, pp. 226–28, doi:10.1038/s41592-021-01087-6.","ama":"Pinkard H, Stuurman N, Ivanov IE, et al. Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. 2021;18(3):226-228. doi:10.1038/s41592-021-01087-6","apa":"Pinkard, H., Stuurman, N., Ivanov, I. E., Anthony, N. M., Ouyang, W., Li, B., … Waller, L. (2021). Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-021-01087-6","ieee":"H. Pinkard et al., “Pycro-Manager: Open-source software for customized and reproducible microscope control,” Nature Methods, vol. 18, no. 3. Springer Nature, pp. 226–228, 2021.","short":"H. Pinkard, N. Stuurman, I.E. Ivanov, N.M. Anthony, W. Ouyang, B. Li, B. Yang, M.A. Tsuchida, B. Chhun, G. Zhang, R. Mei, M. Anderson, D.P. Shepherd, I. Hunt-Isaak, R.L. Dunn, W. Jahr, S. Kato, L.A. Royer, J.R. Thiagarajah, K.W. Eliceiri, E. Lundberg, S.B. Mehta, L. Waller, Nature Methods 18 (2021) 226–228.","chicago":"Pinkard, Henry, Nico Stuurman, Ivan E. Ivanov, Nicholas M. Anthony, Wei Ouyang, Bin Li, Bin Yang, et al. “Pycro-Manager: Open-Source Software for Customized and Reproducible Microscope Control.” Nature Methods. Springer Nature, 2021. https://doi.org/10.1038/s41592-021-01087-6.","ista":"Pinkard H, Stuurman N, Ivanov IE, Anthony NM, Ouyang W, Li B, Yang B, Tsuchida MA, Chhun B, Zhang G, Mei R, Anderson M, Shepherd DP, Hunt-Isaak I, Dunn RL, Jahr W, Kato S, Royer LA, Thiagarajah JR, Eliceiri KW, Lundberg E, Mehta SB, Waller L. 2021. Pycro-Manager: Open-source software for customized and reproducible microscope control. Nature Methods. 18(3), 226–228."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank S. van der Walt and K. Marchuk for discussion during development. This project was funded by Packard Fellowship and Chan Zuckerberg Biohub Investigator Awards to L.W.; STROBE: A NSF Science and Technology Center; an NSF Graduate Research Fellowship awarded to H.P.; a Berkeley Institute for Data Science/UCSF Bakar Computational Health Sciences Institute Fellowship awarded to H.P. with support from the Koret Foundation, the Gordon and Betty Moore Foundation, and the Alfred P. Sloan Foundation to the University of California, Berkeley. K.W.E., B.L. and M.T. were funded by the Chan Zuckerberg Initiative and NIH grant P41GM135019.","date_created":"2021-03-21T23:01:20Z","doi":"10.1038/s41592-021-01087-6","date_published":"2021-03-01T00:00:00Z","page":"226-228","publication":"Nature Methods","day":"01","year":"2021","isi":1},{"doi":"10.1083/jcb.202003052","date_published":"2021-03-19T00:00:00Z","date_created":"2021-04-04T22:01:21Z","day":"19","publication":"Journal of Cell Biology","isi":1,"has_accepted_license":"1","year":"2021","publisher":"Rockefeller University Press","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by European Research Council grant 281971, Wellcome Trust Research Career Development Fellowship WT095829AIA and Wellcome Trust Senior Research\r\nFellowship 219482/Z/19/Z to J.L. Gallop, a Wellcome Trust Senior Investigator Award 098357 to B.D. Simons, and an Austrian Science Fund grant (P31639) to E. Hannezo. We acknowledge\r\ncore funding by the Wellcome Trust (092096) and Cancer Research UK (C6946/A14492). U. Dobramysl was supported by a Wellcome Trust Junior Interdisciplinary Fellowship grant\r\n(105602/Z/14/Z) and a Herchel Smith Postdoctoral Fellowship. H. Shimo was supported by a Funai Foundation Overseas scholarship.","title":"Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation","author":[{"full_name":"Dobramysl, Ulrich","last_name":"Dobramysl","first_name":"Ulrich"},{"first_name":"Iris Katharina","full_name":"Jarsch, Iris Katharina","last_name":"Jarsch"},{"first_name":"Yoshiko","full_name":"Inoue, Yoshiko","last_name":"Inoue"},{"first_name":"Hanae","last_name":"Shimo","full_name":"Shimo, Hanae"},{"last_name":"Richier","full_name":"Richier, Benjamin","first_name":"Benjamin"},{"first_name":"Jonathan R.","full_name":"Gadsby, Jonathan R.","last_name":"Gadsby"},{"full_name":"Mason, Julia","last_name":"Mason","first_name":"Julia"},{"last_name":"Szałapak","full_name":"Szałapak, Alicja","first_name":"Alicja"},{"full_name":"Ioannou, Pantelis Savvas","last_name":"Ioannou","first_name":"Pantelis Savvas"},{"last_name":"Correia","full_name":"Correia, Guilherme Pereira","first_name":"Guilherme Pereira"},{"first_name":"Astrid","last_name":"Walrant","full_name":"Walrant, Astrid"},{"full_name":"Butler, Richard","last_name":"Butler","first_name":"Richard"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."},{"first_name":"Jennifer L.","last_name":"Gallop","full_name":"Gallop, Jennifer L."}],"external_id":{"isi":["000663160600002"],"pmid":["33740033"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Dobramysl, Ulrich, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” Journal of Cell Biology, vol. 220, no. 4, e202003052, Rockefeller University Press, 2021, doi:10.1083/jcb.202003052.","apa":"Dobramysl, U., Jarsch, I. K., Inoue, Y., Shimo, H., Richier, B., Gadsby, J. R., … Gallop, J. L. (2021). Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202003052","ama":"Dobramysl U, Jarsch IK, Inoue Y, et al. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. 2021;220(4). doi:10.1083/jcb.202003052","ieee":"U. Dobramysl et al., “Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation,” Journal of Cell Biology, vol. 220, no. 4. Rockefeller University Press, 2021.","short":"U. Dobramysl, I.K. Jarsch, Y. Inoue, H. Shimo, B. Richier, J.R. Gadsby, J. Mason, A. Szałapak, P.S. Ioannou, G.P. Correia, A. Walrant, R. Butler, E.B. Hannezo, B.D. Simons, J.L. Gallop, Journal of Cell Biology 220 (2021).","chicago":"Dobramysl, Ulrich, Iris Katharina Jarsch, Yoshiko Inoue, Hanae Shimo, Benjamin Richier, Jonathan R. Gadsby, Julia Mason, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” Journal of Cell Biology. Rockefeller University Press, 2021. https://doi.org/10.1083/jcb.202003052.","ista":"Dobramysl U, Jarsch IK, Inoue Y, Shimo H, Richier B, Gadsby JR, Mason J, Szałapak A, Ioannou PS, Correia GP, Walrant A, Butler R, Hannezo EB, Simons BD, Gallop JL. 2021. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. 220(4), e202003052."},"project":[{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"}],"article_number":"e202003052","issue":"4","volume":220,"file":[{"file_id":"9310","checksum":"4739ffd90f2c7e05ac5b00f057c58aa2","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-04-06T10:39:08Z","file_name":"2021_JCB_Dobramysl.pdf","date_updated":"2021-04-06T10:39:08Z","file_size":9019720,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15408140"]},"publication_status":"published","month":"03","intvolume":" 220","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Assemblies of actin and its regulators underlie the dynamic morphology of all eukaryotic cells. To understand how actin regulatory proteins work together to generate actin-rich structures such as filopodia, we analyzed the localization of diverse actin regulators within filopodia in Drosophila embryos and in a complementary in vitro system of filopodia-like structures (FLSs). We found that the composition of the regulatory protein complex where actin is incorporated (the filopodial tip complex) is remarkably heterogeneous both in vivo and in vitro. Our data reveal that different pairs of proteins correlate with each other and with actin bundle length, suggesting the presence of functional subcomplexes. This is consistent with a theoretical framework where three or more redundant subcomplexes join the tip complex stochastically, with any two being sufficient to drive filopodia formation. We provide an explanation for the observed heterogeneity and suggest that a mechanism based on multiple components allows stereotypical filopodial dynamics to arise from diverse upstream signaling pathways."}],"department":[{"_id":"EdHa"}],"file_date_updated":"2021-04-06T10:39:08Z","ddc":["576"],"date_updated":"2023-08-07T14:32:28Z","status":"public","type":"journal_article","article_type":"original","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)"},"_id":"9306"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Hensel, Sebastian. “Finite Time Extinction for the 1D Stochastic Porous Medium Equation with Transport Noise.” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 9, Springer Nature, 2021, pp. 892–939, doi:10.1007/s40072-021-00188-9.","ama":"Hensel S. Finite time extinction for the 1D stochastic porous medium equation with transport noise. Stochastics and Partial Differential Equations: Analysis and Computations. 2021;9:892–939. doi:10.1007/s40072-021-00188-9","apa":"Hensel, S. (2021). Finite time extinction for the 1D stochastic porous medium equation with transport noise. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-021-00188-9","short":"S. Hensel, Stochastics and Partial Differential Equations: Analysis and Computations 9 (2021) 892–939.","ieee":"S. Hensel, “Finite time extinction for the 1D stochastic porous medium equation with transport noise,” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 9. Springer Nature, pp. 892–939, 2021.","chicago":"Hensel, Sebastian. “Finite Time Extinction for the 1D Stochastic Porous Medium Equation with Transport Noise.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2021. https://doi.org/10.1007/s40072-021-00188-9.","ista":"Hensel S. 2021. Finite time extinction for the 1D stochastic porous medium equation with transport noise. Stochastics and Partial Differential Equations: Analysis and Computations. 9, 892–939."},"title":"Finite time extinction for the 1D stochastic porous medium equation with transport noise","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000631001700001"]},"author":[{"orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","last_name":"Hensel","first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication":"Stochastics and Partial Differential Equations: Analysis and Computations","day":"21","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-04-04T22:01:21Z","date_published":"2021-03-21T00:00:00Z","doi":"10.1007/s40072-021-00188-9","page":"892–939","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 . I am very grateful to M. Gerencsér and J. Maas for proposing this problem as well as helpful discussions. Special thanks go to F. Cornalba for suggesting the additional κ-truncation in Proposition 5. I am also indebted to an anonymous referee for pointing out a gap in a previous version of the proof of Lemma 9 (concerning the treatment of the noise term). The issue is resolved in this version.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","ddc":["510"],"date_updated":"2023-08-07T14:31:59Z","department":[{"_id":"JuFi"}],"file_date_updated":"2021-04-06T09:31:28Z","_id":"9307","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","article_type":"original","language":[{"iso":"eng"}],"file":[{"file_name":"2021_StochPartDiffEquation_Hensel.pdf","date_created":"2021-04-06T09:31:28Z","creator":"dernst","file_size":727005,"date_updated":"2021-04-06T09:31:28Z","success":1,"file_id":"9309","checksum":"6529b609c9209861720ffa4685111bc6","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2194-041X"],"issn":["2194-0401"]},"ec_funded":1,"volume":9,"oa_version":"Published Version","abstract":[{"text":"We establish finite time extinction with probability one for weak solutions of the Cauchy–Dirichlet problem for the 1D stochastic porous medium equation with Stratonovich transport noise and compactly supported smooth initial datum. Heuristically, this is expected to hold because Brownian motion has average spread rate O(t12) whereas the support of solutions to the deterministic PME grows only with rate O(t1m+1). The rigorous proof relies on a contraction principle up to time-dependent shift for Wong–Zakai type approximations, the transformation to a deterministic PME with two copies of a Brownian path as the lateral boundary, and techniques from the theory of viscosity solutions.","lang":"eng"}],"intvolume":" 9","month":"03","scopus_import":"1"},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We report the results of an experimental investigation into the decay of turbulence in plane Couette–Poiseuille flow using ‘quench’ experiments where the flow laminarises after a sudden reduction in Reynolds number Re. Specifically, we study the velocity field in the streamwise–spanwise plane. We show that the spanwise velocity containing rolls decays faster than the streamwise velocity, which displays elongated regions of higher or lower velocity called streaks. At final Reynolds numbers above 425, the decay of streaks displays two stages: first a slow decay when rolls are present and secondly a more rapid decay of streaks alone. The difference in behaviour results from the regeneration of streaks by rolls, called the lift-up effect. We define the turbulent fraction as the portion of the flow containing turbulence and this is estimated by thresholding the spanwise velocity component. It decreases linearly with time in the whole range of final Re. The corresponding decay slope increases linearly with final Re. The extrapolated value at which this decay slope vanishes is Reaz≈656±10, close to Reg≈670 at which turbulence is self-sustained. The decay of the energy computed from the spanwise velocity component is found to be exponential. The corresponding decay rate increases linearly with Re, with an extrapolated vanishing value at ReAz≈688±10. This value is also close to the value at which the turbulence is self-sustained, showing that valuable information on the transition can be obtained over a wide range of Re."}],"intvolume":" 915","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/2008.08851","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"volume":915,"_id":"9297","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-07T14:30:11Z","department":[{"_id":"BjHo"}],"acknowledgement":"We gratefully acknowledge Joran Rolland, Yohann Duguet, Romain Monchaux, S´ebastien Gom´e, Laurette Tuckerman, Dwight Barkley, Olivier Dauchot and Sabine Bottin for fruitful discussions. We thank Xavier Benoit-Gonin, Amaury Fourgeaud, Thierry Darnige, Olivier Brouard and Justine Laurent for technical help. This work has benefited from the ANR TransFlow, and by starting grants obtained by B.S. from CNRS (INSIS) and ESPCI. T.M. was\r\nsupported by a Joliot visiting professorship grant from ESPCI.","oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","publication":"Journal of Fluid Mechanics","day":"17","year":"2021","isi":1,"date_created":"2021-03-28T22:01:42Z","doi":"10.1017/jfm.2021.89","date_published":"2021-03-17T00:00:00Z","article_number":"A65","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Liu, T., et al. “Decay of Streaks and Rolls in Plane Couette-Poiseuille Flow.” Journal of Fluid Mechanics, vol. 915, A65, Cambridge University Press, 2021, doi:10.1017/jfm.2021.89.","short":"T. Liu, B. Semin, L. Klotz, R. Godoy-Diana, J.E. Wesfreid, T. Mullin, Journal of Fluid Mechanics 915 (2021).","ieee":"T. Liu, B. Semin, L. Klotz, R. Godoy-Diana, J. E. Wesfreid, and T. Mullin, “Decay of streaks and rolls in plane Couette-Poiseuille flow,” Journal of Fluid Mechanics, vol. 915. Cambridge University Press, 2021.","ama":"Liu T, Semin B, Klotz L, Godoy-Diana R, Wesfreid JE, Mullin T. Decay of streaks and rolls in plane Couette-Poiseuille flow. Journal of Fluid Mechanics. 2021;915. doi:10.1017/jfm.2021.89","apa":"Liu, T., Semin, B., Klotz, L., Godoy-Diana, R., Wesfreid, J. E., & Mullin, T. (2021). Decay of streaks and rolls in plane Couette-Poiseuille flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.89","chicago":"Liu, T., B. Semin, Lukasz Klotz, R. Godoy-Diana, J. E. Wesfreid, and T. Mullin. “Decay of Streaks and Rolls in Plane Couette-Poiseuille Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.89.","ista":"Liu T, Semin B, Klotz L, Godoy-Diana R, Wesfreid JE, Mullin T. 2021. Decay of streaks and rolls in plane Couette-Poiseuille flow. Journal of Fluid Mechanics. 915, A65."},"title":"Decay of streaks and rolls in plane Couette-Poiseuille flow","article_processing_charge":"No","external_id":{"arxiv":["2008.08851"],"isi":["000629677500001"]},"author":[{"first_name":"T.","full_name":"Liu, T.","last_name":"Liu"},{"last_name":"Semin","full_name":"Semin, B.","first_name":"B."},{"full_name":"Klotz, Lukasz","orcid":"0000-0003-1740-7635","last_name":"Klotz","first_name":"Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Godoy-Diana, R.","last_name":"Godoy-Diana","first_name":"R."},{"first_name":"J. E.","full_name":"Wesfreid, J. E.","last_name":"Wesfreid"},{"first_name":"T.","full_name":"Mullin, T.","last_name":"Mullin"}]},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1097-0118"],"issn":["0364-9024"]},"ec_funded":1,"issue":"3","volume":97,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Hill's Conjecture states that the crossing number cr(𝐾𝑛) of the complete graph 𝐾𝑛 in the plane (equivalently, the sphere) is 14⌊𝑛2⌋⌊𝑛−12⌋⌊𝑛−22⌋⌊𝑛−32⌋=𝑛4/64+𝑂(𝑛3) . Moon proved that the expected number of crossings in a spherical drawing in which the points are randomly distributed and joined by geodesics is precisely 𝑛4/64+𝑂(𝑛3) , thus matching asymptotically the conjectured value of cr(𝐾𝑛) . Let cr𝑃(𝐺) denote the crossing number of a graph 𝐺 in the projective plane. Recently, Elkies proved that the expected number of crossings in a naturally defined random projective plane drawing of 𝐾𝑛 is (𝑛4/8𝜋2)+𝑂(𝑛3) . In analogy with the relation of Moon's result to Hill's conjecture, Elkies asked if lim𝑛→∞ cr𝑃(𝐾𝑛)/𝑛4=1/8𝜋2 . We construct drawings of 𝐾𝑛 in the projective plane that disprove this."}],"intvolume":" 97","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.02287"}],"scopus_import":"1","date_updated":"2023-08-07T14:26:15Z","department":[{"_id":"UlWa"}],"_id":"9295","status":"public","type":"journal_article","article_type":"original","publication":"Journal of Graph Theory","day":"23","year":"2021","isi":1,"date_created":"2021-03-28T22:01:41Z","doi":"10.1002/jgt.22665","date_published":"2021-03-23T00:00:00Z","page":"426-440","acknowledgement":"We thank two reviewers for their corrections and suggestions on the original version of this\r\npaper. This project has received funding from NSERC Grant 50503-10940-500 and from the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement No 754411, IST, Klosterneuburg, Austria.","oa":1,"publisher":"Wiley","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"A. M. Arroyo Guevara, D. Mcquillan, R. B. Richter, G. Salazar, and M. Sullivan, “Drawings of complete graphs in the projective plane,” Journal of Graph Theory, vol. 97, no. 3. Wiley, pp. 426–440, 2021.","short":"A.M. Arroyo Guevara, D. Mcquillan, R.B. Richter, G. Salazar, M. Sullivan, Journal of Graph Theory 97 (2021) 426–440.","ama":"Arroyo Guevara AM, Mcquillan D, Richter RB, Salazar G, Sullivan M. Drawings of complete graphs in the projective plane. Journal of Graph Theory. 2021;97(3):426-440. doi:10.1002/jgt.22665","apa":"Arroyo Guevara, A. M., Mcquillan, D., Richter, R. B., Salazar, G., & Sullivan, M. (2021). 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Wiley, 2021. https://doi.org/10.1002/jgt.22665."},"title":"Drawings of complete graphs in the projective plane","article_processing_charge":"No","external_id":{"isi":["000631693200001"],"arxiv":["2002.02287"]},"author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M","last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670"},{"first_name":"Dan","full_name":"Mcquillan, Dan","last_name":"Mcquillan"},{"first_name":"R. Bruce","last_name":"Richter","full_name":"Richter, R. 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Developmental Cell. 2021;56(6):723-725. doi:10.1016/j.devcel.2021.03.002"},"month":"03","intvolume":" 56","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2021.03.002"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"In this issue of Developmental Cell, Doyle and colleagues identify periodic anterior contraction as a characteristic feature of fibroblasts and mesenchymal cancer cells embedded in 3D collagen gels. This contractile mechanism generates a matrix prestrain required for crawling in fibrous 3D environments."}],"volume":56,"issue":"6","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"9294","department":[{"_id":"MiSi"}],"date_updated":"2023-08-07T14:26:47Z"},{"article_number":"109125","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"}],"citation":{"mla":"Zhang, Xiaomin, et al. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods, vol. 357, no. 6, 109125, Elsevier, 2021, doi:10.1016/j.jneumeth.2021.109125.","ieee":"X. Zhang, A. Schlögl, D. H. Vandael, and P. M. Jonas, “MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo,” Journal of Neuroscience Methods, vol. 357, no. 6. Elsevier, 2021.","short":"X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021).","apa":"Zhang, X., Schlögl, A., Vandael, D. H., & Jonas, P. M. (2021). MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2021.109125","ama":"Zhang X, Schlögl A, Vandael DH, Jonas PM. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 2021;357(6). doi:10.1016/j.jneumeth.2021.109125","chicago":"Zhang, Xiaomin, Alois Schlögl, David H Vandael, and Peter M Jonas. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods. Elsevier, 2021. https://doi.org/10.1016/j.jneumeth.2021.109125.","ista":"Zhang X, Schlögl A, Vandael DH, Jonas PM. 2021. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 357(6), 109125."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000661088500005"]},"author":[{"last_name":"Zhang","full_name":"Zhang, Xiaomin","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J.). We thank Drs. Jozsef Csicsvari, Christoph Lampert, and Federico Stella for critically reading previous manuscript versions. We are also grateful to Drs. Josh Merel and Ben Shababo for their help with applying the Bayesian detection method to our data. We also thank Florian Marr for technical assistance, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support.","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2021","has_accepted_license":"1","isi":1,"publication":"Journal of Neuroscience Methods","day":"09","date_created":"2021-04-18T22:01:39Z","date_published":"2021-03-09T00:00:00Z","doi":"10.1016/j.jneumeth.2021.109125","_id":"9329","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-07T14:36:14Z","ddc":["570"],"file_date_updated":"2021-04-19T08:30:22Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.\r\nNew method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.\r\nResults: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.\r\nComparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.\r\nConclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity."}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 357","month":"03","publication_status":"published","publication_identifier":{"eissn":["1872-678X"],"issn":["0165-0270"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9339","checksum":"2a5800d91b96d08b525e17319dcd5e44","file_size":6924738,"date_updated":"2021-04-19T08:30:22Z","creator":"dernst","file_name":"2021_JourNeuroscienceMeth_Zhang.pdf","date_created":"2021-04-19T08:30:22Z"}],"ec_funded":1,"issue":"6","volume":357},{"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9534","checksum":"1e5295fbd9c2a459173ec45a0e8a7c2e","success":1,"date_updated":"2021-06-08T10:04:10Z","file_size":11405875,"creator":"cziletti","date_created":"2021-06-08T10:04:10Z","file_name":"2021_Cell_Petridou.pdf"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"7","volume":184,"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"text":"Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"04","intvolume":" 184","date_updated":"2023-08-07T14:33:59Z","ddc":["570"],"department":[{"_id":"CaHe"},{"_id":"EdHa"}],"file_date_updated":"2021-06-08T10:04:10Z","_id":"9316","type":"journal_article","article_type":"original","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","has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Cell","page":"1914-1928.e19","doi":"10.1016/j.cell.2021.02.017","date_published":"2021-04-01T00:00:00Z","date_created":"2021-04-11T22:01:14Z","acknowledgement":"We thank Carl Goodrich and the members of the Heisenberg and Hannezo groups, in particular Reka Korei, for help, technical advice, and discussions; and the Bioimaging and zebrafish facilities of the IST Austria for continuous support. This work was supported by the Elise Richter Program of Austrian Science Fund (FWF) to N.I.P. ( V 736-B26 ) and the European Union (European Research Council Advanced Grant 742573 to C.-P.H. and European Research Council Starting Grant 851288 to E.H.).","quality_controlled":"1","publisher":"Elsevier","oa":1,"citation":{"mla":"Petridou, Nicoletta, et al. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell, vol. 184, no. 7, Elsevier, 2021, p. 1914–1928.e19, doi:10.1016/j.cell.2021.02.017.","ama":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 2021;184(7):1914-1928.e19. doi:10.1016/j.cell.2021.02.017","apa":"Petridou, N., Corominas-Murtra, B., Heisenberg, C.-P. J., & Hannezo, E. B. (2021). Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.02.017","ieee":"N. Petridou, B. Corominas-Murtra, C.-P. J. Heisenberg, and E. B. Hannezo, “Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions,” Cell, vol. 184, no. 7. Elsevier, p. 1914–1928.e19, 2021.","short":"N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell 184 (2021) 1914–1928.e19.","chicago":"Petridou, Nicoletta, Bernat Corominas-Murtra, Carl-Philipp J Heisenberg, and Edouard B Hannezo. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.02.017.","ista":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. 2021. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 184(7), 1914–1928.e19."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Petridou","full_name":"Petridou, Nicoletta","orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Nicoletta"},{"full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"article_processing_charge":"No","external_id":{"isi":["000636734000022"],"pmid":["33730596"]},"title":"Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"2693FD8C-B435-11E9-9278-68D0E5697425","name":"Tissue material properties in embryonic development","grant_number":"V00736"}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Given a locally finite X⊆Rd and a radius r≥0, the k-fold cover of X and r consists of all points in Rd that have k or more points of X within distance r. We consider two filtrations—one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k—and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in Rd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module of Delaunay mosaics that is isomorphic to the persistence module of the multi-covers."}],"intvolume":" 65","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"59b4e1e827e494209bcb4aae22e1d347","file_id":"10394","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_DisCompGeo_Edelsbrunner_Osang.pdf","date_created":"2021-12-01T10:56:53Z","file_size":677704,"date_updated":"2021-12-01T10:56:53Z","creator":"cchlebak"}],"publication_status":"published","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"187"}]},"volume":65,"_id":"9317","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","ddc":["516"],"date_updated":"2023-08-07T14:35:44Z","department":[{"_id":"HeEd"}],"file_date_updated":"2021-12-01T10:56:53Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha), and by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF)\r\nOpen Access funding provided by the Institute of Science and Technology (IST Austria).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Discrete and Computational Geometry","day":"31","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-04-11T22:01:15Z","date_published":"2021-03-31T00:00:00Z","doi":"10.1007/s00454-021-00281-9","page":"1296–1313","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-021-00281-9.","ista":"Edelsbrunner H, Osang GF. 2021. The multi-cover persistence of Euclidean balls. Discrete and Computational Geometry. 65, 1296–1313.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “The Multi-Cover Persistence of Euclidean Balls.” Discrete and Computational Geometry, vol. 65, Springer Nature, 2021, pp. 1296–1313, doi:10.1007/s00454-021-00281-9.","apa":"Edelsbrunner, H., & Osang, G. F. (2021). The multi-cover persistence of Euclidean balls. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-021-00281-9","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. Discrete and Computational Geometry. 2021;65:1296–1313. doi:10.1007/s00454-021-00281-9","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” Discrete and Computational Geometry, vol. 65. Springer Nature, pp. 1296–1313, 2021.","short":"H. Edelsbrunner, G.F. Osang, Discrete and Computational Geometry 65 (2021) 1296–1313."},"title":"The multi-cover persistence of Euclidean balls","external_id":{"isi":["000635460400001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Osang, Georg F","last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}]},{"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","article_type":"original","status":"public","_id":"9318","department":[{"_id":"RoSe"}],"file_date_updated":"2021-04-12T07:15:58Z","date_updated":"2023-08-07T14:35:06Z","ddc":["510"],"scopus_import":"1","intvolume":" 9","month":"03","abstract":[{"lang":"eng","text":"We consider a system of N bosons in the mean-field scaling regime for a class of interactions including the repulsive Coulomb potential. We derive an asymptotic expansion of the low-energy eigenstates and the corresponding energies, which provides corrections to Bogoliubov theory to any order in 1/N."}],"oa_version":"Published Version","ec_funded":1,"volume":9,"publication_status":"published","publication_identifier":{"eissn":["20505094"]},"language":[{"iso":"eng"}],"file":[{"checksum":"17a3e6786d1e930cf0c14a880a6d7e92","file_id":"9319","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-04-12T07:15:58Z","file_name":"2021_ForumMath_Bossmann.pdf","creator":"dernst","date_updated":"2021-04-12T07:15:58Z","file_size":883851}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e28","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000634006900001"]},"author":[{"full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343","last_name":"Bossmann","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea"},{"id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P","full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889","last_name":"Petrat"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"title":"Asymptotic expansion of low-energy excitations for weakly interacting bosons","citation":{"ama":"Bossmann L, Petrat SP, Seiringer R. Asymptotic expansion of low-energy excitations for weakly interacting bosons. Forum of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.22","apa":"Bossmann, L., Petrat, S. P., & Seiringer, R. (2021). Asymptotic expansion of low-energy excitations for weakly interacting bosons. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2021.22","short":"L. Bossmann, S.P. Petrat, R. Seiringer, Forum of Mathematics, Sigma 9 (2021).","ieee":"L. Bossmann, S. P. Petrat, and R. Seiringer, “Asymptotic expansion of low-energy excitations for weakly interacting bosons,” Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021.","mla":"Bossmann, Lea, et al. “Asymptotic Expansion of Low-Energy Excitations for Weakly Interacting Bosons.” Forum of Mathematics, Sigma, vol. 9, e28, Cambridge University Press, 2021, doi:10.1017/fms.2021.22.","ista":"Bossmann L, Petrat SP, Seiringer R. 2021. Asymptotic expansion of low-energy excitations for weakly interacting bosons. Forum of Mathematics, Sigma. 9, e28.","chicago":"Bossmann, Lea, Sören P Petrat, and Robert Seiringer. “Asymptotic Expansion of Low-Energy Excitations for Weakly Interacting Bosons.” Forum of Mathematics, Sigma. Cambridge University Press, 2021. https://doi.org/10.1017/fms.2021.22."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","acknowledgement":"The first author gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411. The third author was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227).","date_created":"2021-04-11T22:01:15Z","doi":"10.1017/fms.2021.22","date_published":"2021-03-26T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Forum of Mathematics, Sigma","day":"26"},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2010.09168","open_access":"1"}],"month":"04","intvolume":" 118","abstract":[{"text":"Quantum entanglement has been generated and verified in cold-atom experiments and used to make atom-interferometric measurements below the shot-noise limit. However, current state-of-the-art cold-atom devices exploit separable (i.e., unentangled) atomic states. This perspective piece asks the question: can entanglement usefully improve cold-atom sensors, in the sense that it gives new sensing capabilities unachievable with current state-of-the-art devices? We briefly review the state-of-the-art in precision cold-atom sensing, focusing on clocks and inertial sensors, identifying the potential benefits entanglement could bring to these devices, and the challenges that need to be overcome to realize these benefits. We survey demonstrated methods of generating metrologically useful entanglement in cold-atom systems, note their relative strengths and weaknesses, and assess their prospects for near-to-medium term quantum-enhanced cold-atom sensing.","lang":"eng"}],"oa_version":"Preprint","volume":118,"issue":"14","publication_identifier":{"issn":["00036951"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"9331","department":[{"_id":"OnHo"}],"date_updated":"2023-08-07T14:36:42Z","publisher":"AIP Publishing","quality_controlled":"1","oa":1,"acknowledgement":"We acknowledge fruitful discussions with John Close, Chris Freier, Kyle Hardman, Joseph Hope, and Paul Wigley, and insightful suggestions made by Franck Pereira dos Santos on behalf of the Atom Interferometry and Inertial Sensors team at SYRTE. S.S.S. was supported by an Australian Research Council Discovery Early Career Researcher Award (DECRA), Project No. DE200100495. O.H. was supported by IST Austria.","doi":"10.1063/5.0050235","date_published":"2021-04-07T00:00:00Z","date_created":"2021-04-18T22:01:40Z","isi":1,"year":"2021","day":"07","publication":"Applied Physics Letters","article_number":"140501","author":[{"full_name":"Szigeti, Stuart S.","last_name":"Szigeti","first_name":"Stuart S."},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X"},{"first_name":"Simon A.","last_name":"Haine","full_name":"Haine, Simon A."}],"external_id":{"isi":["000637702100001"],"arxiv":["2010.09168"]},"article_processing_charge":"No","title":"Improving cold-atom sensors with quantum entanglement: Prospects and challenges","citation":{"ieee":"S. S. Szigeti, O. Hosten, and S. A. Haine, “Improving cold-atom sensors with quantum entanglement: Prospects and challenges,” Applied Physics Letters, vol. 118, no. 14. AIP Publishing, 2021.","short":"S.S. Szigeti, O. Hosten, S.A. Haine, Applied Physics Letters 118 (2021).","apa":"Szigeti, S. S., Hosten, O., & Haine, S. A. (2021). Improving cold-atom sensors with quantum entanglement: Prospects and challenges. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0050235","ama":"Szigeti SS, Hosten O, Haine SA. Improving cold-atom sensors with quantum entanglement: Prospects and challenges. Applied Physics Letters. 2021;118(14). doi:10.1063/5.0050235","mla":"Szigeti, Stuart S., et al. “Improving Cold-Atom Sensors with Quantum Entanglement: Prospects and Challenges.” Applied Physics Letters, vol. 118, no. 14, 140501, AIP Publishing, 2021, doi:10.1063/5.0050235.","ista":"Szigeti SS, Hosten O, Haine SA. 2021. Improving cold-atom sensors with quantum entanglement: Prospects and challenges. Applied Physics Letters. 118(14), 140501.","chicago":"Szigeti, Stuart S., Onur Hosten, and Simon A. Haine. “Improving Cold-Atom Sensors with Quantum Entanglement: Prospects and Challenges.” Applied Physics Letters. AIP Publishing, 2021. https://doi.org/10.1063/5.0050235."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"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","article_type":"original","status":"public","_id":"9330","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"file_date_updated":"2021-04-19T10:10:56Z","date_updated":"2023-08-08T13:08:47Z","ddc":["570"],"scopus_import":"1","intvolume":" 118","month":"04","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium channels have been linked to synaptic functions and neurological disease. Here we show that α2δ subunits are essential for the formation and organization of glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown model, we demonstrate a failure in presynaptic differentiation evidenced by defective presynaptic calcium channel clustering and calcium influx, smaller presynaptic active zones, and a strongly reduced accumulation of presynaptic vesicle-associated proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms as synaptic organizers is highly redundant, as each individual α2δ isoform can rescue presynaptic calcium channel trafficking and expression of synaptic proteins. Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can fully rescue presynaptic synapsin expression but only partially calcium channel trafficking, suggesting that the regulatory role of α2δ subunits is independent from its role as a calcium channel subunit. Our findings influence the current view on excitatory synapse formation. First, our study suggests that postsynaptic differentiation is secondary to presynaptic differentiation. Second, the dependence of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation points for the organization of synapses. Finally, our results suggest that α2δ subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning the synaptic active zone with the postsynaptic density."}],"oa_version":"Published Version","ec_funded":1,"volume":118,"issue":"14","publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-04-19T10:10:56Z","file_name":"2021_PNAS_Schoepf.pdf","creator":"dernst","date_updated":"2021-04-19T10:10:56Z","file_size":2603911,"checksum":"dd014f68ae9d7d8d8fc4139a24e04506","file_id":"9340","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"external_id":{"isi":["000637398300002"]},"article_processing_charge":"No","author":[{"first_name":"Clemens L.","full_name":"Schöpf, Clemens L.","last_name":"Schöpf"},{"full_name":"Ablinger, Cornelia","last_name":"Ablinger","first_name":"Cornelia"},{"full_name":"Geisler, Stefanie M.","last_name":"Geisler","first_name":"Stefanie M."},{"full_name":"Stanika, Ruslan I.","last_name":"Stanika","first_name":"Ruslan I."},{"full_name":"Campiglio, Marta","last_name":"Campiglio","first_name":"Marta"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benedikt","full_name":"Nimmervoll, Benedikt","last_name":"Nimmervoll"},{"first_name":"Bettina","full_name":"Schlick, Bettina","last_name":"Schlick"},{"full_name":"Brockhaus, Johannes","last_name":"Brockhaus","first_name":"Johannes"},{"last_name":"Missler","full_name":"Missler, Markus","first_name":"Markus"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"full_name":"Obermair, Gerald J.","last_name":"Obermair","first_name":"Gerald J."}],"title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","citation":{"mla":"Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS, vol. 118, no. 14, National Academy of Sciences, 2021, doi:10.1073/pnas.1920827118.","ama":"Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 2021;118(14). doi:10.1073/pnas.1920827118","apa":"Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M., Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1920827118","short":"C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann, B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair, PNAS 118 (2021).","ieee":"C. L. Schöpf et al., “Presynaptic α2δ subunits are key organizers of glutamatergic synapses,” PNAS, vol. 118, no. 14. National Academy of Sciences, 2021.","chicago":"Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika, Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.1920827118.","ista":"Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 118(14)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","acknowledgement":"We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the team of the Electron Microscopy Facility at the Institute of Science and Technology Austria for technical support related to ultrastructural analysis; Hermann Dietrich and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical discussions and reading the manuscript. This study was supported by Austrian Science Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.), European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S., S.M.G., and C.A.","date_created":"2021-04-18T22:01:40Z","doi":"10.1073/pnas.1920827118","date_published":"2021-04-06T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"PNAS","day":"06"},{"language":[{"iso":"eng"}],"file":[{"date_created":"2021-04-19T10:54:55Z","file_name":"2021_JourMolecularScience_Oetvoes.pdf","creator":"dernst","date_updated":"2021-04-19T10:54:55Z","file_size":2769717,"checksum":"26ada2531ad1f9c01a1664de0431f1fe","file_id":"9342","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"volume":22,"issue":"8","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner."}],"intvolume":" 22","month":"04","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-08T13:09:58Z","department":[{"_id":"EvBe"}],"file_date_updated":"2021-04-19T10:54:55Z","_id":"9332","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","publication":"International Journal of Molecular Sciences","day":"08","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-04-18T22:01:41Z","date_published":"2021-04-08T00:00:00Z","doi":"10.3390/ijms22083862","acknowledgement":"This research was supported by a postdoctoral fellowship of the Carl Tryggers Foundation (to K.Ö.) and by grants from Vetenskapsrådet (Nr.: 621-2004-2921 to L.B.) and VINNOVA (to L.B. and S.R.).\r\nWe thank Frederic Berger, Hidehiro Fukaki, Malcolm Bennett, Claudia Köhler, Jiri Friml for providing pRBR1::RBR1-RFP, ssl2-1, slr-1, pPKL::PKL-GFP seeds and the DR5 expressing vector, respectively. Authors are grateful to Hayashi Kenichiro for providing the auxinol compound and to Rishi Bhalerao for stimulating discussions. The technical help of Adeline Rigal and Thomas Vain with the auxinol experiments is much appreciated.","oa":1,"publisher":"MDPI","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Ötvös K, Miskolczi P, Marhavý P, Cruz-Ramírez A, Benková E, Robert S, Bakó L. 2021. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. 22(8), 3862.","chicago":"Ötvös, Krisztina, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva Benková, Stéphanie Robert, and László Bakó. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22083862.","ieee":"K. Ötvös et al., “Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis,” International Journal of Molecular Sciences, vol. 22, no. 8. MDPI, 2021.","short":"K. Ötvös, P. Miskolczi, P. Marhavý, A. Cruz-Ramírez, E. Benková, S. Robert, L. Bakó, International Journal of Molecular Sciences 22 (2021).","apa":"Ötvös, K., Miskolczi, P., Marhavý, P., Cruz-Ramírez, A., Benková, E., Robert, S., & Bakó, L. (2021). Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22083862","ama":"Ötvös K, Miskolczi P, Marhavý P, et al. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. 2021;22(8). doi:10.3390/ijms22083862","mla":"Ötvös, Krisztina, et al. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” International Journal of Molecular Sciences, vol. 22, no. 8, 3862, MDPI, 2021, doi:10.3390/ijms22083862."},"title":"Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis","external_id":{"isi":["000644394800001"]},"article_processing_charge":"No","author":[{"first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","last_name":"Ötvös"},{"full_name":"Miskolczi, Pál","last_name":"Miskolczi","first_name":"Pál"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Marhavý, Peter","orcid":"0000-0001-5227-5741","last_name":"Marhavý"},{"first_name":"Alfredo","last_name":"Cruz-Ramírez","full_name":"Cruz-Ramírez, Alfredo"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"last_name":"Bakó","full_name":"Bakó, László","first_name":"László"}],"article_number":"3862"},{"scopus_import":"1","month":"04","intvolume":" 111","abstract":[{"text":"We revise a previous result about the Fröhlich dynamics in the strong coupling limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα, where φ0 is the electron ground state of the Pekar energy functional and ξα the associated coherent state of the phonons, can be approximated by a global phase for times small compared to α2. In the present note we prove that a similar approximation holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons that is generated by an operator proportional to α−2 and quadratic in creation and annihilation operators. Our result implies that the electron ground state remains close to its initial state for times of order α2, while the phonon fluctuations around the coherent state ξα can be described by a time-dependent Bogoliubov transformation.","lang":"eng"}],"oa_version":"Published Version","volume":111,"publication_identifier":{"issn":["03779017"],"eissn":["15730530"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9341","checksum":"be56c0845a43c0c5c772ee0b5053f7d7","creator":"dernst","file_size":438084,"date_updated":"2021-04-19T10:40:01Z","file_name":"2021_LettersMathPhysics_Mitrouskas.pdf","date_created":"2021-04-19T10:40:01Z"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","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","_id":"9333","department":[{"_id":"RoSe"}],"file_date_updated":"2021-04-19T10:40:01Z","date_updated":"2023-08-08T13:09:28Z","ddc":["510"],"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"I thank Marcel Griesemer for many interesting discussions about the Fröhlich polaron and also for valuable comments on this manuscript. Helpful discussions with Nikolai Leopold and Robert Seiringer are also gratefully acknowledged. This work was partially supported by the Deutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral Theory and Dynamics of Quantum Systems. Open Access funding enabled and organized by Projekt DEAL.","date_published":"2021-04-05T00:00:00Z","doi":"10.1007/s11005-021-01380-7","date_created":"2021-04-18T22:01:41Z","has_accepted_license":"1","isi":1,"year":"2021","day":"05","publication":"Letters in Mathematical Physics","article_number":"45","author":[{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"}],"external_id":{"isi":["000637359300002"]},"article_processing_charge":"No","title":"A note on the Fröhlich dynamics in the strong coupling limit","citation":{"mla":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” Letters in Mathematical Physics, vol. 111, 45, Springer Nature, 2021, doi:10.1007/s11005-021-01380-7.","ama":"Mitrouskas DJ. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 2021;111. doi:10.1007/s11005-021-01380-7","apa":"Mitrouskas, D. J. (2021). A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-021-01380-7","ieee":"D. J. Mitrouskas, “A note on the Fröhlich dynamics in the strong coupling limit,” Letters in Mathematical Physics, vol. 111. Springer Nature, 2021.","short":"D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021).","chicago":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” Letters in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s11005-021-01380-7.","ista":"Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 111, 45."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"title":"The waiting time phenomenon in spatially discretized porous medium and thin film equations","author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"last_name":"Matthes","full_name":"Matthes, Daniel","first_name":"Daniel"}],"external_id":{"isi":["000625044600003"],"arxiv":["1911.04185"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Fischer, Julian L, and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/19M1300017.","ista":"Fischer JL, Matthes D. 2021. The waiting time phenomenon in spatially discretized porous medium and thin film equations. SIAM Journal on Numerical Analysis. 59(1), 60–87.","mla":"Fischer, Julian L., and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” SIAM Journal on Numerical Analysis, vol. 59, no. 1, Society for Industrial and Applied Mathematics, 2021, pp. 60–87, doi:10.1137/19M1300017.","ieee":"J. L. Fischer and D. Matthes, “The waiting time phenomenon in spatially discretized porous medium and thin film equations,” SIAM Journal on Numerical Analysis, vol. 59, no. 1. Society for Industrial and Applied Mathematics, pp. 60–87, 2021.","short":"J.L. Fischer, D. Matthes, SIAM Journal on Numerical Analysis 59 (2021) 60–87.","ama":"Fischer JL, Matthes D. The waiting time phenomenon in spatially discretized porous medium and thin film equations. SIAM Journal on Numerical Analysis. 2021;59(1):60-87. doi:10.1137/19M1300017","apa":"Fischer, J. L., & Matthes, D. (2021). The waiting time phenomenon in spatially discretized porous medium and thin film equations. SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1300017"},"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","oa":1,"acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics”.","doi":"10.1137/19M1300017","date_published":"2021-01-01T00:00:00Z","date_created":"2021-04-18T22:01:42Z","page":"60-87","day":"01","publication":"SIAM Journal on Numerical Analysis","isi":1,"year":"2021","status":"public","type":"journal_article","article_type":"original","_id":"9335","department":[{"_id":"JuFi"}],"date_updated":"2023-08-08T13:10:40Z","month":"01","intvolume":" 59","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1911.04185","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Various degenerate diffusion equations exhibit a waiting time phenomenon: depending on the “flatness” of the compactly supported initial datum at the boundary of the support, the support of the solution may not expand for a certain amount of time. We show that this phenomenon is captured by particular Lagrangian discretizations of the porous medium and the thin film equations, and we obtain sufficient criteria for the occurrence of waiting times that are consistent with the known ones for the original PDEs. For the spatially discrete solution, the waiting time phenomenon refers to a deviation of the edge of support from its original position by a quantity comparable to the mesh width, over a mesh-independent time interval. Our proof is based on estimates on the fluid velocity in Lagrangian coordinates. Combining weighted entropy estimates with an iteration technique à la Stampacchia leads to upper bounds on free boundary propagation. Numerical simulations show that the phenomenon is already clearly visible for relatively coarse discretizations."}],"volume":59,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0036-1429"]},"publication_status":"published"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).","ieee":"P. F. Lenne et al., “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” Physical biology, vol. 18, no. 4. IOP Publishing, 2021.","ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 2021;18(4). doi:10.1088/1478-3975/abd0db","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abd0db","mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” Physical Biology, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:10.1088/1478-3975/abd0db.","ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501.","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” Physical Biology. IOP Publishing, 2021. https://doi.org/10.1088/1478-3975/abd0db."},"title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","author":[{"last_name":"Lenne","full_name":"Lenne, Pierre François","first_name":"Pierre François"},{"first_name":"Edwin","full_name":"Munro, Edwin","last_name":"Munro"},{"first_name":"Idse","last_name":"Heemskerk","full_name":"Heemskerk, Idse"},{"full_name":"Warmflash, Aryeh","last_name":"Warmflash","first_name":"Aryeh"},{"full_name":"Bocanegra, Laura","last_name":"Bocanegra","first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kishi","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuchen","full_name":"Long, Yuchen","last_name":"Long"},{"first_name":"Antoine","full_name":"Fruleux, Antoine","last_name":"Fruleux"},{"first_name":"Arezki","last_name":"Boudaoud","full_name":"Boudaoud, Arezki"},{"first_name":"Timothy E.","full_name":"Saunders, Timothy E.","last_name":"Saunders"},{"last_name":"Caldarelli","full_name":"Caldarelli, Paolo","first_name":"Paolo"},{"first_name":"Arthur","last_name":"Michaut","full_name":"Michaut, Arthur"},{"last_name":"Gros","full_name":"Gros, Jerome","first_name":"Jerome"},{"first_name":"Yonit","last_name":"Maroudas-Sacks","full_name":"Maroudas-Sacks, Yonit"},{"last_name":"Keren","full_name":"Keren, Kinneret","first_name":"Kinneret"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"full_name":"Gartner, Zev J.","last_name":"Gartner","first_name":"Zev J."},{"first_name":"Benjamin","last_name":"Stormo","full_name":"Stormo, Benjamin"},{"full_name":"Gladfelter, Amy","last_name":"Gladfelter","first_name":"Amy"},{"full_name":"Rodrigues, Alan","last_name":"Rodrigues","first_name":"Alan"},{"first_name":"Amy","last_name":"Shyer","full_name":"Shyer, Amy"},{"full_name":"Minc, Nicolas","last_name":"Minc","first_name":"Nicolas"},{"first_name":"Jean Léon","last_name":"Maître","full_name":"Maître, Jean Léon"},{"first_name":"Stefano","full_name":"Di Talia, Stefano","last_name":"Di Talia"},{"full_name":"Khamaisi, Bassma","last_name":"Khamaisi","first_name":"Bassma"},{"full_name":"Sprinzak, David","last_name":"Sprinzak","first_name":"David"},{"first_name":"Sham","full_name":"Tlili, Sham","last_name":"Tlili"}],"article_processing_charge":"No","external_id":{"isi":["000640396400001"],"pmid":["33276350"]},"article_number":"041501","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"},{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"day":"14","publication":"Physical biology","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1088/1478-3975/abd0db","date_published":"2021-04-14T00:00:00Z","date_created":"2021-04-25T22:01:29Z","acknowledgement":"The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).","publisher":"IOP Publishing","quality_controlled":"1","oa":1,"ddc":["570"],"date_updated":"2023-08-08T13:15:46Z","file_date_updated":"2021-04-27T08:38:35Z","department":[{"_id":"AnKi"},{"_id":"EdHa"}],"_id":"9349","status":"public","type":"journal_article","article_type":"original","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":[{"file_name":"2021_PhysBio_Lenne.pdf","date_created":"2021-04-27T08:38:35Z","creator":"cziletti","file_size":6296324,"date_updated":"2021-04-27T08:38:35Z","success":1,"file_id":"9355","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1478-3975"]},"publication_status":"published","volume":18,"issue":"4","related_material":{"record":[{"relation":"dissertation_contains","id":"13081","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development."}],"month":"04","intvolume":" 18","scopus_import":"1"},{"article_number":"eabf2690","title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","article_processing_charge":"No","external_id":{"isi":["000636455600027"],"pmid":["33811076"]},"author":[{"full_name":"Duan, J.","last_name":"Duan","first_name":"J."},{"last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, G.","first_name":"G."},{"last_name":"Voronin","full_name":"Voronin, K. V.","first_name":"K. V."},{"full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Taboada-Gutiérrez, J.","last_name":"Taboada-Gutiérrez","first_name":"J."},{"full_name":"Volkov, V. S.","last_name":"Volkov","first_name":"V. S."},{"first_name":"J.","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, J."},{"first_name":"A. Y.","full_name":"Nikitin, A. Y.","last_name":"Nikitin"},{"full_name":"Alonso-González, P.","last_name":"Alonso-González","first_name":"P."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Duan, J., et al. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” Science Advances, vol. 7, no. 14, eabf2690, AAAS, 2021, doi:10.1126/sciadv.abf2690.","ama":"Duan J, Álvarez-Pérez G, Voronin KV, et al. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 2021;7(14). doi:10.1126/sciadv.abf2690","apa":"Duan, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., Taboada-Gutiérrez, J., Volkov, V. S., … Alonso-González, P. (2021). Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abf2690","short":"J. Duan, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, J. Taboada-Gutiérrez, V.S. Volkov, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","ieee":"J. Duan et al., “Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition,” Science Advances, vol. 7, no. 14. AAAS, 2021.","chicago":"Duan, J., G. Álvarez-Pérez, K. V. Voronin, Ivan Prieto Gonzalez, J. Taboada-Gutiérrez, V. S. Volkov, J. Martín-Sánchez, A. Y. Nikitin, and P. Alonso-González. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” Science Advances. AAAS, 2021. https://doi.org/10.1126/sciadv.abf2690.","ista":"Duan J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Taboada-Gutiérrez J, Volkov VS, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2021. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 7(14), eabf2690."},"oa":1,"publisher":"AAAS","quality_controlled":"1","acknowledgement":"G.Á.-P. and J.T.-G. acknowledge support through the Severo Ochoa Program from the government of the Principality of Asturias (grant nos. PA20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). K.V.V. and V.S.V. acknowledge the Ministry of Science and Higher Education of the Russian Federation (no. 0714-2020-0002). J. M.-S. acknowledges financial support through the Ramón y Cajal Program from the government of Spain and FSE (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT201788358-C3-3-R), and the Basque Department of Education (PIBA-2020-1-0014). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA. ","date_created":"2021-04-18T22:01:42Z","doi":"10.1126/sciadv.abf2690","date_published":"2021-04-02T00:00:00Z","publication":"Science Advances","day":"02","year":"2021","isi":1,"has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","_id":"9334","file_date_updated":"2021-04-19T11:17:29Z","department":[{"_id":"NanoFab"}],"ddc":["530"],"date_updated":"2023-08-08T13:11:31Z","intvolume":" 7","month":"04","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Polaritons with directional in-plane propagation and ultralow losses in van der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale. However, these polaritons present a crucial limitation: their directional propagation is intrinsically determined by the crystal structure of the host material, imposing forbidden directions of propagation. Here, we demonstrate that directional polaritons (in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide) can be directed along forbidden directions by inducing an optical topological transition, which emerges when the slab is placed on a substrate with a given negative permittivity (4H–silicon carbide). By visualizing the transition in real space, we observe exotic polaritonic states between mutually orthogonal hyperbolic regimes, which unveil the topological origin of the transition: a gap opening in the dispersion. This work provides insights into optical topological transitions in vdW crystals, which introduce a route to direct light at the nanoscale."}],"issue":"14","volume":7,"language":[{"iso":"eng"}],"file":[{"file_size":717489,"date_updated":"2021-04-19T11:17:29Z","creator":"dernst","file_name":"2021_ScienceAdv_Duan.pdf","date_created":"2021-04-19T11:17:29Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"4b383d4a1d484a71bbc64ecf401bbdbb","file_id":"9343"}],"publication_status":"published","publication_identifier":{"eissn":["23752548"]}},{"publication":"Annales Henri Poincare","day":"08","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-04-25T22:01:30Z","doi":"10.1007/s00023-021-01044-1","date_published":"2021-04-08T00:00:00Z","page":"2595-2618","acknowledgement":"The authors gratefully acknowledge Gérard Ben Arous for suggesting this kind of result. K.L.K. was partially supported by NSF CAREER Award DMS-125479 and a Simons Sabbatical Fellowship. S.R. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. B. S. gratefully acknowledges partial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose–Einstein condensates” and from the European Research Council through the ERC-AdG CLaQS. Funding Open access funding provided by Institute of Science and Technology (IST Austria).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"K. Kirkpatrick, S. A. E. Rademacher, and B. Schlein, “A large deviation principle in many-body quantum dynamics,” Annales Henri Poincare, vol. 22. Springer Nature, pp. 2595–2618, 2021.","short":"K. Kirkpatrick, S.A.E. Rademacher, B. Schlein, Annales Henri Poincare 22 (2021) 2595–2618.","ama":"Kirkpatrick K, Rademacher SAE, Schlein B. A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. 2021;22:2595-2618. doi:10.1007/s00023-021-01044-1","apa":"Kirkpatrick, K., Rademacher, S. A. E., & Schlein, B. (2021). A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-021-01044-1","mla":"Kirkpatrick, Kay, et al. “A Large Deviation Principle in Many-Body Quantum Dynamics.” Annales Henri Poincare, vol. 22, Springer Nature, 2021, pp. 2595–618, doi:10.1007/s00023-021-01044-1.","ista":"Kirkpatrick K, Rademacher SAE, Schlein B. 2021. A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. 22, 2595–2618.","chicago":"Kirkpatrick, Kay, Simone Anna Elvira Rademacher, and Benjamin Schlein. “A Large Deviation Principle in Many-Body Quantum Dynamics.” Annales Henri Poincare. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01044-1."},"title":"A large deviation principle in many-body quantum dynamics","external_id":{"arxiv":["2010.13754"],"isi":["000638022600001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Kay","last_name":"Kirkpatrick","full_name":"Kirkpatrick, Kay"},{"first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","file_size":522669,"date_updated":"2021-10-15T11:15:40Z","file_name":"2021_Annales_Kirkpatrick.pdf","date_created":"2021-10-15T11:15:40Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10143","checksum":"1a0fb963f2f415ba470881a794f20eb6"}],"publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"ec_funded":1,"volume":22,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider the many-body quantum evolution of a factorized initial data, in the mean-field regime. We show that fluctuations around the limiting Hartree dynamics satisfy large deviation estimates that are consistent with central limit theorems that have been established in the last years. "}],"intvolume":" 22","month":"04","scopus_import":"1","ddc":["530"],"date_updated":"2023-08-08T13:14:40Z","department":[{"_id":"RoSe"}],"file_date_updated":"2021-10-15T11:15:40Z","_id":"9351","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"},{"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Mentorship is experience and/or knowledge‐based guidance. Mentors support, sponsor and advocate for mentees. Having one or more mentors when you seek advice can significantly influence and improve your research endeavours, well‐being and career development. Positive mentee–mentor relationships are vital for maintaining work–life balance and success in careers. Early‐career researchers (ECRs), in particular, can benefit from mentorship to navigate challenges in academic and nonacademic life and careers. Yet, strategies for selecting mentors and maintaining interactions with them are often underdiscussed within research environments. In this Words of Advice, we provide recommendations for ECRs to seek and manage mentorship interactions. Our article draws from our experiences as ECRs and published work, to provide suggestions for mentees to proactively promote beneficial mentorship interactions. The recommended practices highlight the importance of identifying mentorship needs, planning and selecting multiple and diverse mentors, setting goals, and maintaining constructive, and mutually beneficial working relationships with mentors.","lang":"eng"}],"month":"04","main_file_link":[{"url":"https://doi.org/10.1111/febs.15823","open_access":"1"}],"alternative_title":["Words of Advice"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1742-4658"],"issn":["1742-464X"]},"_id":"9336","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-08T13:12:55Z","department":[{"_id":"CaHe"}],"acknowledgement":"The authors thank Nicholas Asby of the University of Chicago for valuable comments on an earlier version of this work. A.P.S. was partially supported by the NARSAD Young Investigator Grant 27705. S.J.H was supported by the National Institutes of Health grant R35GM133732.","oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"FEBS Journal","day":"05","year":"2021","isi":1,"date_created":"2021-04-18T22:01:43Z","date_published":"2021-04-05T00:00:00Z","doi":"10.1111/febs.15823","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Sarabipour, S., Hainer, S. J., Arslan, F. N., De Winde, C. M., Furlong, E., Bielczyk, N., … Davla, S. (2021). Building and sustaining mentor interactions as a mentee. FEBS Journal. Wiley. https://doi.org/10.1111/febs.15823","ama":"Sarabipour S, Hainer SJ, Arslan FN, et al. Building and sustaining mentor interactions as a mentee. FEBS Journal. 2021. doi:10.1111/febs.15823","ieee":"S. Sarabipour et al., “Building and sustaining mentor interactions as a mentee,” FEBS Journal. Wiley, 2021.","short":"S. Sarabipour, S.J. Hainer, F.N. Arslan, C.M. De Winde, E. Furlong, N. Bielczyk, N.M. Jadavji, A.P. Shah, S. Davla, FEBS Journal (2021).","mla":"Sarabipour, Sarvenaz, et al. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal, Wiley, 2021, doi:10.1111/febs.15823.","ista":"Sarabipour S, Hainer SJ, Arslan FN, De Winde CM, Furlong E, Bielczyk N, Jadavji NM, Shah AP, Davla S. 2021. Building and sustaining mentor interactions as a mentee. FEBS Journal.","chicago":"Sarabipour, Sarvenaz, Sarah J. Hainer, Feyza N Arslan, Charlotte M. De Winde, Emily Furlong, Natalia Bielczyk, Nafisa M. Jadavji, Aparna P. Shah, and Sejal Davla. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal. Wiley, 2021. https://doi.org/10.1111/febs.15823."},"title":"Building and sustaining mentor interactions as a mentee","external_id":{"pmid":["33818917"],"isi":["000636678800001"]},"article_processing_charge":"No","author":[{"first_name":"Sarvenaz","last_name":"Sarabipour","full_name":"Sarabipour, Sarvenaz"},{"first_name":"Sarah J.","last_name":"Hainer","full_name":"Hainer, Sarah J."},{"last_name":"Arslan","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Winde, Charlotte M.","last_name":"De Winde","first_name":"Charlotte M."},{"last_name":"Furlong","full_name":"Furlong, Emily","first_name":"Emily"},{"full_name":"Bielczyk, Natalia","last_name":"Bielczyk","first_name":"Natalia"},{"full_name":"Jadavji, Nafisa M.","last_name":"Jadavji","first_name":"Nafisa M."},{"first_name":"Aparna P.","last_name":"Shah","full_name":"Shah, Aparna P."},{"first_name":"Sejal","last_name":"Davla","full_name":"Davla, Sejal"}]},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12368"}]},"volume":120,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Intercellular adhesion is the key to multicellularity, and its malfunction plays an important role in various developmental and disease-related processes. Although it has been intensively studied by both biologists and physicists, a commonly accepted definition of cell-cell adhesion is still being debated. Cell-cell adhesion has been described at the molecular scale as a function of adhesion receptors controlling binding affinity, at the cellular scale as resistance to detachment forces or modulation of surface tension, and at the tissue scale as a regulator of cellular rearrangements and morphogenesis. In this review, we aim to summarize and discuss recent advances in the molecular, cellular, and theoretical description of cell-cell adhesion, ranging from biomimetic models to the complexity of cells and tissues in an organismal context. In particular, we will focus on cadherin-mediated cell-cell adhesion and the role of adhesion signaling and mechanosensation therein, two processes central for understanding the biological and physical basis of cell-cell adhesion."}],"intvolume":" 120","month":"10","main_file_link":[{"open_access":"1","url":"https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view"}],"scopus_import":"1","date_updated":"2023-08-08T13:14:10Z","department":[{"_id":"CaHe"}],"_id":"9350","status":"public","type":"journal_article","article_type":"original","publication":"Biophysical Journal","day":"05","year":"2021","isi":1,"date_created":"2021-04-25T22:01:30Z","date_published":"2021-10-05T00:00:00Z","doi":"10.1016/j.bpj.2021.03.025","page":"4182-4192","acknowledgement":"T.S. acknowledges funding by the research program “The Active Matter Physics of Collective Metastasis,” which is financed by the Dutch Research Council (NWO).","oa":1,"publisher":"Biophysical Society","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together: when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192.","chicago":"Arslan, Feyza N, Julia Eckert, Thomas Schmidt, and Carl-Philipp J Heisenberg. “Holding It Together: When Cadherin Meets Cadherin.” Biophysical Journal. Biophysical Society, 2021. https://doi.org/10.1016/j.bpj.2021.03.025.","ieee":"F. N. Arslan, J. Eckert, T. Schmidt, and C.-P. J. Heisenberg, “Holding it together: when cadherin meets cadherin,” Biophysical Journal, vol. 120. Biophysical Society, pp. 4182–4192, 2021.","short":"F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal 120 (2021) 4182–4192.","apa":"Arslan, F. N., Eckert, J., Schmidt, T., & Heisenberg, C.-P. J. (2021). Holding it together: when cadherin meets cadherin. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2021.03.025","ama":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. Holding it together: when cadherin meets cadherin. Biophysical Journal. 2021;120:4182-4192. doi:10.1016/j.bpj.2021.03.025","mla":"Arslan, Feyza N., et al. “Holding It Together: When Cadherin Meets Cadherin.” Biophysical Journal, vol. 120, Biophysical Society, 2021, pp. 4182–92, doi:10.1016/j.bpj.2021.03.025."},"title":"Holding it together: when cadherin meets cadherin","article_processing_charge":"No","external_id":{"isi":["000704646900006"],"pmid":["33794149"]},"author":[{"first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","last_name":"Arslan"},{"full_name":"Eckert, Julia","last_name":"Eckert","first_name":"Julia"},{"full_name":"Schmidt, Thomas","last_name":"Schmidt","first_name":"Thomas"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}]},{"oa_version":"Preprint","abstract":[{"text":"We consider the stochastic quantization of a quartic double-well energy functional in the semiclassical regime and derive optimal asymptotics for the exponentially small splitting of the ground state energy. Our result provides an infinite-dimensional version of some sharp tunneling estimates known in finite dimensions for semiclassical Witten Laplacians in degree zero. From a stochastic point of view it proves that the L2 spectral gap of the stochastic one-dimensional Allen-Cahn equation in finite volume satisfies a Kramers-type formula in the limit of vanishing noise. We work with finite-dimensional lattice approximations and establish semiclassical estimates which are uniform in the dimension. Our key estimate shows that the constant separating the two exponentially small eigenvalues from the rest of the spectrum can be taken independently of the dimension.","lang":"eng"}],"intvolume":" 281","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.03187"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"volume":281,"issue":"3","_id":"9348","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-08T13:15:11Z","department":[{"_id":"RoSe"}],"acknowledgement":"GDG gratefully acknowledges the financial support of HIM Bonn in the framework of the 2019 Junior Trimester Programs “Kinetic Theory” and “Randomness, PDEs and Nonlinear Fluctuations” and the hospitality at the University of Rome La Sapienza during his frequent visits.","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Journal of Functional Analysis","day":"07","year":"2021","isi":1,"date_created":"2021-04-25T22:01:29Z","doi":"10.1016/j.jfa.2021.109029","date_published":"2021-04-07T00:00:00Z","article_number":"109029","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well Model in Infinite Dimension.” Journal of Functional Analysis, vol. 281, no. 3, 109029, Elsevier, 2021, doi:10.1016/j.jfa.2021.109029.","ieee":"M. Brooks and G. Di Gesù, “Sharp tunneling estimates for a double-well model in infinite dimension,” Journal of Functional Analysis, vol. 281, no. 3. Elsevier, 2021.","short":"M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021).","apa":"Brooks, M., & Di Gesù, G. (2021). Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109029","ama":"Brooks M, Di Gesù G. Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. 2021;281(3). doi:10.1016/j.jfa.2021.109029","chicago":"Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well Model in Infinite Dimension.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109029.","ista":"Brooks M, Di Gesù G. 2021. Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. 281(3), 109029."},"title":"Sharp tunneling estimates for a double-well model in infinite dimension","article_processing_charge":"No","external_id":{"arxiv":["1911.03187"],"isi":["000644702800005"]},"author":[{"last_name":"Brooks","orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris","first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"},{"first_name":"Giacomo","last_name":"Di Gesù","full_name":"Di Gesù, Giacomo"}]},{"issue":"2","volume":59,"publication_identifier":{"issn":["0036-1429"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.11646"}],"month":"03","intvolume":" 59","abstract":[{"text":"This paper provides an a priori error analysis of a localized orthogonal decomposition method for the numerical stochastic homogenization of a model random diffusion problem. If the uniformly elliptic and bounded random coefficient field of the model problem is stationary and satisfies a quantitative decorrelation assumption in the form of the spectral gap inequality, then the expected $L^2$ error of the method can be estimated, up to logarithmic factors, by $H+(\\varepsilon/H)^{d/2}$, $\\varepsilon$ being the small correlation length of the random coefficient and $H$ the width of the coarse finite element mesh that determines the spatial resolution. The proof bridges recent results of numerical homogenization and quantitative stochastic homogenization.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"JuFi"}],"date_updated":"2023-08-08T13:13:37Z","type":"journal_article","article_type":"original","status":"public","_id":"9352","page":"660-674","doi":"10.1137/19M1308992","date_published":"2021-03-09T00:00:00Z","date_created":"2021-04-25T22:01:31Z","isi":1,"year":"2021","day":"09","publication":"SIAM Journal on Numerical Analysis","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","oa":1,"acknowledgement":"This work was initiated while the authors enjoyed the kind hospitality of the Hausdorff Institute for Mathematics in Bonn during the trimester program Multiscale Problems: Algorithms, Numerical Analysis, and Computation. D. Peterseim would like to acknowledge the kind hospitality of the Erwin Schrödinger International Institute for Mathematics and Physics (ESI), where parts of this research were developed under the frame of the thematic program Numerical Analysis of Complex PDE Models in the Sciences.","author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"first_name":"Dietmar","last_name":"Gallistl","full_name":"Gallistl, Dietmar"},{"last_name":"Peterseim","full_name":"Peterseim, Dietmar","first_name":"Dietmar"}],"article_processing_charge":"No","external_id":{"arxiv":["1912.11646"],"isi":["000646030400003"]},"title":"A priori error analysis of a numerical stochastic homogenization method","citation":{"chicago":"Fischer, Julian L, Dietmar Gallistl, and Dietmar Peterseim. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/19M1308992.","ista":"Fischer JL, Gallistl D, Peterseim D. 2021. A priori error analysis of a numerical stochastic homogenization method. SIAM Journal on Numerical Analysis. 59(2), 660–674.","mla":"Fischer, Julian L., et al. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” SIAM Journal on Numerical Analysis, vol. 59, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 660–74, doi:10.1137/19M1308992.","ama":"Fischer JL, Gallistl D, Peterseim D. A priori error analysis of a numerical stochastic homogenization method. SIAM Journal on Numerical Analysis. 2021;59(2):660-674. doi:10.1137/19M1308992","apa":"Fischer, J. L., Gallistl, D., & Peterseim, D. (2021). A priori error analysis of a numerical stochastic homogenization method. SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1308992","short":"J.L. Fischer, D. Gallistl, D. Peterseim, SIAM Journal on Numerical Analysis 59 (2021) 660–674.","ieee":"J. L. Fischer, D. Gallistl, and D. Peterseim, “A priori error analysis of a numerical stochastic homogenization method,” SIAM Journal on Numerical Analysis, vol. 59, no. 2. Society for Industrial and Applied Mathematics, pp. 660–674, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"acknowledgement":"We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice, S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for help with statistical analysis.","date_published":"2021-04-01T00:00:00Z","doi":"10.1371/journal.pgen.1009479","date_created":"2021-05-02T22:01:29Z","page":"e1009479","day":"01","publication":"PLoS genetics","has_accepted_license":"1","isi":1,"year":"2021","title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","author":[{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571"},{"first_name":"Nikolas","last_name":"Furthmann","full_name":"Furthmann, Nikolas"},{"last_name":"Crossman","full_name":"Crossman, Samuel H.","first_name":"Samuel H."},{"full_name":"Tichy, Alexandra Madelaine","last_name":"Tichy","first_name":"Alexandra Madelaine"},{"first_name":"Nina","full_name":"Hoyer, Nina","last_name":"Hoyer"},{"first_name":"Meike","full_name":"Petersen, Meike","last_name":"Petersen"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Zheden, Vanessa","last_name":"Zheden"},{"id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Bicher","full_name":"Bicher, Julia"},{"last_name":"Gschaider-Reichhart","full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus"},{"first_name":"Peter","last_name":"Soba","full_name":"Soba, Peter"},{"first_name":"Konstanze F.","full_name":"Winklhofer, Konstanze F.","last_name":"Winklhofer"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000640606700001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M, Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 17(4), e1009479.","chicago":"Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS Genetics. Public Library of Science, 2021. https://doi.org/10.1371/journal.pgen.1009479.","ieee":"Á. Inglés Prieto et al., “Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease,” PLoS genetics, vol. 17, no. 4. Public Library of Science, p. e1009479, 2021.","short":"Á. Inglés Prieto, N. Furthmann, S.H. Crossman, A.M. Tichy, N. Hoyer, M. Petersen, V. Zheden, J. Bicher, E. Gschaider-Reichhart, A. György, D.E. Siekhaus, P. Soba, K.F. Winklhofer, H.L. Janovjak, PLoS Genetics 17 (2021) e1009479.","ama":"Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 2021;17(4):e1009479. doi:10.1371/journal.pgen.1009479","apa":"Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N., Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1009479","mla":"Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS Genetics, vol. 17, no. 4, Public Library of Science, 2021, p. e1009479, doi:10.1371/journal.pgen.1009479."},"month":"04","intvolume":" 17","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Optogenetics has been harnessed to shed new mechanistic light on current and future therapeutic strategies. This has been to date achieved by the regulation of ion flow and electrical signals in neuronal cells and neural circuits that are known to be affected by disease. In contrast, the optogenetic delivery of trophic biochemical signals, which support cell survival and are implicated in degenerative disorders, has never been demonstrated in an animal model of disease. Here, we reengineered the human and Drosophila melanogaster REarranged during Transfection (hRET and dRET) receptors to be activated by light, creating one-component optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation, these receptors robustly induced the MAPK/ERK proliferative signaling pathway in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD), light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results demonstrate that a light-activated receptor can ameliorate disease hallmarks in a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific and reversible and thus has the potential to inspire novel strategies towards a spatio-temporal regulation of tissue repair."}],"issue":"4","volume":17,"file":[{"date_created":"2021-05-04T09:05:27Z","file_name":"2021_PLOS_Ingles-Prieto.pdf","creator":"kschuh","date_updated":"2021-05-04T09:05:27Z","file_size":3072764,"file_id":"9369","checksum":"82a74668f863e8dfb22fdd4f845c92ce","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15537404"]},"publication_status":"published","status":"public","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)"},"_id":"9363","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"file_date_updated":"2021-05-04T09:05:27Z","ddc":["570"],"date_updated":"2023-08-08T13:17:47Z"},{"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"628622","title":"High rates of genome rearrangements and pathogenicity of Shigella spp","author":[{"full_name":"Seferbekova, Zaira","last_name":"Seferbekova","first_name":"Zaira"},{"first_name":"Alexey","full_name":"Zabelkin, Alexey","last_name":"Zabelkin"},{"full_name":"Yakovleva, Yulia","last_name":"Yakovleva","first_name":"Yulia"},{"first_name":"Robert","full_name":"Afasizhev, Robert","last_name":"Afasizhev"},{"full_name":"Dranenko, Natalia O.","last_name":"Dranenko","first_name":"Natalia O."},{"first_name":"Nikita","full_name":"Alexeev, Nikita","last_name":"Alexeev"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","last_name":"Bochkareva","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639"}],"external_id":{"isi":["000643713300001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.628622.","ista":"Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 12, 628622.","mla":"Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers in Microbiology, vol. 12, 628622, Frontiers, 2021, doi:10.3389/fmicb.2021.628622.","ama":"Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.628622","apa":"Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O., Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.628622","short":"Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N. Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).","ieee":"Z. Seferbekova et al., “High rates of genome rearrangements and pathogenicity of Shigella spp,” Frontiers in Microbiology, vol. 12. Frontiers, 2021."},"quality_controlled":"1","publisher":"Frontiers","oa":1,"acknowledgement":"We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos.","date_published":"2021-04-12T00:00:00Z","doi":"10.3389/fmicb.2021.628622","date_created":"2021-05-09T22:01:38Z","day":"12","publication":"Frontiers in Microbiology","isi":1,"has_accepted_license":"1","year":"2021","status":"public","article_type":"original","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)"},"_id":"9380","department":[{"_id":"FyKo"}],"file_date_updated":"2021-05-11T13:05:52Z","ddc":["570"],"date_updated":"2023-08-08T13:30:39Z","month":"04","intvolume":" 12","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands."}],"volume":12,"ec_funded":1,"file":[{"date_created":"2021-05-11T13:05:52Z","file_name":"2021_Frontiers_Microbiology_Seferbekova.pdf","creator":"kschuh","date_updated":"2021-05-11T13:05:52Z","file_size":14362316,"checksum":"2f856543add59273a482a7f326fc0400","file_id":"9384","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published"},{"project":[{"name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425"},{"_id":"26B96266-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Algebro-Geometric Applications of Factorization Homology","grant_number":"M02751"}],"citation":{"chicago":"Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” Geometry & Topology. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/gt.2021.25.813.","ista":"Ho QP. 2021. Homological stability and densities of generalized configuration spaces. Geometry & Topology. 25(2), 813–912.","mla":"Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” Geometry & Topology, vol. 25, no. 2, Mathematical Sciences Publishers, 2021, pp. 813–912, doi:10.2140/gt.2021.25.813.","apa":"Ho, Q. P. (2021). Homological stability and densities of generalized configuration spaces. Geometry & Topology. Mathematical Sciences Publishers. https://doi.org/10.2140/gt.2021.25.813","ama":"Ho QP. Homological stability and densities of generalized configuration spaces. Geometry & Topology. 2021;25(2):813-912. doi:10.2140/gt.2021.25.813","short":"Q.P. Ho, Geometry & Topology 25 (2021) 813–912.","ieee":"Q. P. Ho, “Homological stability and densities of generalized configuration spaces,” Geometry & Topology, vol. 25, no. 2. Mathematical Sciences Publishers, pp. 813–912, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Ho","full_name":"Ho, Quoc P","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Quoc P"}],"article_processing_charge":"No","external_id":{"arxiv":["1802.07948"],"isi":["000682738600005"]},"title":"Homological stability and densities of generalized configuration spaces","acknowledgement":"This paper owes an obvious intellectual debt to the illuminating treatments of factorization homology by J.\r\nFrancis, D. Gaitsgory, and J. Lurie in [GL,G1, FG]. The author would like to thank B. Farb and J. Wolfson for\r\nbringing the question of explaining coincidences in homological densities to his attention. Moreover, the author\r\nthanks J. Wolfson for many helpful conversations on the subject, O. Randal-Williams for many comments which\r\ngreatly help improve the exposition, and G. C. Drummond-Cole for many useful conversations on L∞-algebras.\r\nFinally, the author is grateful to the anonymous referee for carefully reading the manuscript and for providing\r\nnumerous comments which greatly helped improve the clarity and precision of the exposition.\r\nThis work is supported by the Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 of\r\nthe European Research Council and the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization\r\nHomology,” Austrian Science Fund (FWF): M 2751.","publisher":"Mathematical Sciences Publishers","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"27","publication":"Geometry & Topology","page":"813-912","date_published":"2021-04-27T00:00:00Z","doi":"10.2140/gt.2021.25.813","date_created":"2021-05-02T06:59:33Z","_id":"9359","article_type":"original","type":"journal_article","status":"public","keyword":["Generalized configuration spaces","homological stability","homological densities","chiral algebras","chiral homology","factorization algebras","Koszul duality","Ran space"],"date_updated":"2023-08-08T13:28:59Z","ddc":["514","516","512"],"file_date_updated":"2021-05-03T06:54:06Z","department":[{"_id":"TaHa"}],"abstract":[{"lang":"eng","text":"We prove that the factorization homologies of a scheme with coefficients in truncated polynomial algebras compute the cohomologies of its generalized configuration spaces. Using Koszul duality between commutative algebras and Lie algebras, we obtain new expressions for the cohomologies of the latter. As a consequence, we obtain a uniform and conceptual approach for treating homological stability, homological densities, and arithmetic densities of generalized configuration spaces. Our results categorify, generalize, and in fact provide a conceptual understanding of the coincidences appearing in the work of Farb--Wolfson--Wood. Our computation of the stable homological densities also yields rational homotopy types, answering a question posed by Vakil--Wood. Our approach hinges on the study of homological stability of cohomological Chevalley complexes, which is of independent interest.\r\n"}],"oa_version":"Submitted Version","month":"04","intvolume":" 25","publication_identifier":{"issn":["1364-0380"]},"publication_status":"published","file":[{"file_size":479268,"date_updated":"2021-05-03T06:54:06Z","creator":"qho","file_name":"densities.pdf","date_created":"2021-05-03T06:54:06Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"643a8d2d6f06f0888dcd7503f55d0920","file_id":"9366"}],"language":[{"iso":"eng"}],"issue":"2","volume":25,"ec_funded":1},{"date_updated":"2023-08-08T13:26:12Z","ddc":["570"],"department":[{"_id":"Bio"}],"file_date_updated":"2021-05-04T12:41:38Z","_id":"9361","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","publication_identifier":{"eissn":["23795042"]},"publication_status":"published","file":[{"date_created":"2021-05-04T12:41:38Z","file_name":"2021_mSphere_Gast.pdf","creator":"kschuh","date_updated":"2021-05-04T12:41:38Z","file_size":3379349,"file_id":"9370","checksum":"310748d140c8838335c1314431095898","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":6,"issue":"2","abstract":[{"text":"The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 6","citation":{"ista":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 6(2), e01024-20.","chicago":"Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” MSphere. American Society for Microbiology, 2021. https://doi.org/10.1128/mSphere.01024-20.","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","ieee":"M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein,” mSphere, vol. 6, no. 2. American Society for Microbiology, 2021.","ama":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 2021;6(2). doi:10.1128/mSphere.01024-20","apa":"Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., & Plattet, P. (2021). Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. MSphere. American Society for Microbiology. https://doi.org/10.1128/mSphere.01024-20","mla":"Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” MSphere, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:10.1128/mSphere.01024-20."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Matthieu","full_name":"Gast, Matthieu","last_name":"Gast"},{"full_name":"Kadzioch, Nicole P.","last_name":"Kadzioch","first_name":"Nicole P."},{"last_name":"Milius","full_name":"Milius, Doreen","id":"384050BC-F248-11E8-B48F-1D18A9856A87","first_name":"Doreen"},{"first_name":"Francesco","full_name":"Origgi, Francesco","last_name":"Origgi"},{"full_name":"Plattet, Philippe","last_name":"Plattet","first_name":"Philippe"}],"article_processing_charge":"No","external_id":{"pmid":["33853875"],"isi":["000663823400025"]},"title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","article_number":"e01024-20","has_accepted_license":"1","isi":1,"year":"2021","day":"14","publication":"mSphere","date_published":"2021-04-14T00:00:00Z","doi":"10.1128/mSphere.01024-20","date_created":"2021-05-02T22:01:28Z","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","quality_controlled":"1","publisher":"American Society for Microbiology","oa":1},{"_id":"9376","type":"journal_article","article_type":"original","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","keyword":["multistability","mechanism","computational design","rigidity"],"date_updated":"2023-08-08T13:31:38Z","ddc":["000"],"file_date_updated":"2021-12-17T08:13:51Z","department":[{"_id":"BeBi"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"text":"This paper presents a method for designing planar multistable compliant structures. Given a sequence of desired stable states and the corresponding poses of the structure, we identify the topology and geometric realization of a mechanism—consisting of bars and joints—that is able to physically reproduce the desired multistable behavior. In order to solve this problem efficiently, we build on insights from minimally rigid graph theory to identify simple but effective topologies for the mechanism. We then optimize its geometric parameters, such as joint positions and bar lengths, to obtain correct transitions between the given poses. Simultaneously, we ensure adequate stability of each pose based on an effective approximate error metric related to the elastic energy Hessian of the bars in the mechanism. As demonstrated by our results, we obtain functional multistable mechanisms of manageable complexity that can be fabricated using 3D printing. Further, we evaluated the effectiveness of our method on a large number of examples in the simulation and fabricated several physical prototypes.","lang":"eng"}],"oa_version":"Published Version","month":"10","intvolume":" 40","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"publication_status":"published","file":[{"file_id":"9377","checksum":"8564b3118457d4c8939a8ef2b1a2f16c","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Multistable-authorversion.pdf","date_created":"2021-05-08T17:36:59Z","file_size":18926557,"date_updated":"2021-05-08T17:36:59Z","creator":"bbickel"},{"checksum":"3b6e874e30bfa1bfc3ad3498710145a1","file_id":"9378","success":1,"access_level":"open_access","relation":"main_file","content_type":"video/mp4","date_created":"2021-05-08T17:38:22Z","file_name":"multistable-video.mp4","creator":"bbickel","date_updated":"2021-05-08T17:38:22Z","file_size":76542901},{"creator":"bbickel","date_updated":"2021-12-17T08:13:51Z","file_size":3367072,"date_created":"2021-12-17T08:13:51Z","title":"Supplementary Material for “Computational Design of Planar Multistable Compliant Structures”","file_name":"multistable-supplementary material.pdf","access_level":"open_access","relation":"supplementary_material","description":"This document provides additional results and analyzes the robustness and limitations of our approach.","content_type":"application/pdf","file_id":"10562","checksum":"20dc3bc42e1a912a5b0247c116772098"}],"language":[{"iso":"eng"}],"issue":"5","volume":40,"ec_funded":1,"article_number":"186","project":[{"grant_number":"642841","name":"Distributed 3D Object Design","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ista":"Zhang R, Auzinger T, Bickel B. 2021. Computational design of planar multistable compliant structures. ACM Transactions on Graphics. 40(5), 186.","chicago":"Zhang, Ran, Thomas Auzinger, and Bernd Bickel. “Computational Design of Planar Multistable Compliant Structures.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453477.","short":"R. Zhang, T. Auzinger, B. Bickel, ACM Transactions on Graphics 40 (2021).","ieee":"R. Zhang, T. Auzinger, and B. Bickel, “Computational design of planar multistable compliant structures,” ACM Transactions on Graphics, vol. 40, no. 5. Association for Computing Machinery, 2021.","ama":"Zhang R, Auzinger T, Bickel B. Computational design of planar multistable compliant structures. ACM Transactions on Graphics. 2021;40(5). doi:10.1145/3453477","apa":"Zhang, R., Auzinger, T., & Bickel, B. (2021). Computational design of planar multistable compliant structures. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3453477","mla":"Zhang, Ran, et al. “Computational Design of Planar Multistable Compliant Structures.” ACM Transactions on Graphics, vol. 40, no. 5, 186, Association for Computing Machinery, 2021, doi:10.1145/3453477."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran","last_name":"Zhang","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X"},{"full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","last_name":"Auzinger","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000752079300003"]},"title":"Computational design of planar multistable compliant structures","acknowledgement":"We would like to thank everyone who contributed to this paper, the authors of artworks for all the examples, including @macrovec-tor_official and Wikimedia for the FLAG semaphore, and @pikisuper-star for the FIGURINE. The photos of iconic poses in the teaser were supplied by (from left to right): Mike Hewitt/Olympics Day 8 - Athletics/Gettty Images, Oneinchpunch/Basketball player training on acourt in New york city/Shutterstock, and Andrew Redington/TigerWoods/Getty Images. We also want to express our gratitude to Christian Hafner for insightful discussions, the IST Austria machine shop SSU, all proof-readers, and anonymous reviewers. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"08","publication":"ACM Transactions on Graphics","date_published":"2021-10-08T00:00:00Z","doi":"10.1145/3453477","date_created":"2021-05-08T17:37:08Z"},{"publication":"PNAS","day":"21","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-05-07T17:10:21Z","date_published":"2021-06-21T00:00:00Z","doi":"10.1073/pnas.2015005118","acknowledgement":"We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 118(25), e2015005118.","chicago":"Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118.","short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, PNAS 118 (2021).","ieee":"J. I. Meier et al., “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings of the National Academy of Sciences, 2021.","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2015005118","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118","mla":"Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118."},"title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","article_processing_charge":"No","external_id":{"isi":["000671755600001"],"pmid":["34155138"]},"author":[{"last_name":"Meier","full_name":"Meier, Joana I.","first_name":"Joana I."},{"first_name":"Patricio A.","full_name":"Salazar, Patricio A.","last_name":"Salazar"},{"full_name":"Kučka, Marek","last_name":"Kučka","first_name":"Marek"},{"full_name":"Davies, Robert William","last_name":"Davies","first_name":"Robert William"},{"full_name":"Dréau, Andreea","last_name":"Dréau","first_name":"Andreea"},{"first_name":"Ismael","last_name":"Aldás","full_name":"Aldás, Ismael"},{"first_name":"Olivia Box","last_name":"Power","full_name":"Power, Olivia Box"},{"first_name":"Nicola J.","full_name":"Nadeau, Nicola J.","last_name":"Nadeau"},{"first_name":"Jon R.","last_name":"Bridle","full_name":"Bridle, Jon R."},{"last_name":"Rolian","full_name":"Rolian, Campbell","first_name":"Campbell"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"last_name":"McMillan","full_name":"McMillan, W. Owen","first_name":"W. Owen"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"article_number":"e2015005118","language":[{"iso":"eng"}],"file":[{"file_id":"10835","checksum":"cb30c6166b2132ee60d616b31a1a7c29","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-03-08T08:18:16Z","file_name":"2021_PNAS_Meier.pdf","creator":"dernst","date_updated":"2022-03-08T08:18:16Z","file_size":20592929}],"publication_status":"published","publication_identifier":{"eissn":["0027-8424"]},"issue":"25","volume":118,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations."}],"intvolume":" 118","month":"06","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-08T13:33:09Z","file_date_updated":"2022-03-08T08:18:16Z","department":[{"_id":"NiBa"}],"_id":"9375","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original"},{"file_date_updated":"2021-10-15T08:26:02Z","department":[{"_id":"NiBa"}],"date_updated":"2023-08-08T13:34:08Z","ddc":["570"],"article_type":"original","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","_id":"9394","related_material":{"record":[{"id":"12987","status":"public","relation":"research_data"}]},"issue":"3","volume":5,"ec_funded":1,"publication_identifier":{"eissn":["2056-3744"]},"publication_status":"published","file":[{"checksum":"023b1608e311f0fda30593ba3d0a4e0b","file_id":"10142","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-10-15T08:26:02Z","file_name":"2021_EvolutionLetters_Koch.pdf","creator":"cchlebak","date_updated":"2021-10-15T08:26:02Z","file_size":3021108}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 5","abstract":[{"lang":"eng","text":"Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow."}],"oa_version":"Published Version","author":[{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"last_name":"Morales","full_name":"Morales, Hernán E.","first_name":"Hernán E."},{"last_name":"Larsson","full_name":"Larsson, Jenny","first_name":"Jenny"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"full_name":"Lemmon, E. Moriarty","last_name":"Lemmon","first_name":"E. Moriarty"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"external_id":{"isi":["000647846200001"]},"article_processing_charge":"No","title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","citation":{"ista":"Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213.","chicago":"Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters. Wiley, 2021. https://doi.org/10.1002/evl3.227.","ieee":"E. L. Koch et al., “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” Evolution Letters, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","short":"E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213.","apa":"Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.227","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 2021;5(3):196-213. doi:10.1002/evl3.227","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"page":"196-213","doi":"10.1002/evl3.227","date_published":"2021-05-07T00:00:00Z","date_created":"2021-05-16T22:01:47Z","has_accepted_license":"1","isi":1,"year":"2021","day":"07","publication":"Evolution Letters","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We are very grateful to Irena Senčić for technical assistance and to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for assistance with data collection. RKB was funded by the Natural Environment Research Council and by the European Research Council. KJ was funded by the Swedish Research Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie Grant agreement no. 797747. RF was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie Grant agreement No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE and by National Funds through FCT—Foundation for Science and Technology within the scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628). We are grateful to other members of the Littorina research group for helpful discussions. We thank Claire Mérot and an anonymous referee for insightful comments on an earlier version. "},{"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","article_type":"original","status":"public","_id":"9381","file_date_updated":"2021-05-11T13:50:06Z","department":[{"_id":"KrCh"}],"date_updated":"2023-08-08T13:31:08Z","ddc":["000"],"scopus_import":"1","intvolume":" 17","month":"04","abstract":[{"lang":"eng","text":"A game of rock-paper-scissors is an interesting example of an interaction where none of the pure strategies strictly dominates all others, leading to a cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors dynamics and allow individuals to make behavioural mistakes during the strategy execution. We show that such an assumption can break a cyclic relationship leading to a stable equilibrium emerging with only one strategy surviving. We consider two cases: completely random mistakes when individuals have no bias towards any strategy and a general form of mistakes. Then, we determine conditions for a strategy to dominate all other strategies. However, given that individuals who adopt a dominating strategy are still prone to behavioural mistakes in the observed behaviour, we may still observe extinct strategies. That is, behavioural mistakes in strategy execution stabilise evolutionary dynamics leading to an evolutionary stable and, potentially, mixed co-existence equilibrium."}],"oa_version":"Published Version","ec_funded":1,"volume":17,"issue":"4","publication_status":"published","publication_identifier":{"eissn":["15537358"],"issn":["1553734X"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9385","checksum":"a94ebe0c4116f5047eaa6029e54d2dac","success":1,"creator":"kschuh","date_updated":"2021-05-11T13:50:06Z","file_size":1323820,"date_created":"2021-05-11T13:50:06Z","file_name":"2021_pcbi_Kleshnina.pdf"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"article_number":"e1008523","article_processing_charge":"No","external_id":{"isi":["000639711200001"]},"author":[{"first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina","full_name":"Kleshnina, Maria"},{"full_name":"Streipert, Sabrina S.","last_name":"Streipert","first_name":"Sabrina S."},{"full_name":"Filar, Jerzy A.","last_name":"Filar","first_name":"Jerzy A."},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"title":"Mistakes can stabilise the dynamics of rock-paper-scissors games","citation":{"ama":"Kleshnina M, Streipert SS, Filar JA, Chatterjee K. Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. 2021;17(4). doi:10.1371/journal.pcbi.1008523","apa":"Kleshnina, M., Streipert, S. S., Filar, J. A., & Chatterjee, K. (2021). Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008523","ieee":"M. Kleshnina, S. S. Streipert, J. A. Filar, and K. Chatterjee, “Mistakes can stabilise the dynamics of rock-paper-scissors games,” PLoS Computational Biology, vol. 17, no. 4. Public Library of Science, 2021.","short":"M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational Biology 17 (2021).","mla":"Kleshnina, Maria, et al. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” PLoS Computational Biology, vol. 17, no. 4, e1008523, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008523.","ista":"Kleshnina M, Streipert SS, Filar JA, Chatterjee K. 2021. Mistakes can stabilise the dynamics of rock-paper-scissors games. PLoS Computational Biology. 17(4), e1008523.","chicago":"Kleshnina, Maria, Sabrina S. Streipert, Jerzy A. Filar, and Krishnendu Chatterjee. “Mistakes Can Stabilise the Dynamics of Rock-Paper-Scissors Games.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008523."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","acknowledgement":"Authors would like to thank Christian Hilbe and Martin Nowak for their inspiring and very helpful feedback on the manuscript.","date_created":"2021-05-09T22:01:38Z","date_published":"2021-04-01T00:00:00Z","doi":"10.1371/journal.pcbi.1008523","year":"2021","has_accepted_license":"1","isi":1,"publication":"PLoS Computational Biology","day":"01"},{"issue":"9","volume":31,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["09609822"],"eissn":["18790445"]},"publication_status":"published","month":"05","intvolume":" 31","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not."}],"department":[{"_id":"NiBa"}],"date_updated":"2023-08-08T13:34:38Z","status":"public","type":"journal_article","article_type":"original","_id":"9392","doi":"10.1016/j.cub.2021.03.060","date_published":"2021-05-10T00:00:00Z","date_created":"2021-05-16T22:01:46Z","page":"R428-R429","day":"10","publication":"Current Biology","isi":1,"year":"2021","publisher":"Cell Press","quality_controlled":"1","oa":1,"acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","title":"Quantifying the use of species concepts","author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"article_processing_charge":"No","external_id":{"pmid":["33974865"],"isi":["000654741200004"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060.","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. Current Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060","apa":"Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429."}},{"title":"Two linked loci under mutation-selection balance and Muller’s ratchet","article_processing_charge":"No","external_id":{"isi":["000659161500002"]},"author":[{"last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia"},{"first_name":"Tatiana Yu.","full_name":"Neretina, Tatiana Yu.","last_name":"Neretina"},{"first_name":"Alexey S.","full_name":"Kondrashov, Alexey S.","last_name":"Kondrashov"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.","chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology. Elsevier , 2021. https://doi.org/10.1016/j.jtbi.2021.110729.","short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021).","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” Journal of Theoretical Biology, vol. 524. Elsevier , 2021.","ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524. doi:10.1016/j.jtbi.2021.110729","apa":"Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729","mla":"Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology, vol. 524, 110729, Elsevier , 2021, doi:10.1016/j.jtbi.2021.110729."},"article_number":"110729","date_created":"2021-05-12T05:58:42Z","doi":"10.1016/j.jtbi.2021.110729","date_published":"2021-04-24T00:00:00Z","publication":"Journal of Theoretical Biology","day":"24","year":"2021","isi":1,"oa":1,"publisher":"Elsevier ","quality_controlled":"1","acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","department":[{"_id":"GradSch"}],"date_updated":"2023-08-08T13:32:40Z","keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"status":"public","article_type":"original","type":"journal_article","_id":"9387","volume":524,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-5193"]},"intvolume":" 524","month":"04","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/477489v1","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift."}]},{"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","_id":"12987","title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"first_name":"Eva","last_name":"Koch","full_name":"Koch, Eva"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"last_name":"Larsson","full_name":"Larsson, Jenny","first_name":"Jenny"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"last_name":"Lemmon","full_name":"Lemmon, Alan R.","first_name":"Alan R."},{"full_name":"Lemmon, E. Moriarty","last_name":"Lemmon","first_name":"E. Moriarty"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.","ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4","apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4","short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021).","ieee":"E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","mla":"Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4."},"date_updated":"2023-08-08T13:34:07Z","month":"04","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.zgmsbccb4","open_access":"1"}],"publisher":"Dryad","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome."}],"date_created":"2023-05-16T12:34:09Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","doi":"10.5061/DRYAD.ZGMSBCCB4","date_published":"2021-04-10T00:00:00Z","related_material":{"record":[{"id":"9394","status":"public","relation":"used_in_publication"}]},"day":"10","year":"2021","has_accepted_license":"1"},{"acknowledgement":"The authors would like to thank anonymous reviewers for their constructive comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao are supported by Fundamental Research Funds for the Central Universities. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant agreement No 715767).","oa":1,"quality_controlled":"1","publisher":"IEEE","year":"2021","isi":1,"has_accepted_license":"1","publication":"IEEE Transactions on Visualization and Computer Graphics","day":"01","date_created":"2021-05-23T22:01:42Z","doi":"10.1109/TVCG.2019.2957218","date_published":"2021-06-01T00:00:00Z","article_number":"2881-2895","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021).","ieee":"X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021.","ama":"Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218","apa":"Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021). Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218","mla":"Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:10.1109/TVCG.2019.2957218.","ista":"Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 27(6), 2881–2895.","chicago":"Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["31804937"],"isi":["000649620700009"]},"article_processing_charge":"No","author":[{"first_name":"Xudong","last_name":"Feng","full_name":"Feng, Xudong"},{"last_name":"Liu","full_name":"Liu, Jiafeng","first_name":"Jiafeng"},{"first_name":"Huamin","last_name":"Wang","full_name":"Wang, Huamin"},{"first_name":"Yin","last_name":"Yang","full_name":"Yang, Yin"},{"last_name":"Bao","full_name":"Bao, Hujun","first_name":"Hujun"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Weiwei","full_name":"Xu, Weiwei","last_name":"Xu"}],"title":"Computational design of skinned Quad-Robots","abstract":[{"text":"We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 27","month":"06","publication_status":"published","publication_identifier":{"issn":["19410506"],"eissn":["10772626"]},"language":[{"iso":"eng"}],"file":[{"checksum":"a78e6ac94e33ade4ffaea66943d5f7dc","file_id":"9427","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-05-25T15:08:49Z","file_name":"2021_TVCG_Feng.pdf","date_updated":"2021-05-25T15:08:49Z","file_size":6183002,"creator":"kschuh"}],"ec_funded":1,"volume":27,"issue":"6","_id":"9408","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","date_updated":"2023-08-08T13:45:46Z","ddc":["000"],"file_date_updated":"2021-05-25T15:08:49Z","department":[{"_id":"BeBi"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021.","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913.","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913."},"title":"Adaptation at different points along antibiotic concentration gradients","external_id":{"isi":["000651501400001"],"pmid":[" 33975485"]},"article_processing_charge":"No","author":[{"last_name":"Lagator","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"last_name":"Uecker","full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"}],"article_number":"20200913","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication":"Biology letters","day":"12","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-05-23T22:01:43Z","date_published":"2021-05-12T00:00:00Z","doi":"10.1098/rsbl.2020.0913","acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","oa":1,"quality_controlled":"1","publisher":"Royal Society of London","ddc":["570"],"date_updated":"2023-08-08T13:44:35Z","file_date_updated":"2021-05-25T14:09:03Z","department":[{"_id":"NiBa"}],"_id":"9410","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","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"9c13c1f5af7609c97c741f11d293188a","file_id":"9425","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_BiologyLetters_Lagator.pdf","date_created":"2021-05-25T14:09:03Z","creator":"kschuh","file_size":726759,"date_updated":"2021-05-25T14:09:03Z"}],"publication_status":"published","publication_identifier":{"eissn":["1744957X"]},"ec_funded":1,"issue":"5","volume":17,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.","lang":"eng"}],"intvolume":" 17","month":"05","scopus_import":"1"},{"_id":"9412","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","date_updated":"2023-08-08T13:39:19Z","ddc":["510"],"department":[{"_id":"LaEr"}],"file_date_updated":"2021-05-25T13:24:19Z","abstract":[{"lang":"eng","text":"We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 26","month":"03","publication_status":"published","publication_identifier":{"eissn":["10836489"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9423","checksum":"864ab003ad4cffea783f65aa8c2ba69f","success":1,"date_updated":"2021-05-25T13:24:19Z","file_size":865148,"creator":"kschuh","date_created":"2021-05-25T13:24:19Z","file_name":"2021_EJP_Cipolloni.pdf"}],"ec_funded":1,"volume":26,"article_number":"24","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24.","mla":"Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” Electronic Journal of Probability, vol. 26. Institute of Mathematical Statistics, 2021.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021).","ama":"Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 2021;26. doi:10.1214/21-EJP591","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2002.02438"],"isi":["000641855600001"]},"article_processing_charge":"No","author":[{"last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"}],"title":"Fluctuation around the circular law for random matrices with real entries","oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","year":"2021","isi":1,"has_accepted_license":"1","publication":"Electronic Journal of Probability","day":"23","date_created":"2021-05-23T22:01:44Z","date_published":"2021-03-23T00:00:00Z","doi":"10.1214/21-EJP591"},{"doi":"10.1038/s41467-021-22725-9","date_published":"2021-05-10T00:00:00Z","date_created":"2021-05-23T22:01:42Z","day":"10","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2021","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"The authors thank Malte Schröder for valuable discussions and creating the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion. The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster of Excellence Physics of Life of TU Dresden.","title":"Discontinuous epidemic transition due to limited testing","author":[{"last_name":"Scarselli","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"last_name":"Timme","full_name":"Timme, Marc","first_name":"Marc"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"article_processing_charge":"No","external_id":{"isi":["000687305500044"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586.","chicago":"Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-22725-9.","ieee":"D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic transition due to limited testing,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).","apa":"Scarselli, D., Budanur, N. B., Timme, M., & Hof, B. (2021). Discontinuous epidemic transition due to limited testing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-22725-9","ama":"Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition due to limited testing. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22725-9","mla":"Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications, vol. 12, no. 1, 2586, Springer Nature, 2021, doi:10.1038/s41467-021-22725-9."},"article_number":"2586","volume":12,"issue":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/smashing-the-covid-curve/","relation":"press_release","description":"News on IST Homepage"}]},"file":[{"creator":"kschuh","file_size":1176573,"date_updated":"2021-05-25T14:18:40Z","file_name":"2021_NatureCommunications_Scarselli.pdf","date_created":"2021-05-25T14:18:40Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9426","checksum":"fe26c1b8a7da1ae07a6c03f80ff06ea1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","month":"05","intvolume":" 12","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"High impact epidemics constitute one of the largest threats humanity is facing in the 21st century. In the absence of pharmaceutical interventions, physical distancing together with testing, contact tracing and quarantining are crucial in slowing down epidemic dynamics. Yet, here we show that if testing capacities are limited, containment may fail dramatically because such combined countermeasures drastically change the rules of the epidemic transition: Instead of continuous, the response to countermeasures becomes discontinuous. Rather than following the conventional exponential growth, the outbreak that is initially strongly suppressed eventually accelerates and scales faster than exponential during an explosive growth period. As a consequence, containment measures either suffice to stop the outbreak at low total case numbers or fail catastrophically if marginally too weak, thus implying large uncertainties in reliably estimating overall epidemic dynamics, both during initial phases and during second wave scenarios."}],"file_date_updated":"2021-05-25T14:18:40Z","department":[{"_id":"BjHo"}],"ddc":["570"],"date_updated":"2023-08-08T13:45:13Z","status":"public","article_type":"original","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)"},"_id":"9407"},{"abstract":[{"lang":"eng","text":"The dynamics of a triangular magnetocapillary swimmer is studied using the lattice Boltzmann method. We extend on our previous work, which deals with the self-assembly and a specific type of the swimmer motion characterized by the swimmer’s maximum velocity centred around the particle’s inverse viscous time. Here, we identify additional regimes of motion. First, modifying the ratio of surface tension and magnetic forces allows to study the swimmer propagation in the regime of significantly lower frequencies mainly defined by the strength of the magnetocapillary potential. Second, introducing a constant magnetic contribution in each of the particles in addition to their magnetic moment induced by external fields leads to another regime characterized by strong in-plane swimmer reorientations that resemble experimental observations."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 44","month":"04","publication_status":"published","publication_identifier":{"issn":["12928941"],"eissn":["1292895X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-05-25T11:32:14Z","file_size":2507870,"creator":"kschuh","date_created":"2021-05-25T11:32:14Z","file_name":"2021_EPJE_Sukhov.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0ef342d011afbe3c5cb058fda9a3f395","file_id":"9422","success":1}],"issue":"4","volume":44,"_id":"9411","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","date_updated":"2023-08-08T13:36:28Z","ddc":["530"],"file_date_updated":"2021-05-25T11:32:14Z","department":[{"_id":"ScWa"}],"acknowledgement":"This work was financially supported by the DFG Priority Programme SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA 4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing time.","oa":1,"quality_controlled":"1","publisher":"Springer","year":"2021","isi":1,"has_accepted_license":"1","publication":"European Physical Journal E","day":"24","date_created":"2021-05-23T22:01:44Z","doi":"10.1140/epje/s10189-021-00065-2","date_published":"2021-04-24T00:00:00Z","article_number":"59","citation":{"ista":"Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 44(4), 59.","chicago":"Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2.","apa":"Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2","ama":"Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2","ieee":"A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,” European Physical Journal E, vol. 44, no. 4. Springer, 2021.","short":"A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard, N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021).","mla":"Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000643251300001"]},"author":[{"last_name":"Sukhov","full_name":"Sukhov, Alexander","first_name":"Alexander"},{"first_name":"Maxime","last_name":"Hubert","full_name":"Hubert, Maxime"},{"last_name":"Grosjean","orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M"},{"last_name":"Trosman","full_name":"Trosman, Oleg","first_name":"Oleg"},{"first_name":"Sebastian","full_name":"Ziegler, Sebastian","last_name":"Ziegler"},{"first_name":"Ylona","last_name":"Collard","full_name":"Collard, Ylona"},{"first_name":"Nicolas","last_name":"Vandewalle","full_name":"Vandewalle, Nicolas"},{"first_name":"Ana Sunčana","full_name":"Smith, Ana Sunčana","last_name":"Smith"},{"first_name":"Jens","full_name":"Harting, Jens","last_name":"Harting"}],"title":"Regimes of motion of magnetocapillary swimmers"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1059-1524"],"eissn":["1939-4586"]},"license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","ec_funded":1,"volume":32,"issue":"9","oa_version":"Published Version","abstract":[{"text":"Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.","lang":"eng"}],"intvolume":" 32","month":"04","main_file_link":[{"url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723","open_access":"1"}],"scopus_import":"1","date_updated":"2023-08-08T13:36:02Z","department":[{"_id":"MaLo"}],"_id":"9414","status":"public","tmp":{"short":"CC BY-NC-SA (3.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)"},"type":"journal_article","article_type":"original","publication":"Molecular Biology of the Cell","day":"19","year":"2021","isi":1,"date_created":"2021-05-23T22:01:45Z","doi":"10.1091/MBC.E20-11-0723","date_published":"2021-04-19T00:00:00Z","page":"869-879","acknowledgement":"The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753.","oa":1,"quality_controlled":"1","publisher":"American Society for Cell Biology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.","ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879. doi:10.1091/MBC.E20-11-0723","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723","ieee":"K. Ishihara et al., “Spatial variation of microtubule depolymerization in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","short":"K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose, J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.","chicago":"Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.","ista":"Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 32(9), 869–879."},"title":"Spatial variation of microtubule depolymerization in large asters","article_processing_charge":"No","external_id":{"isi":["000641574700005"]},"author":[{"last_name":"Ishihara","full_name":"Ishihara, Keisuke","first_name":"Keisuke"},{"last_name":"Decker","full_name":"Decker, Franziska","first_name":"Franziska"},{"first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R"},{"last_name":"Pelletier","full_name":"Pelletier, James F.","first_name":"James F."},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Brugués, Jan","last_name":"Brugués","first_name":"Jan"},{"first_name":"Timothy J.","last_name":"Mitchison","full_name":"Mitchison, Timothy J."}],"project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}]},{"month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace's unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision.","lang":"eng"}],"file":[{"creator":"esarac","date_updated":"2021-06-16T08:23:54Z","file_size":641990,"date_created":"2021-06-16T08:23:54Z","file_name":"qam.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9557","checksum":"6e4cba3f72775f479c5b1b75d1a4a0c4","success":1}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"conference","conference":{"name":"LICS: Symposium on Logic in Computer Science","start_date":"2021-06-29","end_date":"2021-07-02","location":"Online"},"_id":"9356","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2021-06-16T08:23:54Z","ddc":["000"],"date_updated":"2023-08-08T13:52:56Z","quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","oa":1,"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","date_published":"2021-06-29T00:00:00Z","doi":"10.1109/LICS52264.2021.9470547","date_created":"2021-04-30T17:30:47Z","day":"29","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","isi":1,"has_accepted_license":"1","year":"2021","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"9470547","title":"Quantitative and approximate monitoring","author":[{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"article_processing_charge":"No","external_id":{"arxiv":["2105.08353"],"isi":["000947350400021"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 9470547, Institute of Electrical and Electronics Engineers, 2021, doi:10.1109/LICS52264.2021.9470547.","ieee":"T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Online, 2021.","short":"T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021.","apa":"Henzinger, T. A., & Sarac, N. E. (2021). Quantitative and approximate monitoring. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Online: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470547","ama":"Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021. doi:10.1109/LICS52264.2021.9470547","chicago":"Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470547.","ista":"Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 9470547."}},{"date_updated":"2023-08-08T13:51:14Z","department":[{"_id":"GaTk"}],"_id":"9439","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"publication_status":"published","volume":24,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks."}],"month":"05","intvolume":" 24","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/669200 ","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009.","chicago":"Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.","apa":"Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0","ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.","short":"W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.","mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0."},"title":"Efficient and adaptive sensory codes","author":[{"first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski"},{"last_name":"Hermundstad","full_name":"Hermundstad, Ann M.","first_name":"Ann M."}],"external_id":{"isi":["000652577300003"]},"article_processing_charge":"No","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"day":"20","publication":"Nature Neuroscience","isi":1,"year":"2021","doi":"10.1038/s41593-021-00846-0","date_published":"2021-05-20T00:00:00Z","date_created":"2021-05-30T22:01:24Z","page":"998-1009","acknowledgement":"We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"page":"2431-2453","date_created":"2021-06-02T13:13:58Z","date_published":"2021-07-01T00:00:00Z","doi":"10.1093/plcell/koab122","year":"2021","has_accepted_license":"1","isi":1,"publication":"Plant Cell","day":"01","oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","acknowledgement":"We would also like to thank Lothar Willmitzer for the lipidomic analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany). We thank Manuela Vega from SCI for her technical assistance in image analysis. We thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1 clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga, Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom (Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1 construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University). We thank Plan Propio from the University of Málaga for financial support.\r\nFunding","external_id":{"isi":["000703938100026"],"pmid":["33944955"]},"article_processing_charge":"No","author":[{"first_name":"N","full_name":"Ruiz-Lopez, N","last_name":"Ruiz-Lopez"},{"first_name":"J","last_name":"Pérez-Sancho","full_name":"Pérez-Sancho, J"},{"full_name":"Esteban Del Valle, A","last_name":"Esteban Del Valle","first_name":"A"},{"first_name":"RP","full_name":"Haslam, RP","last_name":"Haslam"},{"first_name":"S","last_name":"Vanneste","full_name":"Vanneste, S"},{"first_name":"R","last_name":"Catalá","full_name":"Catalá, R"},{"first_name":"C","full_name":"Perea-Resa, C","last_name":"Perea-Resa"},{"first_name":"D","last_name":"Van Damme","full_name":"Van Damme, D"},{"full_name":"García-Hernández, S","last_name":"García-Hernández","first_name":"S"},{"last_name":"Albert","full_name":"Albert, A","first_name":"A"},{"first_name":"J","full_name":"Vallarino, J","last_name":"Vallarino"},{"first_name":"J","last_name":"Lin","full_name":"Lin, J"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Macho","full_name":"Macho, AP","first_name":"AP"},{"first_name":"J","last_name":"Salinas","full_name":"Salinas, J"},{"last_name":"Rosado","full_name":"Rosado, A","first_name":"A"},{"first_name":"JA","full_name":"Napier, JA","last_name":"Napier"},{"first_name":"V","last_name":"Amorim-Silva","full_name":"Amorim-Silva, V"},{"first_name":"MA","last_name":"Botella","full_name":"Botella, MA"}],"title":"Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress","citation":{"mla":"Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:10.1093/plcell/koab122.","ama":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122","apa":"Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste, S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122","short":"N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste, R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino, J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva, M. Botella, Plant Cell 33 (2021) 2431–2453.","ieee":"N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021.","chicago":"Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste, R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.","ista":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J, Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ec_funded":1,"volume":33,"issue":"7","publication_status":"published","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-10-14T13:36:38Z","file_name":"2021_PlantCell_RuizLopez.pdf","creator":"cchlebak","date_updated":"2021-10-14T13:36:38Z","file_size":2952028,"file_id":"10141","checksum":"22d596678d00310d793611864a6d0fcd","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 33","month":"07","abstract":[{"text":"Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"JiFr"}],"file_date_updated":"2021-10-14T13:36:38Z","date_updated":"2023-08-08T13:54:32Z","ddc":["580"],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","_id":"9443"},{"file_date_updated":"2021-06-09T15:21:14Z","department":[{"_id":"FlSc"}],"ddc":["570"],"date_updated":"2023-08-08T13:53:53Z","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"type":"journal_article","article_type":"original","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)"},"_id":"9431","volume":12,"issue":"1","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","relation":"press_release"}]},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9538","checksum":"53ccc53d09a9111143839dbe7784e663","success":1,"date_updated":"2021-06-09T15:21:14Z","file_size":6166295,"creator":"kschuh","date_created":"2021-06-09T15:21:14Z","file_name":"2021_NatureCommunications_Obr.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","month":"05","intvolume":" 12","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","author":[{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin","last_name":"Obr"},{"last_name":"Ricana","full_name":"Ricana, Clifton L.","first_name":"Clifton L."},{"last_name":"Nikulin","full_name":"Nikulin, Nadia","first_name":"Nadia"},{"last_name":"Feathers","full_name":"Feathers, Jon-Philip R.","first_name":"Jon-Philip R."},{"full_name":"Klanschnig, Marco","last_name":"Klanschnig","first_name":"Marco"},{"first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","full_name":"Thader, Andreas","last_name":"Thader"},{"first_name":"Marc C.","full_name":"Johnson, Marc C.","last_name":"Johnson"},{"last_name":"Vogt","full_name":"Vogt, Volker M.","first_name":"Volker M."},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"},{"first_name":"Robert A.","full_name":"Dick, Robert A.","last_name":"Dick"}],"external_id":{"isi":["000659145000011"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).","ieee":"M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021.","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0"},"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"article_number":"3226","date_published":"2021-05-28T00:00:00Z","doi":"10.1038/s41467-021-23506-0","date_created":"2021-05-28T14:25:50Z","day":"28","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2021","quality_controlled":"1","publisher":"Nature Research","oa":1,"acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF)."},{"date_created":"2021-06-06T22:01:30Z","doi":"10.1017/jfm.2021.371","date_published":"2021-07-25T00:00:00Z","publication":"Journal of Fluid Mechanics","day":"25","year":"2021","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","acknowledgement":"The anonymous referees are kindly acknowledged for their useful suggestions andcomments.","title":"Suppression of turbulence and travelling waves in a vertical heated pipe","external_id":{"isi":["000653785000001"],"arxiv":["2008.13486"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena","full_name":"Marensi, Elena","last_name":"Marensi"},{"first_name":"Shuisheng","full_name":"He, Shuisheng","last_name":"He"},{"last_name":"Willis","full_name":"Willis, Ashley P.","first_name":"Ashley P."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17.","chicago":"Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371.","ieee":"E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919. Cambridge University Press, 2021.","short":"E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021).","ama":"Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371","apa":"Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.371","mla":"Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge University Press, 2021, doi:10.1017/jfm.2021.371."},"article_number":"A17","volume":919,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9766","checksum":"867ad077e45c181c2c5ec1311ba27c41","file_size":4087358,"date_updated":"2021-08-03T09:53:28Z","creator":"kschuh","file_name":"2021_JournalFluidMechanics_Marensi.pdf","date_created":"2021-08-03T09:53:28Z"}],"publication_status":"published","publication_identifier":{"eissn":["14697645"],"issn":["00221120"]},"intvolume":" 919","month":"07","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy forces. As the suppression of turbulence leads to severe heat transfer deterioration, this is an important and undesirable phenomenon in both heating and cooling applications. Vertical flow is often considered, as the axial buoyancy force can help drive the flow. With heating measured by the buoyancy parameter 𝐶, our direct numerical simulations show that shear-driven turbulence may either be completely laminarised or it transitions to a relatively quiescent convection-driven state. Buoyancy forces cause a flattening of the base flow profile, which in isothermal pipe flow has recently been linked to complete suppression of turbulence (Kühnen et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol. 863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch travelling-wave solution analysed here, which is believed to mediate transition to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy. A linear instability of the laminar base flow is responsible for the appearance of the relatively quiescent convection driven state for 𝐶≳4 across the range of Reynolds numbers considered. In the suppression of turbulence, however, i.e. in the transition from turbulence, we find clearer association with the analysis of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical systems approach, which describes better the transition to turbulence. The laminarisation criterion He et al. propose, based on an apparent Reynolds number of the flow as measured by its driving pressure gradient, is found to capture the critical 𝐶=𝐶𝑐𝑟(𝑅𝑒) above which the flow will be laminarised or switch to the convection-driven type. Our analysis suggests that it is the weakened rolls, rather than the streaks, which appear to be critical for laminarisation."}],"file_date_updated":"2021-08-03T09:53:28Z","department":[{"_id":"BjHo"}],"ddc":["530"],"date_updated":"2023-08-08T13:58:41Z","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)"},"type":"journal_article","article_type":"original","_id":"9467"},{"_id":"9470","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-08-08T13:59:18Z","ddc":["570"],"file_date_updated":"2021-06-11T15:34:53Z","department":[{"_id":"NiBa"}],"abstract":[{"text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 30","month":"06","publication_status":"published","publication_identifier":{"issn":["09621083"],"eissn":["1365294X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"e6f4731365bde2614b333040a08265d8","file_id":"9545","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_MolecularEcology_Berdan.pdf","date_created":"2021-06-11T15:34:53Z","file_size":1031978,"date_updated":"2021-06-11T15:34:53Z","creator":"kschuh"}],"ec_funded":1,"issue":"12","volume":30,"project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.","chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936","mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000652056400001"]},"article_processing_charge":"No","author":[{"full_name":"Berdan, Emma L.","last_name":"Berdan","first_name":"Emma L."},{"first_name":"Alexandre","full_name":"Blanckaert, Alexandre","last_name":"Blanckaert"},{"last_name":"Slotte","full_name":"Slotte, Tanja","first_name":"Tanja"},{"full_name":"Suh, Alexander","last_name":"Suh","first_name":"Alexander"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fragata, Inês","last_name":"Fragata","first_name":"Inês"}],"title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018).","oa":1,"publisher":"Wiley","quality_controlled":"1","year":"2021","isi":1,"has_accepted_license":"1","publication":"Molecular Ecology","day":"01","page":"2710-2723","date_created":"2021-06-06T22:01:31Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1111/mec.15936"},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2001.06053","open_access":"1"}],"month":"05","intvolume":" 35","abstract":[{"text":"Motivated by the successful application of geometry to proving the Harary--Hill conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical” drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$ connecting pairs of vertices. Such a drawing has three properties: (1) every edge $e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$ has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$ at most once, in either a crossing or an end of $e$. We use properties (1)--(3) to define a pseudospherical drawing of $G$. Our main result is that for the complete graph, properties (1)--(3) are equivalent to the same three properties but with “precisely two crossings” in (2) replaced by “at most two crossings.” The proof requires a result in the geometric transversal theory of arrangements of pseudocircles. This is proved using the surprising result that the absence of special arcs (coherent spirals) in an arrangement of simple closed curves characterizes the fact that any two curves in the arrangement have at most two crossings. Our studies provide the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles crossing twice.\r\n","lang":"eng"}],"oa_version":"Preprint","volume":35,"issue":"2","ec_funded":1,"publication_identifier":{"issn":["08954801"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"9468","department":[{"_id":"UlWa"}],"date_updated":"2023-08-08T13:58:12Z","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"page":"1050-1076","doi":"10.1137/20M1313234","date_published":"2021-05-20T00:00:00Z","date_created":"2021-06-06T22:01:30Z","isi":1,"year":"2021","day":"20","publication":"SIAM Journal on Discrete Mathematics","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M"},{"last_name":"Richter","full_name":"Richter, R. Bruce","first_name":"R. Bruce"},{"first_name":"Matthew","last_name":"Sunohara","full_name":"Sunohara, Matthew"}],"external_id":{"arxiv":["2001.06053"],"isi":["000674142200022"]},"article_processing_charge":"No","title":"Extending drawings of complete graphs into arrangements of pseudocircles","citation":{"mla":"Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics, vol. 35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76, doi:10.1137/20M1313234.","ama":"Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 2021;35(2):1050-1076. doi:10.1137/20M1313234","apa":"Arroyo Guevara, A. M., Richter, R. B., & Sunohara, M. (2021). Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1313234","ieee":"A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings of complete graphs into arrangements of pseudocircles,” SIAM Journal on Discrete Mathematics, vol. 35, no. 2. Society for Industrial and Applied Mathematics, pp. 1050–1076, 2021.","short":"A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete Mathematics 35 (2021) 1050–1076.","chicago":"Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/20M1313234.","ista":"Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 35(2), 1050–1076."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"title":"Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons","external_id":{"arxiv":["2009.00992"],"isi":["000656508600008"]},"article_processing_charge":"No","author":[{"last_name":"Deuchert","full_name":"Deuchert, Andreas","first_name":"Andreas"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096.","ista":"Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6), 109096.","mla":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096.","ieee":"A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons,” Journal of Functional Analysis, vol. 281, no. 6. Elsevier, 2021.","short":"A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).","apa":"Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096","ama":"Deuchert A, Seiringer R. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 2021;281(6). doi:10.1016/j.jfa.2021.109096"},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"article_number":"109096","date_created":"2021-06-06T22:01:28Z","date_published":"2021-09-15T00:00:00Z","doi":"10.1016/j.jfa.2021.109096","publication":"Journal of Functional Analysis","day":"15","year":"2021","isi":1,"oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.","department":[{"_id":"RoSe"}],"date_updated":"2023-08-08T13:56:27Z","status":"public","article_type":"original","type":"journal_article","_id":"9462","ec_funded":1,"volume":281,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"intvolume":" 281","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.00992"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We consider a system of N trapped bosons with repulsive interactions in a combined semiclassical mean-field limit at positive temperature. We show that the free energy is well approximated by the minimum of the Hartree free energy functional – a natural extension of the Hartree energy functional to positive temperatures. The Hartree free energy functional converges in the same limit to a semiclassical free energy functional, and we show that the system displays Bose–Einstein condensation if and only if it occurs in the semiclassical free energy functional. This allows us to show that for weak coupling the critical temperature decreases due to the repulsive interactions.","lang":"eng"}]},{"year":"2021","isi":1,"publication":"Optimization Methods and Software","day":"12","date_created":"2021-06-06T22:01:30Z","doi":"10.1080/10556788.2021.1924715","date_published":"2021-05-12T00:00:00Z","acknowledgement":"The authors are grateful to the anonymous referees and the handling Editor for their insightful comments which have improved the earlier version of the manuscript greatly. The second author is grateful to the University of Hafr Al Batin. The last author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","publisher":"Taylor and Francis","quality_controlled":"1","citation":{"mla":"Iyiola, Olaniyi S., et al. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” Optimization Methods and Software, Taylor and Francis, 2021, doi:10.1080/10556788.2021.1924715.","ieee":"O. S. Iyiola, C. D. Enyi, and Y. Shehu, “Reflected three-operator splitting method for monotone inclusion problem,” Optimization Methods and Software. Taylor and Francis, 2021.","short":"O.S. Iyiola, C.D. Enyi, Y. Shehu, Optimization Methods and Software (2021).","apa":"Iyiola, O. S., Enyi, C. D., & Shehu, Y. (2021). Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software. Taylor and Francis. https://doi.org/10.1080/10556788.2021.1924715","ama":"Iyiola OS, Enyi CD, Shehu Y. Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software. 2021. doi:10.1080/10556788.2021.1924715","chicago":"Iyiola, Olaniyi S., Cyril D. Enyi, and Yekini Shehu. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” Optimization Methods and Software. Taylor and Francis, 2021. https://doi.org/10.1080/10556788.2021.1924715.","ista":"Iyiola OS, Enyi CD, Shehu Y. 2021. Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000650507600001"]},"author":[{"first_name":"Olaniyi S.","last_name":"Iyiola","full_name":"Iyiola, Olaniyi S."},{"last_name":"Enyi","full_name":"Enyi, Cyril D.","first_name":"Cyril D."},{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu"}],"title":"Reflected three-operator splitting method for monotone inclusion problem","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","publication_identifier":{"eissn":["1029-4937"],"issn":["1055-6788"]},"language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"In this paper, we consider reflected three-operator splitting methods for monotone inclusion problems in real Hilbert spaces. To do this, we first obtain weak convergence analysis and nonasymptotic O(1/n) convergence rate of the reflected Krasnosel'skiĭ-Mann iteration for finding a fixed point of nonexpansive mapping in real Hilbert spaces under some seemingly easy to implement conditions on the iterative parameters. We then apply our results to three-operator splitting for the monotone inclusion problem and consequently obtain the corresponding convergence analysis. Furthermore, we derive reflected primal-dual algorithms for highly structured monotone inclusion problems. Some numerical implementations are drawn from splitting methods to support the theoretical analysis.","lang":"eng"}],"oa_version":"None","scopus_import":"1","month":"05","date_updated":"2023-08-08T13:57:43Z","department":[{"_id":"VlKo"}],"_id":"9469","type":"journal_article","article_type":"original","status":"public"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23854-x","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","ieee":"M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:10.1038/s41467-021-23854-x."},"title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","external_id":{"pmid":["34108481"],"isi":["000664874700014"]},"article_processing_charge":"No","author":[{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ingrid","full_name":"Rössler, Ingrid","last_name":"Rössler"},{"last_name":"Klein","full_name":"Klein, Isabella","first_name":"Isabella"},{"first_name":"Christina","last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina"},{"first_name":"Gertrude","full_name":"Zisser, Gertrude","last_name":"Zisser"},{"first_name":"Christian C.","full_name":"Gruber, Christian C.","last_name":"Gruber"},{"full_name":"Gruber, Karl","last_name":"Gruber","first_name":"Karl"},{"first_name":"David","last_name":"Haselbach","full_name":"Haselbach, David"},{"first_name":"Helmut","full_name":"Bergler, Helmut","last_name":"Bergler"}],"article_number":"3483","publication":"Nature Communications","day":"09","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-06-10T14:57:45Z","doi":"10.1038/s41467-021-23854-x","date_published":"2021-06-09T00:00:00Z","acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","ddc":["570"],"date_updated":"2023-08-08T14:05:26Z","file_date_updated":"2021-06-15T18:55:59Z","department":[{"_id":"EM-Fac"}],"_id":"9540","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"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","language":[{"iso":"eng"}],"file":[{"file_size":3397292,"date_updated":"2021-06-15T18:55:59Z","creator":"cziletti","file_name":"2021_NatureComm_Prattes.pdf","date_created":"2021-06-15T18:55:59Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"40fc24c1310930990b52a8ad1142ee97","file_id":"9556"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"issue":"1","volume":12,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"intvolume":" 12","month":"06"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-021-03613-0"}],"scopus_import":"1","intvolume":" 594","month":"06","abstract":[{"lang":"eng","text":"AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning1. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties. "}],"pmid":1,"oa_version":"Published Version","volume":594,"publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"9549","department":[{"_id":"PeJo"}],"date_updated":"2023-08-08T13:59:51Z","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank members of the Greger laboratory, B. Herguedas, J. Krieger and J.-N. Dohrke for comments on the manuscript; J. Krieger and J.-N. Dohrke for discussion, J. Krieger for help with the normal mode analysis, B. Köhegyi for help with cryo-EM imaging, V. Chang and K. Suzuki for helping to generate the CNIH2-1D4-HA stable cell line, M. Carvalho for assistance at early stages of this project, the LMB scientific computing and the cryo-EM facility for support, P. Emsley for help with model building, T. Nakane for helpful comments with RELION 3.1 and R. Warshamanage for helping with EMDA cryo-EM-map processing. We acknowledge the Diamond Light Source for access and support of the Cryo-EM facilities at the UK national electron bio10 imaging centre (eBIC), proposal EM17434, funded by the Wellcome Trust, MRC and BBSRC. This work was supported by grants from the Medical Research Council, as part of United Kingdom Research and Innovation (also known as UK Research and Innovation) (MC_U105174197) and BBSRC (BB/N002113/1) to I.H.G.","page":"454-458","date_created":"2021-06-13T22:01:33Z","date_published":"2021-06-02T00:00:00Z","doi":"10.1038/s41586-021-03613-0","year":"2021","isi":1,"publication":"Nature","day":"02","external_id":{"isi":["000657238100003"],"pmid":["34079129"]},"article_processing_charge":"No","author":[{"first_name":"Danyang","last_name":"Zhang","full_name":"Zhang, Danyang"},{"first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"last_name":"Matthews","full_name":"Matthews, Peter M.","first_name":"Peter M."},{"last_name":"Cais","full_name":"Cais, Ondrej","first_name":"Ondrej"},{"last_name":"Greger","full_name":"Greger, Ingo H.","first_name":"Ingo H."}],"title":"Gating and modulation of a hetero-octameric AMPA glutamate receptor","citation":{"mla":"Zhang, Danyang, et al. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature, vol. 594, Springer Nature, 2021, pp. 454–58, doi:10.1038/s41586-021-03613-0.","ieee":"D. Zhang, J. Watson, P. M. Matthews, O. Cais, and I. H. Greger, “Gating and modulation of a hetero-octameric AMPA glutamate receptor,” Nature, vol. 594. Springer Nature, pp. 454–458, 2021.","short":"D. Zhang, J. Watson, P.M. Matthews, O. Cais, I.H. Greger, Nature 594 (2021) 454–458.","ama":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 2021;594:454-458. doi:10.1038/s41586-021-03613-0","apa":"Zhang, D., Watson, J., Matthews, P. M., Cais, O., & Greger, I. H. (2021). Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03613-0","chicago":"Zhang, Danyang, Jake Watson, Peter M. Matthews, Ondrej Cais, and Ingo H. Greger. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03613-0.","ista":"Zhang D, Watson J, Matthews PM, Cais O, Greger IH. 2021. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 594, 454–458."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","acknowledgement":"The first author is supported in part by Hong Kong RGC Grant GRF 16301519 and NSFC 11871425. The second author is supported in part by ERC Advanced Grant RANMAT 338804. The third author is supported in part by Swedish Research Council Grant VR-2017-05195 and the Knut and Alice Wallenberg Foundation","date_created":"2021-06-13T22:01:33Z","doi":"10.1017/fms.2021.38","date_published":"2021-05-27T00:00:00Z","publication":"Forum of Mathematics, Sigma","day":"27","year":"2021","isi":1,"has_accepted_license":"1","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"article_number":"e44","title":"Equipartition principle for Wigner matrices","article_processing_charge":"No","external_id":{"arxiv":["2008.07061"],"isi":["000654960800001"]},"author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"last_name":"Schnelli","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Bao Z, Erdös L, Schnelli K. 2021. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 9, e44.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2021. https://doi.org/10.1017/fms.2021.38.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021.","short":"Z. Bao, L. Erdös, K. Schnelli, Forum of Mathematics, Sigma 9 (2021).","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2021). Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2021.38","ama":"Bao Z, Erdös L, Schnelli K. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.38","mla":"Bao, Zhigang, et al. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 9, e44, Cambridge University Press, 2021, doi:10.1017/fms.2021.38."},"intvolume":" 9","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We prove that the energy of any eigenvector of a sum of several independent large Wigner matrices is equally distributed among these matrices with very high precision. This shows a particularly strong microcanonical form of the equipartition principle for quantum systems whose components are modelled by Wigner matrices. ","lang":"eng"}],"ec_funded":1,"volume":9,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"9555","checksum":"47c986578de132200d41e6d391905519","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_ForumMath_Bao.pdf","date_created":"2021-06-15T14:40:45Z","file_size":483458,"date_updated":"2021-06-15T14:40:45Z","creator":"cziletti"}],"publication_status":"published","publication_identifier":{"eissn":["20505094"]},"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":"9550","department":[{"_id":"LaEr"}],"file_date_updated":"2021-06-15T14:40:45Z","ddc":["510"],"date_updated":"2023-08-08T14:03:40Z"},{"publication_status":"published","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"language":[{"iso":"eng"}],"volume":103,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13080"}]},"issue":"23","abstract":[{"lang":"eng","text":"We present conductance-matrix measurements in long, three-terminal hybrid superconductor-semiconductor nanowires, and compare with theoretical predictions of a magnetic-field-driven, topological quantum phase transition. By examining the nonlocal conductance, we identify the closure of the excitation gap in the bulk of the semiconductor before the emergence of zero-bias peaks, ruling out spurious gap-closure signatures from localized states. We observe that after the gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends, inconsistent with a simple picture of clean topological superconductivity."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2006.01275","open_access":"1"}],"scopus_import":"1","intvolume":" 103","month":"06","date_updated":"2023-08-08T14:08:08Z","department":[{"_id":"AnHi"}],"_id":"9570","type":"journal_article","article_type":"original","status":"public","year":"2021","isi":1,"publication":"Physical Review B","day":"15","date_created":"2021-06-20T22:01:33Z","doi":"10.1103/PhysRevB.103.235201","date_published":"2021-06-15T00:00:00Z","acknowledgement":"We acknowledge insightful discussions with K. Flensberg, E. B. Hansen, T. Karzig, R. Lutchyn, D. Pikulin, E. Prada, and R. Aguado. This work was supported by Microsoft Project Q and the Danmarks Grundforskningsfond. C.M.M. acknowledges support from the Villum Fonden. A.P.H. and L.C. contributed equally to this work.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","citation":{"short":"D. Puglia, E.A. Martinez, G.C. Ménard, A. Pöschl, S. Gronin, G.C. Gardner, R. Kallaher, M.J. Manfra, C.M. Marcus, A.P. Higginbotham, L. Casparis, Physical Review B 103 (2021).","ieee":"D. Puglia et al., “Closing of the induced gap in a hybrid superconductor-semiconductor nanowire,” Physical Review B, vol. 103, no. 23. American Physical Society, 2021.","ama":"Puglia D, Martinez EA, Ménard GC, et al. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 2021;103(23). doi:10.1103/PhysRevB.103.235201","apa":"Puglia, D., Martinez, E. A., Ménard, G. C., Pöschl, A., Gronin, S., Gardner, G. C., … Casparis, L. (2021). Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.103.235201","mla":"Puglia, Denise, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Physical Review B, vol. 103, no. 23, 235201, American Physical Society, 2021, doi:10.1103/PhysRevB.103.235201.","ista":"Puglia D, Martinez EA, Ménard GC, Pöschl A, Gronin S, Gardner GC, Kallaher R, Manfra MJ, Marcus CM, Higginbotham AP, Casparis L. 2021. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 103(23), 235201.","chicago":"Puglia, Denise, E. A. Martinez, G. C. Ménard, A. Pöschl, S. Gronin, G. C. Gardner, R. Kallaher, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.103.235201."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2006.01275"],"isi":["000661512500002"]},"article_processing_charge":"No","author":[{"first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","last_name":"Puglia","full_name":"Puglia, Denise"},{"full_name":"Martinez, E. A.","last_name":"Martinez","first_name":"E. A."},{"first_name":"G. C.","last_name":"Ménard","full_name":"Ménard, G. C."},{"full_name":"Pöschl, A.","last_name":"Pöschl","first_name":"A."},{"first_name":"S.","full_name":"Gronin, S.","last_name":"Gronin"},{"last_name":"Gardner","full_name":"Gardner, G. C.","first_name":"G. C."},{"first_name":"R.","full_name":"Kallaher, R.","last_name":"Kallaher"},{"full_name":"Manfra, M. J.","last_name":"Manfra","first_name":"M. J."},{"full_name":"Marcus, C. M.","last_name":"Marcus","first_name":"C. M."},{"last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Casparis, L.","last_name":"Casparis","first_name":"L."}],"title":"Closing of the induced gap in a hybrid superconductor-semiconductor nanowire","article_number":"235201"},{"author":[{"last_name":"Ivanov","full_name":"Ivanov, Grigory","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"last_name":"Tsiutsiurupa","full_name":"Tsiutsiurupa, Igor","first_name":"Igor"}],"external_id":{"arxiv":["2008.09543"],"isi":["000656507500001"]},"article_processing_charge":"No","title":"Functional Löwner ellipsoids","citation":{"mla":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis, vol. 31, Springer, 2021, pp. 11493–528, doi:10.1007/s12220-021-00691-4.","short":"G. Ivanov, I. Tsiutsiurupa, Journal of Geometric Analysis 31 (2021) 11493–11528.","ieee":"G. Ivanov and I. Tsiutsiurupa, “Functional Löwner ellipsoids,” Journal of Geometric Analysis, vol. 31. Springer, pp. 11493–11528, 2021.","apa":"Ivanov, G., & Tsiutsiurupa, I. (2021). Functional Löwner ellipsoids. Journal of Geometric Analysis. Springer. https://doi.org/10.1007/s12220-021-00691-4","ama":"Ivanov G, Tsiutsiurupa I. Functional Löwner ellipsoids. Journal of Geometric Analysis. 2021;31:11493-11528. doi:10.1007/s12220-021-00691-4","chicago":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis. Springer, 2021. https://doi.org/10.1007/s12220-021-00691-4.","ista":"Ivanov G, Tsiutsiurupa I. 2021. Functional Löwner ellipsoids. Journal of Geometric Analysis. 31, 11493–11528."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"11493-11528","date_published":"2021-05-31T00:00:00Z","doi":"10.1007/s12220-021-00691-4","date_created":"2021-06-13T22:01:32Z","isi":1,"year":"2021","day":"31","publication":"Journal of Geometric Analysis","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"The authors acknowledge the support of the grant of the Russian Government N 075-15-2019-1926.","department":[{"_id":"UlWa"}],"date_updated":"2023-08-08T14:04:49Z","type":"journal_article","article_type":"original","status":"public","_id":"9548","volume":31,"publication_identifier":{"eissn":["1559-002X"],"issn":["1050-6926"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.09543"}],"month":"05","intvolume":" 31","abstract":[{"text":"We extend the notion of the minimal volume ellipsoid containing a convex body in Rd to the setting of logarithmically concave functions. We consider a vast class of logarithmically concave functions whose superlevel sets are concentric ellipsoids. For a fixed function from this class, we consider the set of all its “affine” positions. For any log-concave function f on Rd, we consider functions belonging to this set of “affine” positions, and find the one with the minimal integral under the condition that it is pointwise greater than or equal to f. We study the properties of existence and uniqueness of the solution to this problem. For any s∈[0,+∞), we consider the construction dual to the recently defined John s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint: arXiv:2006.09934, 2020). We prove that such a construction determines a unique function and call it the Löwner s-function of f. We study the Löwner s-functions as s tends to zero and to infinity. Finally, extending the notion of the outer volume ratio, we define the outer integral ratio of a log-concave function and give an asymptotically tight bound on it.","lang":"eng"}],"oa_version":"Preprint"},{"year":"2021","day":"09","date_created":"2023-05-23T17:11:28Z","doi":"10.5281/ZENODO.4592435","related_material":{"link":[{"relation":"software","url":"https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3"}],"record":[{"relation":"used_in_publication","id":"9570","status":"public"}]},"date_published":"2021-03-09T00:00:00Z","abstract":[{"text":"Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the raw data for these extended datasets as well.","lang":"eng"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4592460","open_access":"1"}],"publisher":"Zenodo","month":"03","citation":{"mla":"Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435.","apa":"Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G., … Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435","ama":"Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435","ieee":"D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021.","short":"D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher, M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021).","chicago":"Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435.","ista":"Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R, Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435."},"date_updated":"2023-08-08T14:08:07Z","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise","last_name":"Puglia","full_name":"Puglia, Denise"},{"full_name":"Martinez, Esteban","last_name":"Martinez","first_name":"Esteban"},{"first_name":"Gerbold","last_name":"Menard","full_name":"Menard, Gerbold"},{"first_name":"Andreas","last_name":"Pöschl","full_name":"Pöschl, Andreas"},{"last_name":"Gronin","full_name":"Gronin, Sergei","first_name":"Sergei"},{"first_name":"Geoffrey","last_name":"Gardner","full_name":"Gardner, Geoffrey"},{"first_name":"Ray","last_name":"Kallaher","full_name":"Kallaher, Ray"},{"first_name":"Michael","last_name":"Manfra","full_name":"Manfra, Michael"},{"full_name":"Marcus, Charles","last_name":"Marcus","first_name":"Charles"},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham"},{"first_name":"Lucas","last_name":"Casparis","full_name":"Casparis, Lucas"}],"title":"Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire","department":[{"_id":"AnHi"}],"_id":"13080","type":"research_data_reference","status":"public"},{"day":"18","publication":"RSC Advances","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-06-18T00:00:00Z","doi":"10.1039/d1ra03428f","date_created":"2021-06-19T07:27:45Z","page":"21702-21715","acknowledgement":"The research is funded by Higher Education Commission (HEC) Pakistan under start-up research grant program (SRGP) Project no. 2454.","publisher":"Royal Society of Chemistry","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Dar MS, Akram KB, Sohail A, Arif F, Zabihi F, Yang S, Munir S, Zhu M, Abid M, Nauman M. 2021. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 11(35), 21702–21715.","chicago":"Dar, M. S., Khush Bakhat Akram, Ayesha Sohail, Fatima Arif, Fatemeh Zabihi, Shengyuan Yang, Shamsa Munir, Meifang Zhu, M. Abid, and Muhammad Nauman. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1ra03428f.","apa":"Dar, M. S., Akram, K. B., Sohail, A., Arif, F., Zabihi, F., Yang, S., … Nauman, M. (2021). Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. Royal Society of Chemistry. https://doi.org/10.1039/d1ra03428f","ama":"Dar MS, Akram KB, Sohail A, et al. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 2021;11(35):21702-21715. doi:10.1039/d1ra03428f","ieee":"M. S. Dar et al., “Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling,” RSC Advances, vol. 11, no. 35. Royal Society of Chemistry, pp. 21702–21715, 2021.","short":"M.S. Dar, K.B. Akram, A. Sohail, F. Arif, F. Zabihi, S. Yang, S. Munir, M. Zhu, M. Abid, M. Nauman, RSC Advances 11 (2021) 21702–21715.","mla":"Dar, M. S., et al. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances, vol. 11, no. 35, Royal Society of Chemistry, 2021, pp. 21702–15, doi:10.1039/d1ra03428f."},"title":"Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling","author":[{"last_name":"Dar","full_name":"Dar, M. S.","first_name":"M. S."},{"first_name":"Khush Bakhat","full_name":"Akram, Khush Bakhat","last_name":"Akram"},{"last_name":"Sohail","full_name":"Sohail, Ayesha","first_name":"Ayesha"},{"last_name":"Arif","full_name":"Arif, Fatima","first_name":"Fatima"},{"full_name":"Zabihi, Fatemeh","last_name":"Zabihi","first_name":"Fatemeh"},{"last_name":"Yang","full_name":"Yang, Shengyuan","first_name":"Shengyuan"},{"full_name":"Munir, Shamsa","last_name":"Munir","first_name":"Shamsa"},{"full_name":"Zhu, Meifang","last_name":"Zhu","first_name":"Meifang"},{"first_name":"M.","last_name":"Abid","full_name":"Abid, M."},{"id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad","orcid":"0000-0002-2111-4846","full_name":"Nauman, Muhammad","last_name":"Nauman"}],"article_processing_charge":"No","external_id":{"isi":["000665644000048"]},"file":[{"creator":"asandaue","file_size":2114557,"date_updated":"2021-06-23T13:09:34Z","file_name":"2021_RSCAdvances_Dar.pdf","date_created":"2021-06-23T13:09:34Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"cd582d67ace7151078e46b3a896871a9","file_id":"9596"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2046-2069"]},"publication_status":"published","volume":11,"issue":"35","license":"https://creativecommons.org/licenses/by/3.0/","oa_version":"Published Version","abstract":[{"text":"We report the synthesis and characterization of graphene functionalized with iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia application. We adopted the wet chemical procedure, using various contents of Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids. The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface combined with their biocompatibility and high thermal conductivity make them an excellent material for magnetic hyperthermia. The morphological and magnetic properties of the nanohybrids were studied using scanning electron microscopy (SEM) and a vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength 9.1 mT for studying their hyperthermic performance. The localized antitumor effects were investigated with artificial neural network modeling. A neural net time-series model was developed for the assessment of the best nanohybrid composition to serve the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with External Input (NARX) models were obtained, one for each of the components. The assessment of the accuracy of the predicted results has been done on the basis of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training phase i.e., 0.44703, which is where the model achieved optimal results after 71 epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications in low dosage with the highest specific absorption rate (SAR) and mean squared error values.","lang":"eng"}],"month":"06","intvolume":" 11","ddc":["540"],"date_updated":"2023-08-08T14:23:21Z","department":[{"_id":"KiMo"}],"file_date_updated":"2021-06-23T13:09:34Z","_id":"9569","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"}},{"date_created":"2021-06-16T15:45:36Z","date_published":"2021-06-18T00:00:00Z","doi":"10.1103/PhysRevLett.126.244502","publication":"Physical Review Letters","day":"18","year":"2021","isi":1,"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster.","title":"Coarse graining the state space of a turbulent flow using periodic orbits","external_id":{"isi":["000663310100008"],"arxiv":["2007.02584"]},"article_processing_charge":"No","author":[{"first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"},{"last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Yalniz, G., Hof, B., & Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.126.244502","ama":"Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 2021;126(24). doi:10.1103/PhysRevLett.126.244502","ieee":"G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” Physical Review Letters, vol. 126, no. 24. American Physical Society, 2021.","short":"G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).","mla":"Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:10.1103/PhysRevLett.126.244502.","ista":"Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502.","chicago":"Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.244502."},"project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"article_number":"244502","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/turbulent-flow-simplified/"}]},"issue":"24","volume":126,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"intvolume":" 126","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.02584"}],"oa_version":"Preprint","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"date_updated":"2023-08-08T14:08:36Z","status":"public","article_type":"letter_note","type":"journal_article","_id":"9558"},{"date_updated":"2023-08-10T13:36:50Z","ddc":["570"],"department":[{"_id":"PreCl"}],"file_date_updated":"2021-06-28T11:35:30Z","_id":"9607","type":"journal_article","article_type":"original","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","publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","file":[{"date_created":"2021-06-28T11:35:30Z","file_name":"2021_ELife_Bespalov.pdf","creator":"asandaue","date_updated":"2021-06-28T11:35:30Z","file_size":2500720,"file_id":"9609","checksum":"885b746051a7a6b6e24e3d2781a48fde","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":10,"abstract":[{"lang":"eng","text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"05","intvolume":" 10","citation":{"ieee":"A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.63294","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. eLife. 2021;10. doi:10.7554/eLife.63294","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294.","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Bespalov","full_name":"Bespalov, Anton","first_name":"Anton"},{"full_name":"Bernard, René","last_name":"Bernard","first_name":"René"},{"last_name":"Gilis","full_name":"Gilis, Anja","first_name":"Anja"},{"first_name":"Björn","last_name":"Gerlach","full_name":"Gerlach, Björn"},{"first_name":"Javier","full_name":"Guillén, Javier","last_name":"Guillén"},{"first_name":"Vincent","last_name":"Castagné","full_name":"Castagné, Vincent"},{"last_name":"Lefevre","full_name":"Lefevre, Isabel A.","first_name":"Isabel A."},{"first_name":"Fiona","full_name":"Ducrey, Fiona","last_name":"Ducrey"},{"full_name":"Monk, Lee","last_name":"Monk","first_name":"Lee"},{"first_name":"Sandrine","last_name":"Bongiovanni","full_name":"Bongiovanni, Sandrine"},{"first_name":"Bruce","last_name":"Altevogt","full_name":"Altevogt, Bruce"},{"first_name":"María","last_name":"Arroyo-Araujo","full_name":"Arroyo-Araujo, María"},{"first_name":"Lior","full_name":"Bikovski, Lior","last_name":"Bikovski"},{"first_name":"Natasja","full_name":"De Bruin, Natasja","last_name":"De Bruin"},{"first_name":"Esmeralda","full_name":"Castaños-Vélez, Esmeralda","last_name":"Castaños-Vélez"},{"first_name":"Alexander","last_name":"Dityatev","full_name":"Dityatev, Alexander"},{"first_name":"Christoph H.","full_name":"Emmerich, Christoph H.","last_name":"Emmerich"},{"last_name":"Fares","full_name":"Fares, Raafat","first_name":"Raafat"},{"first_name":"Chantelle","last_name":"Ferland-Beckham","full_name":"Ferland-Beckham, Chantelle"},{"first_name":"Christelle","full_name":"Froger-Colléaux, Christelle","last_name":"Froger-Colléaux"},{"first_name":"Valerie","full_name":"Gailus-Durner, Valerie","last_name":"Gailus-Durner"},{"full_name":"Hölter, Sabine M.","last_name":"Hölter","first_name":"Sabine M."},{"first_name":"Martine Cj","last_name":"Hofmann","full_name":"Hofmann, Martine Cj"},{"first_name":"Patricia","full_name":"Kabitzke, Patricia","last_name":"Kabitzke"},{"first_name":"Martien Jh","last_name":"Kas","full_name":"Kas, Martien Jh"},{"first_name":"Claudia","full_name":"Kurreck, Claudia","last_name":"Kurreck"},{"full_name":"Moser, Paul","last_name":"Moser","first_name":"Paul"},{"first_name":"Malgorzata","full_name":"Pietraszek, Malgorzata","last_name":"Pietraszek"},{"first_name":"Piotr","last_name":"Popik","full_name":"Popik, Piotr"},{"first_name":"Heidrun","full_name":"Potschka, Heidrun","last_name":"Potschka"},{"last_name":"Prado Montes De Oca","full_name":"Prado Montes De Oca, Ernesto","first_name":"Ernesto"},{"last_name":"Restivo","full_name":"Restivo, Leonardo","first_name":"Leonardo"},{"first_name":"Gernot","full_name":"Riedel, Gernot","last_name":"Riedel"},{"full_name":"Ritskes-Hoitinga, Merel","last_name":"Ritskes-Hoitinga","first_name":"Merel"},{"full_name":"Samardzic, Janko","last_name":"Samardzic","first_name":"Janko"},{"id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Schunn","full_name":"Schunn, Michael","orcid":"0000-0003-4326-5300"},{"first_name":"Claudia","last_name":"Stöger","full_name":"Stöger, Claudia"},{"last_name":"Voikar","full_name":"Voikar, Vootele","first_name":"Vootele"},{"full_name":"Vollert, Jan","last_name":"Vollert","first_name":"Jan"},{"full_name":"Wever, Kimberley E.","last_name":"Wever","first_name":"Kimberley E."},{"last_name":"Wuyts","full_name":"Wuyts, Kathleen","first_name":"Kathleen"},{"first_name":"Malcolm R.","full_name":"Macleod, Malcolm R.","last_name":"Macleod"},{"last_name":"Dirnagl","full_name":"Dirnagl, Ulrich","first_name":"Ulrich"},{"last_name":"Steckler","full_name":"Steckler, Thomas","first_name":"Thomas"}],"article_processing_charge":"No","external_id":{"pmid":["34028353"],"isi":["000661272000001"]},"title":"Introduction to the EQIPD quality system","has_accepted_license":"1","isi":1,"year":"2021","day":"24","publication":"eLife","date_published":"2021-05-24T00:00:00Z","doi":"10.7554/eLife.63294","date_created":"2021-06-27T22:01:49Z","acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1},{"oa_version":"Published Version","abstract":[{"text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"intvolume":" 12","month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"75dd89d09945185b2d14b2434a0bcb50","file_id":"9608","creator":"asandaue","file_size":2156554,"date_updated":"2021-06-28T08:04:22Z","file_name":"2021_NatureCommunications_Santini.pdf","date_created":"2021-06-28T08:04:22Z"}],"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"volume":12,"issue":"1","_id":"9601","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","ddc":["570"],"date_updated":"2023-08-10T13:53:23Z","department":[{"_id":"SiHi"}],"file_date_updated":"2021-06-28T08:04:22Z","acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature Communications","day":"12","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-06-27T22:01:46Z","doi":"10.1038/s41467-021-23510-4","date_published":"2021-07-12T00:00:00Z","article_number":"3804","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23510-4","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23510-4","ieee":"L. Santini et al., “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021).","mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:10.1038/s41467-021-23510-4.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804.","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23510-4."},"title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","article_processing_charge":"No","external_id":{"isi":["000667248600005"]},"author":[{"first_name":"Laura","last_name":"Santini","full_name":"Santini, Laura"},{"full_name":"Halbritter, Florian","last_name":"Halbritter","first_name":"Florian"},{"last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian","first_name":"Fabian"},{"first_name":"Toru","last_name":"Suzuki","full_name":"Suzuki, Toru"},{"first_name":"Maki","last_name":"Asami","full_name":"Asami, Maki"},{"last_name":"Ma","full_name":"Ma, Xiaoyan","first_name":"Xiaoyan"},{"first_name":"Julia","last_name":"Ramesmayer","full_name":"Ramesmayer, Julia"},{"first_name":"Andreas","last_name":"Lackner","full_name":"Lackner, Andreas"},{"first_name":"Nick","full_name":"Warr, Nick","last_name":"Warr"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Ernest","full_name":"Laue, Ernest","last_name":"Laue"},{"full_name":"Farlik, Matthias","last_name":"Farlik","first_name":"Matthias"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"last_name":"Beyer","full_name":"Beyer, Andreas","first_name":"Andreas"},{"first_name":"Anthony C.F.","full_name":"Perry, Anthony C.F.","last_name":"Perry"},{"first_name":"Martin","full_name":"Leeb, Martin","last_name":"Leeb"}]},{"project":[{"grant_number":"Z00342","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Pach","full_name":"Pach, János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János"},{"first_name":"István","full_name":"Tomon, István","last_name":"Tomon"}],"external_id":{"isi":["000702280800002"]},"article_processing_charge":"No","title":"Erdős-Hajnal-type results for monotone paths","citation":{"ista":"Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. 151, 21–37.","chicago":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B. Elsevier, 2021. https://doi.org/10.1016/j.jctb.2021.05.004.","apa":"Pach, J., & Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. Elsevier. https://doi.org/10.1016/j.jctb.2021.05.004","ama":"Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory Series B. 2021;151:21-37. doi:10.1016/j.jctb.2021.05.004","short":"J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37.","ieee":"J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” Journal of Combinatorial Theory. Series B, vol. 151. Elsevier, pp. 21–37, 2021.","mla":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B, vol. 151, Elsevier, 2021, pp. 21–37, doi:10.1016/j.jctb.2021.05.004."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"We would like to thank the anonymous referees for their useful comments and suggestions. János Pach is partially supported by Austrian Science Fund (FWF) grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially supported by Swiss National Science Foundation grant no. 200021_196965, and thanks the support of MIPT Moscow. Both authors are partially supported by The Russian Government in the framework of MegaGrant no. 075-15-2019-1926.","page":"21-37","doi":"10.1016/j.jctb.2021.05.004","date_published":"2021-06-09T00:00:00Z","date_created":"2021-06-27T22:01:47Z","isi":1,"has_accepted_license":"1","year":"2021","day":"09","publication":"Journal of Combinatorial Theory. Series B","article_type":"original","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","_id":"9602","file_date_updated":"2021-06-28T13:33:23Z","department":[{"_id":"HeEd"}],"date_updated":"2023-08-10T13:38:00Z","ddc":["510"],"scopus_import":"1","month":"06","intvolume":" 151","abstract":[{"text":"An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees.","lang":"eng"}],"oa_version":"Published Version","volume":151,"publication_identifier":{"issn":["0095-8956"]},"publication_status":"published","file":[{"creator":"asandaue","file_size":418168,"date_updated":"2021-06-28T13:33:23Z","file_name":"2021_JournalOfCombinatorialTheory_Pach.pdf","date_created":"2021-06-28T13:33:23Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"15fbc9064cd9d1c777ac0043b78c8f12","file_id":"9612"}],"language":[{"iso":"eng"}]},{"volume":103,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["24699934"],"issn":["24699926"]},"intvolume":" 103","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/2009.06491","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results.","lang":"eng"}],"department":[{"_id":"MiLe"}],"date_updated":"2023-08-10T13:37:25Z","status":"public","type":"journal_article","article_type":"letter_note","_id":"9606","date_created":"2021-06-27T22:01:49Z","doi":"10.1103/PhysRevA.103.L061303","date_published":"2021-06-01T00:00:00Z","publication":"Physical Review A","day":"01","year":"2021","isi":1,"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"G.B. acknowledges support from the Austrian Science Fund (FWF), under Project No. M2641-N27. This work was\r\npartially supported by the University of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss, Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning Moritz and Markus Bohlen for providing their experimental\r\ndata.","title":"Propagation of first and second sound in a two-dimensional Fermi superfluid","article_processing_charge":"No","external_id":{"isi":["000662296700014"],"arxiv":["2009.06491"]},"author":[{"first_name":"A.","last_name":"Tononi","full_name":"Tononi, A."},{"last_name":"Cappellaro","orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660"},{"last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"first_name":"L.","last_name":"Salasnich","full_name":"Salasnich, L."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6), L061303.","chicago":"Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.L061303.","apa":"Tononi, A., Cappellaro, A., Bighin, G., & Salasnich, L. (2021). Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.L061303","ama":"Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 2021;103(6). doi:10.1103/PhysRevA.103.L061303","short":"A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103 (2021).","ieee":"A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first and second sound in a two-dimensional Fermi superfluid,” Physical Review A, vol. 103, no. 6. American Physical Society, 2021.","mla":"Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A, vol. 103, no. 6, L061303, American Physical Society, 2021, doi:10.1103/PhysRevA.103.L061303."},"article_number":"L061303"},{"author":[{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino"},{"full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X","last_name":"Schulz","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Jesús-Cortés, Héctor","last_name":"De Jesús-Cortés","first_name":"Héctor"},{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","last_name":"Maes"},{"first_name":"Balint","id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425","last_name":"Nagy","full_name":"Nagy, Balint"},{"first_name":"Francis","full_name":"Reilly-Andújar, Francis","last_name":"Reilly-Andújar"},{"first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","last_name":"Colombo"},{"first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867"},{"id":"3526230C-F248-11E8-B48F-1D18A9856A87","first_name":"Florianne E","last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E"},{"full_name":"Bear, Mark F.","last_name":"Bear","first_name":"Mark F."},{"orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["34233180"],"isi":["000670188500004"]},"title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","citation":{"ieee":"A. Venturino et al., “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” Cell Reports, vol. 36, no. 1. Elsevier, 2021.","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313.","ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.","chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier, 2021. https://doi.org/10.1016/j.celrep.2021.109313."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"109313","date_published":"2021-07-06T00:00:00Z","doi":"10.1016/j.celrep.2021.109313","date_created":"2021-07-11T22:01:16Z","has_accepted_license":"1","isi":1,"year":"2021","day":"06","publication":"Cell Reports","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","file_date_updated":"2021-07-19T13:32:17Z","department":[{"_id":"SaSi"}],"date_updated":"2023-08-10T14:09:39Z","ddc":["570"],"type":"journal_article","article_type":"original","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","_id":"9642","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/","description":"News on IST Homepage"}]},"volume":36,"issue":"1","ec_funded":1,"publication_identifier":{"eissn":["22111247"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"f056255f6d01fd9a86b5387635928173","file_id":"9693","file_size":56388540,"date_updated":"2021-07-19T13:32:17Z","creator":"cziletti","file_name":"2021_CellReports_Venturino.pdf","date_created":"2021-07-19T13:32:17Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 36","abstract":[{"text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"pmid":1,"oa_version":"Published Version"},{"_id":"9603","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","date_updated":"2023-08-10T13:55:00Z","ddc":["570"],"department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"file_date_updated":"2021-06-28T14:06:24Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division."}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 35","publication_identifier":{"eissn":["22111247"]},"publication_status":"published","file":[{"date_created":"2021-06-28T14:06:24Z","file_name":"2021_CellReports_Contreras.pdf","date_updated":"2021-06-28T14:06:24Z","file_size":7653149,"creator":"asandaue","file_id":"9613","checksum":"d49520fdcbbb5c2f883bddb67cee5d77","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":35,"issue":"12","related_material":{"link":[{"url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/","relation":"press_release","description":"News on IST Homepage"}]},"ec_funded":1,"article_number":"109274","project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"citation":{"ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274.","ieee":"X. Contreras et al., “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12). doi:10.1016/j.celrep.2021.109274","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press, 2021, doi:10.1016/j.celrep.2021.109274."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras","full_name":"Contreras, Ximena"},{"last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"id":"70ADC922-B424-11E9-99E3-BA18E6697425","first_name":"Amarbayasgalan","last_name":"Davaatseren","full_name":"Davaatseren, Amarbayasgalan"},{"full_name":"Hansen, Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"},{"first_name":"Johanna","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","last_name":"Sonntag","full_name":"Sonntag, Johanna"},{"last_name":"Andersen","full_name":"Andersen, Lill","first_name":"Lill"},{"last_name":"Bernthaler","full_name":"Bernthaler, Tina","first_name":"Tina"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"last_name":"Heger","full_name":"Heger, Anna-Magdalena","first_name":"Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Randy L.","last_name":"Johnson","first_name":"Randy L."},{"first_name":"Lindsay A.","full_name":"Schwarz, Lindsay A.","last_name":"Schwarz"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000664463600016"]},"title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.","publisher":"Cell Press","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"22","publication":"Cell Reports","date_published":"2021-06-22T00:00:00Z","doi":"10.1016/j.celrep.2021.109274","date_created":"2021-06-27T22:01:48Z"},{"type":"journal_article","article_type":"original","keyword":["Multidisciplinary"],"status":"public","_id":"9618","department":[{"_id":"MaSe"}],"file_date_updated":"2021-09-23T14:00:05Z","date_updated":"2023-08-10T13:57:07Z","ddc":["539"],"scopus_import":"1","intvolume":" 371","month":"03","abstract":[{"lang":"eng","text":"The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science."}],"pmid":1,"oa_version":"Preprint","ec_funded":1,"volume":371,"issue":"6536","publication_status":"published","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10040","checksum":"0b356fd10ab9bb95177d4c047d4e9c1a","success":1,"date_updated":"2021-09-23T14:00:05Z","file_size":3671159,"creator":"patrickd","date_created":"2021-09-23T14:00:05Z","file_name":"scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf"}],"project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"external_id":{"arxiv":["2012.12276"],"pmid":["33632894"],"isi":["000636043400048"]},"article_processing_charge":"No","author":[{"first_name":"D.","full_name":"Bluvstein, D.","last_name":"Bluvstein"},{"full_name":"Omran, A.","last_name":"Omran","first_name":"A."},{"last_name":"Levine","full_name":"Levine, H.","first_name":"H."},{"first_name":"A.","full_name":"Keesling, A.","last_name":"Keesling"},{"first_name":"G.","last_name":"Semeghini","full_name":"Semeghini, G."},{"full_name":"Ebadi, S.","last_name":"Ebadi","first_name":"S."},{"first_name":"T. T.","last_name":"Wang","full_name":"Wang, T. T."},{"last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios"},{"last_name":"Maskara","full_name":"Maskara, N.","first_name":"N."},{"first_name":"W. W.","last_name":"Ho","full_name":"Ho, W. W."},{"last_name":"Choi","full_name":"Choi, S.","first_name":"S."},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"full_name":"Greiner, M.","last_name":"Greiner","first_name":"M."},{"first_name":"V.","last_name":"Vuletić","full_name":"Vuletić, V."},{"full_name":"Lukin, M. D.","last_name":"Lukin","first_name":"M. D."}],"title":"Controlling quantum many-body dynamics in driven Rydberg atom arrays","citation":{"ista":"Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT, Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 371(6536), 1355–1359.","chicago":"Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science. AAAS, 2021. https://doi.org/10.1126/science.abg2530.","short":"D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T. Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V. Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359.","ieee":"D. Bluvstein et al., “Controlling quantum many-body dynamics in driven Rydberg atom arrays,” Science, vol. 371, no. 6536. AAAS, pp. 1355–1359, 2021.","apa":"Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S., … Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. AAAS. https://doi.org/10.1126/science.abg2530","ama":"Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 2021;371(6536):1355-1359. doi:10.1126/science.abg2530","mla":"Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:10.1126/science.abg2530."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"AAAS","quality_controlled":"1","acknowledgement":"We thank many members of the Harvard AMO community, particularly E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado, H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We acknowledge financial support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research, the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033), and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate (NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K., G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors discussed the results and contributed to the manuscript. Competing interests: M.G., V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a shareholder of QuEra Computing. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and the supplementary materials.","page":"1355-1359","date_created":"2021-06-29T12:04:05Z","date_published":"2021-03-26T00:00:00Z","doi":"10.1126/science.abg2530","year":"2021","isi":1,"has_accepted_license":"1","publication":"Science","day":"26"},{"ddc":["580"],"date_updated":"2023-08-10T14:01:41Z","file_date_updated":"2021-07-19T12:13:34Z","department":[{"_id":"JiFr"}],"_id":"9657","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"date_created":"2021-07-19T12:13:34Z","file_name":"2021_PlantCell_Gao.pdf","date_updated":"2021-07-19T12:13:34Z","file_size":10566921,"creator":"cziletti","checksum":"6715712ec306c321f0204c817b7f8ae7","file_id":"9691","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"volume":33,"issue":"9","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia."}],"intvolume":" 33","month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","ieee":"Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183"},"title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","article_processing_charge":"No","external_id":{"pmid":["34240197"],"isi":["000702165300012"]},"author":[{"first_name":"Z","full_name":"Gao, Z","last_name":"Gao"},{"first_name":"Z","full_name":"Chen, Z","last_name":"Chen"},{"last_name":"Cui","full_name":"Cui, Y","first_name":"Y"},{"first_name":"M","full_name":"Ke, M","last_name":"Ke"},{"full_name":"Xu, H","last_name":"Xu","first_name":"H"},{"first_name":"Q","full_name":"Xu, Q","last_name":"Xu"},{"last_name":"Chen","full_name":"Chen, J","first_name":"J"},{"first_name":"Y","last_name":"Li","full_name":"Li, Y"},{"last_name":"Huang","full_name":"Huang, L","first_name":"L"},{"last_name":"Zhao","full_name":"Zhao, H","first_name":"H"},{"first_name":"D","full_name":"Huang, D","last_name":"Huang"},{"first_name":"S","full_name":"Mai, S","last_name":"Mai"},{"first_name":"T","full_name":"Xu, T","last_name":"Xu"},{"full_name":"Liu, X","last_name":"Liu","first_name":"X"},{"full_name":"Li, S","last_name":"Li","first_name":"S"},{"first_name":"Y","full_name":"Guan, Y","last_name":"Guan"},{"last_name":"Yang","full_name":"Yang, W","first_name":"W"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"J","full_name":"Petrášek, J","last_name":"Petrášek"},{"last_name":"Zhang","full_name":"Zhang, J","first_name":"J"},{"first_name":"X","last_name":"Chen","full_name":"Chen, X"}],"publication":"Plant Cell","day":"07","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-07-14T15:32:43Z","date_published":"2021-07-07T00:00:00Z","doi":"10.1093/plcell/koab183","page":"2981–3003","oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1"},{"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9692","checksum":"5767418926a7f7fb76151de29473dae0","success":1,"creator":"cziletti","date_updated":"2021-07-19T13:02:20Z","file_size":628992,"date_created":"2021-07-19T13:02:20Z","file_name":"2021_NatCoom_Tkadlec.pdf"}],"language":[{"iso":"eng"}],"volume":12,"issue":"1","ec_funded":1,"abstract":[{"text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"06","intvolume":" 12","date_updated":"2023-08-10T14:05:09Z","ddc":["510"],"department":[{"_id":"KrCh"}],"file_date_updated":"2021-07-19T13:02:20Z","_id":"9640","article_type":"original","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","has_accepted_license":"1","isi":1,"year":"2021","day":"29","publication":"Nature Communications","doi":"10.1038/s41467-021-24271-w","date_published":"2021-06-29T00:00:00Z","date_created":"2021-07-11T22:01:15Z","acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-24271-w","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"article_processing_charge":"No","external_id":{"isi":["000671752100003"],"pmid":["34188036"]},"title":"Fast and strong amplifiers of natural selection","article_number":"4009","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}]},{"author":[{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin","last_name":"Qi"},{"first_name":"SS","full_name":"Alotaibi, SS","last_name":"Alotaibi"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"external_id":{"pmid":["34254313"],"isi":["000680587100001"]},"article_processing_charge":"Yes (via OA deal)","title":"PIN-mediated polar auxin transport regulations in plant tropic responses","citation":{"short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” New Phytologist, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522. doi:10.1111/nph.17617","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. Wiley. https://doi.org/10.1111/nph.17617","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:10.1111/nph.17617.","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"510-522","doi":"10.1111/nph.17617","date_published":"2021-10-01T00:00:00Z","date_created":"2021-07-14T15:29:14Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"New Phytologist","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","department":[{"_id":"JiFr"}],"file_date_updated":"2021-10-07T13:42:47Z","date_updated":"2023-08-10T14:02:41Z","ddc":["580"],"type":"journal_article","article_type":"original","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","_id":"9656","issue":"2","volume":232,"ec_funded":1,"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10105","checksum":"6422a6eb329b52d96279daaee0fcf189","success":1,"date_updated":"2021-10-07T13:42:47Z","file_size":1939800,"creator":"kschuh","date_created":"2021-10-07T13:42:47Z","file_name":"2021_NewPhytologist_Han.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 232","abstract":[{"lang":"eng","text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment."}],"pmid":1,"oa_version":"Published Version"},{"date_created":"2021-07-18T22:01:22Z","doi":"10.1088/1367-2630/ac0576","date_published":"2021-06-23T00:00:00Z","publication":"New Journal of Physics","day":"23","year":"2021","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","title":"Morphology of three-body quantum states from machine learning","external_id":{"arxiv":["2102.04961"],"isi":["000664736300001"]},"article_processing_charge":"Yes","author":[{"full_name":"Huber, David","last_name":"Huber","first_name":"David"},{"first_name":"Oleksandr V.","full_name":"Marchukov, Oleksandr V.","last_name":"Marchukov"},{"last_name":"Hammer","full_name":"Hammer, Hans Werner","first_name":"Hans Werner"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac0576.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” New Journal of Physics, vol. 23, no. 6. IOP Publishing, 2021.","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., & Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac0576","ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. New Journal of Physics. 2021;23(6). doi:10.1088/1367-2630/ac0576","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:10.1088/1367-2630/ac0576."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"065009","ec_funded":1,"volume":23,"issue":"6","language":[{"iso":"eng"}],"file":[{"file_name":"2021_NewJPhys_Huber.pdf","date_created":"2021-07-19T11:47:16Z","file_size":3868445,"date_updated":"2021-07-19T11:47:16Z","creator":"cziletti","success":1,"file_id":"9690","checksum":"e39164ce7ea228d287cf8924e1a0f9fe","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["13672630"]},"intvolume":" 23","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.","lang":"eng"}],"department":[{"_id":"MiLe"}],"file_date_updated":"2021-07-19T11:47:16Z","ddc":["530"],"date_updated":"2023-08-10T13:58:09Z","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","article_type":"original","_id":"9679"},{"author":[{"last_name":"Yang","full_name":"Yang, Qiutan","first_name":"Qiutan"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","full_name":"Xue, Shi-lei","last_name":"Xue"},{"first_name":"Chii Jou","full_name":"Chan, Chii Jou","last_name":"Chan"},{"full_name":"Rempfler, Markus","last_name":"Rempfler","first_name":"Markus"},{"full_name":"Vischi, Dario","last_name":"Vischi","first_name":"Dario"},{"first_name":"Francisca","last_name":"Maurer-Gutierrez","full_name":"Maurer-Gutierrez, Francisca"},{"first_name":"Takashi","full_name":"Hiiragi, Takashi","last_name":"Hiiragi"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Prisca","last_name":"Liberali","full_name":"Liberali, Prisca"}],"external_id":{"isi":["000664016300003"],"pmid":["34155381"]},"article_processing_charge":"No","title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","citation":{"mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021, pp. 733–744, doi:10.1038/s41556-021-00700-2.","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","ieee":"Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744, 2021.","apa":"Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2","ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2","chicago":"Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2.","ista":"Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"}],"page":"733–744","date_published":"2021-06-21T00:00:00Z","doi":"10.1038/s41556-021-00700-2","date_created":"2021-07-04T22:01:25Z","isi":1,"year":"2021","day":"21","publication":"Nature Cell Biology","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).","department":[{"_id":"EdHa"}],"date_updated":"2023-08-10T13:57:36Z","type":"journal_article","article_type":"original","status":"public","_id":"9629","volume":23,"ec_funded":1,"publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359","open_access":"1"}],"month":"06","intvolume":" 23","abstract":[{"text":"Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis.","lang":"eng"}],"pmid":1,"oa_version":"Preprint"},{"article_number":"100452","external_id":{"isi":["000703159600010"]},"article_processing_charge":"No","author":[{"last_name":"Su","full_name":"Su, Lizhong","first_name":"Lizhong"},{"full_name":"Hong, Tao","last_name":"Hong","first_name":"Tao"},{"first_name":"Dongyang","full_name":"Wang, Dongyang","last_name":"Wang"},{"last_name":"Wang","full_name":"Wang, Sining","first_name":"Sining"},{"full_name":"Qin, Bingchao","last_name":"Qin","first_name":"Bingchao"},{"full_name":"Zhang, Mengmeng","last_name":"Zhang","first_name":"Mengmeng"},{"first_name":"Xiang","full_name":"Gao, Xiang","last_name":"Gao"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"first_name":"Li Dong","full_name":"Zhao, Li Dong","last_name":"Zhao"}],"title":"Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation","citation":{"ama":"Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 2021;20. doi:10.1016/j.mtphys.2021.100452","apa":"Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021). Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. Elsevier. https://doi.org/10.1016/j.mtphys.2021.100452","ieee":"L. Su et al., “Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,” Materials Today Physics, vol. 20. Elsevier, 2021.","short":"L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D. Zhao, Materials Today Physics 20 (2021).","mla":"Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics, vol. 20, 100452, Elsevier, 2021, doi:10.1016/j.mtphys.2021.100452.","ista":"Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 20, 100452.","chicago":"Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics. Elsevier, 2021. https://doi.org/10.1016/j.mtphys.2021.100452."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","quality_controlled":"1","acknowledgement":"This work was supported by National Natural Science Foundation of China (51772012), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the High Performance Computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM measurements.","date_created":"2021-07-04T22:01:24Z","doi":"10.1016/j.mtphys.2021.100452","date_published":"2021-06-03T00:00:00Z","year":"2021","isi":1,"publication":"Materials Today Physics","day":"03","type":"journal_article","article_type":"original","status":"public","_id":"9626","department":[{"_id":"MaIb"}],"date_updated":"2023-08-10T13:56:31Z","scopus_import":"1","intvolume":" 20","month":"06","abstract":[{"text":"SnSe, a wide-bandgap semiconductor, has attracted significant attention from the thermoelectric (TE) community due to its outstanding TE performance deriving from the ultralow thermal conductivity and advantageous electronic structures. Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap engineering and vacancy compensation. We found that PbTe can significantly reduce the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain boundary could also reduce the intergrain energy barrier which largely enhances the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe. Our findings provide a novel strategy to promote the TE performance in wide-bandgap semiconductors.","lang":"eng"}],"oa_version":"None","volume":20,"publication_status":"published","publication_identifier":{"eissn":["2542-5293"]},"language":[{"iso":"eng"}]},{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses."}],"month":"05","intvolume":" 12","scopus_import":"1","file":[{"date_created":"2021-12-17T11:34:50Z","file_name":"2021_NatureCommunications_Vandael.pdf","date_updated":"2021-12-17T11:34:50Z","file_size":3108845,"creator":"kschuh","file_id":"10563","checksum":"6036a8cdae95e1707c2a04d54e325ff4","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/","relation":"press_release"}]},"issue":"1","volume":12,"ec_funded":1,"_id":"9778","status":"public","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"type":"journal_article","article_type":"original","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)"},"ddc":["570"],"date_updated":"2023-08-10T14:16:16Z","department":[{"_id":"PeJo"}],"file_date_updated":"2021-12-17T11:34:50Z","acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","quality_controlled":"1","publisher":"Springer","oa":1,"day":"18","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1038/s41467-021-23153-5","date_published":"2021-05-18T00:00:00Z","date_created":"2021-08-06T07:22:55Z","article_number":"2912","project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications, vol. 12, no. 1, 2912, Springer, 2021, doi:10.1038/s41467-021-23153-5.","apa":"Vandael, D. H., Okamoto, Y., & Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. Springer. https://doi.org/10.1038/s41467-021-23153-5","ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23153-5","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” Nature Communications, vol. 12, no. 1. Springer, 2021.","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications. Springer, 2021. https://doi.org/10.1038/s41467-021-23153-5.","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912."},"title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","last_name":"Vandael"},{"id":"3337E116-F248-11E8-B48F-1D18A9856A87","first_name":"Yuji","last_name":"Okamoto","orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"external_id":{"isi":["000655481800014"]},"article_processing_charge":"No"},{"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” Theoretical Computer Science, vol. 893. Elsevier, pp. 1–16, 2021.","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021). Long lived transients in gene regulation. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023","chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.","ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16."},"title":"Long lived transients in gene regulation","article_processing_charge":"No","external_id":{"isi":["000710180500002"]},"author":[{"first_name":"Tatjana","full_name":"Petrov, Tatjana","last_name":"Petrov"},{"first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia","last_name":"Igler"},{"first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali","last_name":"Sezgin"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Theoretical Computer Science","day":"04","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-07-11T22:01:18Z","date_published":"2021-06-04T00:00:00Z","doi":"10.1016/j.tcs.2021.05.023","page":"1-16","_id":"9647","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","ddc":["004"],"date_updated":"2023-08-10T14:11:19Z","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"file_date_updated":"2022-05-12T12:13:27Z","oa_version":"Published Version","abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"intvolume":" 893","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"d3aef34cfb13e53bba4cf44d01680793","file_id":"11364","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_TheoreticalComputerScience_Petrov.pdf","date_created":"2022-05-12T12:13:27Z","creator":"dernst","file_size":2566504,"date_updated":"2022-05-12T12:13:27Z"}],"publication_status":"published","publication_identifier":{"issn":["0304-3975"]},"volume":893},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071593.","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593","ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells, vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593."},"title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","author":[{"last_name":"Muench","full_name":"Muench, Nicole A.","first_name":"Nicole A."},{"first_name":"Sonia","last_name":"Patel","full_name":"Patel, Sonia"},{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085"},{"first_name":"Ryan J.","last_name":"Donahue","full_name":"Donahue, Ryan J."},{"first_name":"Akihiro","last_name":"Ikeda","full_name":"Ikeda, Akihiro"},{"full_name":"Nickells, Robert W.","last_name":"Nickells","first_name":"Robert W."}],"external_id":{"isi":["000678193300001"],"pmid":["34201955"]},"article_processing_charge":"Yes","article_number":"1593","day":"25","publication":"Cells","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-06-25T00:00:00Z","doi":"10.3390/cells10071593","date_created":"2021-08-01T22:01:22Z","acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","publisher":"MDPI","quality_controlled":"1","oa":1,"ddc":["570"],"date_updated":"2023-08-10T14:14:53Z","file_date_updated":"2021-08-04T14:01:30Z","department":[{"_id":"SaSi"}],"_id":"9761","status":"public","type":"journal_article","article_type":"original","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":[{"date_created":"2021-08-04T14:01:30Z","file_name":"2021_Cells_Muench.pdf","date_updated":"2021-08-04T14:01:30Z","file_size":4555611,"creator":"cziletti","file_id":"9768","checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20734409"]},"publication_status":"published","volume":10,"issue":"7","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. "}],"month":"06","intvolume":" 10","scopus_import":"1"},{"publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","date_published":"2021-06-30T00:00:00Z","doi":"10.1016/j.nlm.2021.107486","date_created":"2021-07-11T22:01:16Z","day":"30","publication":"Neurobiology of Learning and Memory","isi":1,"has_accepted_license":"1","year":"2021","project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"article_number":"107486","title":"The role of hippocampal mossy cells in novelty detection","author":[{"full_name":"Fredes, Felipe","last_name":"Fredes","first_name":"Felipe"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"article_processing_charge":"No","external_id":{"pmid":["34214666"],"isi":["000677694900004"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486, Elsevier, 2021, doi:10.1016/j.nlm.2021.107486.","apa":"Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486","ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021.","short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021. https://doi.org/10.1016/j.nlm.2021.107486.","ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486."},"month":"06","intvolume":" 183","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation."}],"volume":183,"ec_funded":1,"file":[{"success":1,"file_id":"9694","checksum":"8e8298a9e8c7df146ad23f32c2a63929","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_NeurobLearnMemory_Fredes.pdf","date_created":"2021-07-19T13:46:06Z","creator":"cziletti","file_size":1994793,"date_updated":"2021-07-19T13:46:06Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["10747427"],"eissn":["10959564"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"9641","department":[{"_id":"RySh"}],"file_date_updated":"2021-07-19T13:46:06Z","ddc":["610"],"date_updated":"2023-08-10T14:10:37Z"},{"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450383912"]},"publication_status":"published","month":"06","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2011.14617","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude.","lang":"eng"}],"department":[{"_id":"KrCh"}],"date_updated":"2023-08-10T14:14:08Z","status":"public","type":"conference","conference":{"start_date":"2021-06-20","location":"Online","end_date":"2021-06-26","name":"PLDI: Programming Language Design and Implementation"},"_id":"9646","date_published":"2021-06-01T00:00:00Z","doi":"10.1145/3453483.3454102","date_created":"2021-07-11T22:01:18Z","page":"1171-1186","day":"01","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","isi":1,"year":"2021","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).","title":"Quantitative analysis of assertion violations in probabilistic programs","author":[{"full_name":"Wang, Jinyi","last_name":"Wang","first_name":"Jinyi"},{"first_name":"Yican","full_name":"Sun, Yican","last_name":"Sun"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","full_name":"Fu, Hongfei","last_name":"Fu"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"}],"external_id":{"isi":["000723661700076"],"arxiv":["2011.14617"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186.","chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1171–86. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454102.","ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1171–1186). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454102","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1171–1186.","mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102."},"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}]},{"citation":{"apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076","ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076","ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 772–787.","short":"A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787.","mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–87, doi:10.1145/3453483.3454076.","ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 772–87. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454076."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Ali","full_name":"Asadi, Ali","last_name":"Asadi"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fu, Hongfei","last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"},{"first_name":"Mohammad","last_name":"Mahdavi","full_name":"Mahdavi, Mohammad"}],"external_id":{"isi":["000723661700050"]},"article_processing_charge":"No","title":"Polynomial reachability witnesses via Stellensätze","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"isi":1,"year":"2021","day":"01","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","page":"772-787","date_published":"2021-06-01T00:00:00Z","doi":"10.1145/3453483.3454076","date_created":"2021-07-11T22:01:17Z","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"date_updated":"2023-08-10T14:13:39Z","department":[{"_id":"KrCh"}],"_id":"9645","type":"conference","conference":{"start_date":"2021-06-20","location":"Online","end_date":"2021-06-26","name":" PLDI: Programming Language Design and Implementation"},"status":"public","publication_identifier":{"isbn":["9781450383912"]},"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-03183862/"}],"month":"06"},{"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","article_type":"letter_note","status":"public","_id":"9759","department":[{"_id":"CaHe"}],"file_date_updated":"2021-08-05T12:06:49Z","date_updated":"2023-08-10T14:16:46Z","ddc":["613"],"scopus_import":"1","intvolume":" 17","month":"07","oa_version":"Published Version","pmid":1,"volume":17,"issue":"7","publication_status":"published","publication_identifier":{"issn":["1553734X"],"eissn":["15537358"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-08-05T12:06:49Z","file_name":"2021_PlosCompBio_Bartlett.pdf","date_updated":"2021-08-05T12:06:49Z","file_size":693633,"creator":"cchlebak","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","file_id":"9771","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"article_number":"e1009124","external_id":{"pmid":["34264932"],"isi":["000677713500008"]},"article_processing_charge":"Yes","author":[{"first_name":"Michael John","last_name":"Bartlett","full_name":"Bartlett, Michael John"},{"full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","last_name":"Arslan","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N"},{"last_name":"Bankston","full_name":"Bankston, Adriana","first_name":"Adriana"},{"first_name":"Sarvenaz","last_name":"Sarabipour","full_name":"Sarabipour, Sarvenaz"}],"title":"Ten simple rules to improve academic work- life balance","citation":{"ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” PLoS Computational Biology, vol. 17, no. 7. Public Library of Science, 2021.","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009124.","ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Public Library of Science","acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","date_created":"2021-08-01T22:01:21Z","date_published":"2021-07-15T00:00:00Z","doi":"10.1371/journal.pcbi.1009124","year":"2021","isi":1,"has_accepted_license":"1","publication":"PLoS Computational Biology","day":"15"},{"project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Themistoklis","last_name":"Zisis","full_name":"Zisis, Themistoklis"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz","full_name":"Schwarz, Jan"},{"first_name":"Miriam","full_name":"Balles, Miriam","last_name":"Balles"},{"first_name":"Maibritt","last_name":"Kretschmer","full_name":"Kretschmer, Maibritt"},{"full_name":"Nemethova, Maria","last_name":"Nemethova","first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","last_name":"Chait"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Janina","last_name":"Lange","full_name":"Lange, Janina"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K"},{"full_name":"Zahler, Stefan","last_name":"Zahler","first_name":"Stefan"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","citation":{"short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","ieee":"T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850.","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","page":"35545–35560","doi":"10.1021/acsami.1c09850","date_published":"2021-08-04T00:00:00Z","date_created":"2021-08-08T22:01:28Z","has_accepted_license":"1","isi":1,"year":"2021","day":"04","publication":"ACS Applied Materials and Interfaces","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"9822","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"file_date_updated":"2021-08-09T09:44:03Z","date_updated":"2023-08-10T14:22:48Z","ddc":["620","570"],"scopus_import":"1","month":"08","intvolume":" 13","abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":13,"issue":"30","ec_funded":1,"publication_identifier":{"issn":["19448244"],"eissn":["19448252"]},"publication_status":"published","file":[{"success":1,"file_id":"9833","checksum":"b043a91d9f9200e467b970b692687ed3","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","date_created":"2021-08-09T09:44:03Z","creator":"asandaue","file_size":7123293,"date_updated":"2021-08-09T09:44:03Z"}],"language":[{"iso":"eng"}]},{"intvolume":" 40","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates.","lang":"eng"}],"issue":"4","volume":40,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"51b61b7e5c175e2d7ed8fa3b35f7525a","file_id":"9834","success":1,"creator":"asandaue","date_updated":"2021-08-09T11:41:50Z","file_size":49840741,"date_created":"2021-08-09T11:41:50Z","file_name":"2021_ACMTransactionsOnGraphics_Mallikarjun.pdf"}],"publication_status":"published","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"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":"9819","department":[{"_id":"BeBi"}],"file_date_updated":"2021-08-09T11:41:50Z","ddc":["000"],"date_updated":"2023-08-10T14:25:08Z","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019].","date_created":"2021-08-08T22:01:27Z","date_published":"2021-08-01T00:00:00Z","doi":"10.1145/3450626.3459765","publication":"ACM Transactions on Graphics","day":"01","year":"2021","has_accepted_license":"1","isi":1,"article_number":"44","title":"PhotoApp: Photorealistic appearance editing of head portraits","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2103.07658"],"isi":["000674930900011"]},"author":[{"first_name":"B. R.","last_name":"Mallikarjun","full_name":"Mallikarjun, B. R."},{"full_name":"Tewari, Ayush","last_name":"Tewari","first_name":"Ayush"},{"first_name":"Abdallah","last_name":"Dib","full_name":"Dib, Abdallah"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seidel","full_name":"Seidel, Hans Peter","first_name":"Hans Peter"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"},{"first_name":"Louis","last_name":"Chevallier","full_name":"Chevallier, Louis"},{"first_name":"Mohamed A.","full_name":"Elgharib, Mohamed A.","last_name":"Elgharib"},{"first_name":"Christian","last_name":"Theobalt","full_name":"Theobalt, Christian"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.","chicago":"Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.","short":"B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021).","ieee":"B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","ama":"Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765","apa":"Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459765","mla":"Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459765."}},{"article_number":"e0255267","citation":{"ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267.","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Hledik, Michal","last_name":"Hledik"},{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Beiglböck","full_name":"Beiglböck, Mathias","first_name":"Mathias"},{"first_name":"Anna Nele","last_name":"Herdina","full_name":"Herdina, Anna Nele"},{"full_name":"Strassl, Robert","last_name":"Strassl","first_name":"Robert"},{"last_name":"Posch","full_name":"Posch, Martin","first_name":"Martin"}],"external_id":{"isi":["000685248200095"],"pmid":["34324553"]},"article_processing_charge":"Yes","title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"29","publication":"PLoS ONE","doi":"10.1371/journal.pone.0255267","date_published":"2021-07-29T00:00:00Z","date_created":"2021-08-08T22:01:26Z","_id":"9816","article_type":"original","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":"2023-08-10T14:26:32Z","ddc":["610"],"department":[{"_id":"NiBa"}],"file_date_updated":"2021-08-09T11:52:14Z","abstract":[{"lang":"eng","text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 16","publication_identifier":{"eissn":["1932-6203"]},"publication_status":"published","file":[{"file_size":773921,"date_updated":"2021-08-09T11:52:14Z","creator":"asandaue","file_name":"2021_PLoSONE_Hledík.pdf","date_created":"2021-08-09T11:52:14Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9835","checksum":"ae4df60eb62f4491278588548d0c1f93"}],"language":[{"iso":"eng"}],"volume":16,"issue":"7"},{"abstract":[{"lang":"eng","text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 16","publication_identifier":{"eissn":["19326203"]},"publication_status":"published","file":[{"date_created":"2021-08-09T09:25:41Z","file_name":"2021_PLoSONE_Graff.pdf","creator":"asandaue","date_updated":"2021-08-09T09:25:41Z","file_size":2706919,"checksum":"0277aa155d5db1febd2cb384768bba5f","file_id":"9832","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":16,"issue":"7","_id":"9821","type":"journal_article","article_type":"original","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":"2023-08-10T14:21:42Z","ddc":["006"],"file_date_updated":"2021-08-09T09:25:41Z","department":[{"_id":"HeEd"}],"acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"PLoS ONE","date_published":"2021-07-01T00:00:00Z","doi":"10.1371/journal.pone.0253851","date_created":"2021-08-08T22:01:28Z","article_number":"e0253851","citation":{"ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021).","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851","ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0253851","mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:10.1371/journal.pone.0253851.","ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851.","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0253851."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Grzegorz","last_name":"Graff","full_name":"Graff, Grzegorz"},{"first_name":"Beata","full_name":"Graff, Beata","last_name":"Graff"},{"full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel"},{"first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski","full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866"},{"last_name":"Gąsecki","full_name":"Gąsecki, Dariusz","first_name":"Dariusz"},{"last_name":"Narkiewicz","full_name":"Narkiewicz, Krzysztof","first_name":"Krzysztof"}],"external_id":{"pmid":["34292957"],"isi":["000678124900050"]},"article_processing_charge":"Yes","title":"Persistent homology as a new method of the assessment of heart rate variability"},{"article_number":"125","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813.","apa":"Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., & Myszkowski, K. (2021). The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459813","ama":"Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459813","ieee":"A. Serrano et al., “The effect of shape and illumination on material perception: Model and applications,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","short":"A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021).","chicago":"Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813.","ista":"Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K. 2021. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 40(4), 125."},"title":"The effect of shape and illumination on material perception: Model and applications","article_processing_charge":"No","external_id":{"isi":["000674930900090"]},"author":[{"last_name":"Serrano","full_name":"Serrano, Ana","first_name":"Ana"},{"full_name":"Chen, Bin","last_name":"Chen","first_name":"Bin"},{"last_name":"Wang","full_name":"Wang, Chao","first_name":"Chao"},{"first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael","orcid":"0000-0002-5062-4474","last_name":"Piovarci"},{"full_name":"Seidel, Hans Peter","last_name":"Seidel","first_name":"Hans Peter"},{"first_name":"Piotr","full_name":"Didyk, Piotr","last_name":"Didyk"},{"first_name":"Karol","last_name":"Myszkowski","full_name":"Myszkowski, Karol"}],"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY).","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","publication":"ACM Transactions on Graphics","day":"01","year":"2021","isi":1,"date_created":"2021-08-08T22:01:28Z","date_published":"2021-08-01T00:00:00Z","doi":"10.1145/3450626.3459813","_id":"9820","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-10T14:20:10Z","department":[{"_id":"BeBi"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design."}],"intvolume":" 40","month":"08","main_file_link":[{"open_access":"1","url":"https://zaguan.unizar.es/record/110704/files/texto_completo.pdf"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"issue":"4","volume":40},{"publication":"ACM Transactions on Graphics","day":"01","year":"2021","isi":1,"date_created":"2021-08-08T22:01:27Z","date_published":"2021-08-01T00:00:00Z","doi":"10.1145/3450626.3459816","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459816.","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816","apa":"Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459816","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816.","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168."},"title":"Mechanics-aware deformation of yarn pattern geometry","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000674930900132"]},"author":[{"last_name":"Sperl","full_name":"Sperl, Georg","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Narain","full_name":"Narain, Rahul","first_name":"Rahul"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"article_number":"168","project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"ec_funded":1,"volume":40,"related_material":{"link":[{"description":"News on IST Webpage","url":"https://ist.ac.at/en/news/knitting-virtual-yarn/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"12358"},{"status":"public","id":"9327","relation":"software"}]},"issue":"4","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales.","lang":"eng"}],"intvolume":" 40","month":"08","main_file_link":[{"url":"https://doi.org/10.1145/3450626.3459816","open_access":"1"}],"scopus_import":"1","date_updated":"2023-08-10T14:24:36Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"_id":"9818","status":"public","article_type":"original","type":"journal_article"}]