[{"date_updated":"2023-08-07T14:17:00Z","ddc":["510"],"file_date_updated":"2021-03-22T11:01:09Z","department":[{"_id":"RoSe"}],"_id":"9256","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","status":"public","publication_status":"published","publication_identifier":{"eissn":["15730530"],"issn":["03779017"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9273","checksum":"687fef1525789c0950de90468dd81604","success":1,"creator":"dernst","date_updated":"2021-03-22T11:01:09Z","file_size":397962,"date_created":"2021-03-22T11:01:09Z","file_name":"2021_LettersMathPhysics_Napiorkowski.pdf"}],"license":"https://creativecommons.org/licenses/by/4.0/","issue":"2","volume":111,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 111","month":"03","citation":{"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.","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","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.","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.","ista":"Napiórkowski MM, Seiringer R. 2021. Free energy asymptotics of the quantum Heisenberg spin chain. Letters in Mathematical Physics. 111(2), 31."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"title":"Free energy asymptotics of the quantum Heisenberg spin chain","article_number":"31","year":"2021","has_accepted_license":"1","isi":1,"publication":"Letters in Mathematical Physics","day":"09","date_created":"2021-03-21T23:01:19Z","doi":"10.1007/s11005-021-01375-4","date_published":"2021-03-09T00:00:00Z","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"},{"author":[{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"}],"article_processing_charge":"No","external_id":{"arxiv":["2010.05356"],"isi":["000617037900013"]},"title":"Frequency-multiplexed hybrid optical entangled source based on the Pockels effect","citation":{"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.","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).","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","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","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."},"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","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":[{"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.","lang":"eng"}],"oa_version":"Preprint"},{"article_number":"e2024083118","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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.","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).","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."},"title":"Designing self-assembling kinetics with differentiable statistical physics models","external_id":{"pmid":["33653960"],"isi":["000627429100097"]},"article_processing_charge":"No","author":[{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"},{"first_name":"Ella M.","full_name":"King, Ella M.","last_name":"King"},{"first_name":"Samuel S.","last_name":"Schoenholz","full_name":"Schoenholz, Samuel S."},{"first_name":"Ekin D.","full_name":"Cubuk, Ekin D.","last_name":"Cubuk"},{"last_name":"Brenner","full_name":"Brenner, Michael P.","first_name":"Michael P."}],"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.","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences","day":"09","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-03-21T23:01:20Z","doi":"10.1073/pnas.2024083118","date_published":"2021-03-09T00:00:00Z","_id":"9257","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","ddc":["530"],"date_updated":"2023-08-07T14:19:34Z","file_date_updated":"2021-03-22T12:23:54Z","department":[{"_id":"CaGo"}],"pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 118","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","file_id":"9278","success":1,"date_updated":"2021-03-22T12:23:54Z","file_size":1047954,"creator":"dernst","date_created":"2021-03-22T12:23:54Z","file_name":"2021_PNAS_Goodrich.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":118,"issue":"10"},{"day":"19","publication":"Science Advances","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1126/sciadv.abd9153","date_published":"2021-03-19T00:00:00Z","date_created":"2021-03-22T07:14:03Z","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.","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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."},"title":"Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity","author":[{"full_name":"Mbianda, Johanne","last_name":"Mbianda","first_name":"Johanne"},{"first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M","last_name":"Bakail"},{"first_name":"Christophe","full_name":"André, Christophe","last_name":"André"},{"last_name":"Moal","full_name":"Moal, Gwenaëlle","first_name":"Gwenaëlle"},{"first_name":"Marie E.","full_name":"Perrin, Marie E.","last_name":"Perrin"},{"first_name":"Guillaume","last_name":"Pinna","full_name":"Pinna, Guillaume"},{"first_name":"Raphaël","full_name":"Guerois, Raphaël","last_name":"Guerois"},{"last_name":"Becher","full_name":"Becher, Francois","first_name":"Francois"},{"last_name":"Legrand","full_name":"Legrand, Pierre","first_name":"Pierre"},{"last_name":"Traoré","full_name":"Traoré, Seydou","first_name":"Seydou"},{"first_name":"Céline","last_name":"Douat","full_name":"Douat, Céline"},{"first_name":"Gilles","full_name":"Guichard, Gilles","last_name":"Guichard"},{"last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise","first_name":"Françoise"}],"external_id":{"pmid":["33741589"],"isi":["000633443000011"]},"article_processing_charge":"No","article_number":"eabd9153","file":[{"creator":"dernst","date_updated":"2021-03-22T12:49:00Z","file_size":837156,"date_created":"2021-03-22T12:49:00Z","file_name":"2021_ScienceAdv_Mbianda.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9280","checksum":"737624cd0e630ffa7c52797a690500e3","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","volume":7,"issue":"12","license":"https://creativecommons.org/licenses/by-nc/4.0/","pmid":1,"oa_version":"Published Version","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."}],"month":"03","intvolume":" 7","ddc":["570"],"date_updated":"2023-08-07T14:20:26Z","file_date_updated":"2021-03-22T12:49:00Z","department":[{"_id":"CampIT"}],"_id":"9262","status":"public","type":"journal_article","article_type":"original","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)"}},{"_id":"9259","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":"2023-08-07T14:18:26Z","ddc":["570"],"department":[{"_id":"MiSi"},{"_id":"Bio"}],"file_date_updated":"2021-03-22T12:08:26Z","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"02","publication_status":"published","publication_identifier":{"eissn":["1664-3224"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-03-22T12:08:26Z","file_size":3740146,"creator":"dernst","date_created":"2021-03-22T12:08:26Z","file_name":"2021_FrontiersImmumo_Vaahtomeri.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9277","checksum":"663f5a48375e42afa4bfef58d42ec186","success":1}],"ec_funded":1,"volume":12,"article_number":"630002","project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"grant_number":"Y 564-B12","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"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.","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","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","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.","short":"K. Vaahtomeri, C. Moussion, R. Hauschild, M.K. Sixt, Frontiers in Immunology 12 (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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["33717158"],"isi":["000627134400001"]},"article_processing_charge":"No","author":[{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri"},{"id":"3356F664-F248-11E8-B48F-1D18A9856A87","first_name":"Christine","full_name":"Moussion, Christine","last_name":"Moussion"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"title":"Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium","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.","oa":1,"quality_controlled":"1","publisher":"Frontiers","year":"2021","isi":1,"has_accepted_license":"1","publication":"Frontiers in Immunology","day":"25","date_created":"2021-03-21T23:01:20Z","date_published":"2021-02-25T00:00:00Z","doi":"10.3389/fimmu.2021.630002"},{"date_updated":"2023-08-07T14:17:55Z","ddc":["580"],"file_date_updated":"2021-03-22T11:18:58Z","department":[{"_id":"JiFr"}],"_id":"9254","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":["20411723"]},"language":[{"iso":"eng"}],"file":[{"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","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e1022f3aee349853ded2b2b3e092362d","file_id":"9275","success":1}],"volume":12,"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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"03","citation":{"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.","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.","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.","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.","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).","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000630419400048"],"pmid":["33712581"]},"author":[{"first_name":"Yangjie","full_name":"Hu, Yangjie","last_name":"Hu"},{"first_name":"Moutasem","full_name":"Omary, Moutasem","last_name":"Omary"},{"first_name":"Yun","last_name":"Hu","full_name":"Hu, Yun"},{"first_name":"Ohad","full_name":"Doron, Ohad","last_name":"Doron"},{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","full_name":"Chen, Qingguo","first_name":"Qingguo"},{"last_name":"Megides","full_name":"Megides, Or","first_name":"Or"},{"full_name":"Chekli, Ori","last_name":"Chekli","first_name":"Ori"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"Yunde","last_name":"Zhao","full_name":"Zhao, Yunde"},{"full_name":"Tsarfaty, Ilan","last_name":"Tsarfaty","first_name":"Ilan"},{"full_name":"Shani, Eilon","last_name":"Shani","first_name":"Eilon"}],"title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","article_number":"1657","year":"2021","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"12","date_created":"2021-03-21T23:01:19Z","doi":"10.1038/s41467-021-21802-3","date_published":"2021-03-12T00:00:00Z","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,"quality_controlled":"1","publisher":"Springer Nature"},{"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).","doi":"10.1038/s41534-021-00387-1","date_published":"2021-03-15T00:00:00Z","date_created":"2021-03-21T23:01:19Z","isi":1,"has_accepted_license":"1","year":"2021","day":"15","publication":"npj Quantum Information","article_number":"50","author":[{"first_name":"Matej","last_name":"Pivoluska","full_name":"Pivoluska, Matej"},{"full_name":"Plesch, Martin","last_name":"Plesch","first_name":"Martin"},{"full_name":"Farkas, Máté","last_name":"Farkas","first_name":"Máté"},{"full_name":"Ruzickova, Natalia","last_name":"Ruzickova","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"},{"first_name":"Clara","last_name":"Flegel","full_name":"Flegel, Clara"},{"last_name":"Valencia","full_name":"Valencia, Natalia Herrera","first_name":"Natalia Herrera"},{"last_name":"Mccutcheon","full_name":"Mccutcheon, Will","first_name":"Will"},{"first_name":"Mehul","full_name":"Malik, Mehul","last_name":"Malik"},{"last_name":"Aguilar","full_name":"Aguilar, Edgar A.","first_name":"Edgar A."}],"article_processing_charge":"No","external_id":{"isi":["000629173100001"]},"title":"Semi-device-independent random number generation with flexible assumptions","citation":{"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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"03","intvolume":" 7","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."}],"oa_version":"Published Version","volume":7,"publication_identifier":{"eissn":["2056-6387"]},"publication_status":"published","file":[{"date_updated":"2021-03-22T11:09:34Z","file_size":1360271,"creator":"dernst","date_created":"2021-03-22T11:09:34Z","file_name":"2021_NPJQuantumInformation_Pivoluska.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9274","checksum":"26d3f2a2c8c8fa8c1002028326b45f64","success":1}],"language":[{"iso":"eng"}],"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":"9255","department":[{"_id":"FyKo"}],"file_date_updated":"2021-03-22T11:09:34Z","date_updated":"2023-08-07T14:17:26Z","ddc":["530"]},{"_id":"9260","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)"},"ddc":["510"],"date_updated":"2023-08-07T14:20:00Z","department":[{"_id":"TiBr"}],"file_date_updated":"2021-03-22T12:41:26Z","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"03","intvolume":" 299","scopus_import":"1","file":[{"file_id":"9279","checksum":"8ed9f49568806894744096dbbca0ad7b","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-03-22T12:41:26Z","file_name":"2021_MathZeitschrift_Browning.pdf","date_updated":"2021-03-22T12:41:26Z","file_size":492685,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0025-5874"],"eissn":["1432-1823"]},"publication_status":"published","volume":299,"project":[{"_id":"26A8D266-B435-11E9-9278-68D0E5697425","name":"Between rational and integral points","grant_number":"EP-P026710-2"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","short":"T.D. Browning, S. Yamagishi, Mathematische Zeitschrift 299 (2021) 1071–1101.","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.","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.","ista":"Browning TD, Yamagishi S. 2021. Arithmetic of higher-dimensional orbifolds and a mixed Waring problem. Mathematische Zeitschrift. 299, 1071–1101."},"title":"Arithmetic of higher-dimensional orbifolds and a mixed Waring problem","author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177"},{"first_name":"Shuntaro","last_name":"Yamagishi","full_name":"Yamagishi, Shuntaro"}],"article_processing_charge":"No","external_id":{"isi":["000625573800002"]},"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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"05","publication":"Mathematische Zeitschrift","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1007/s00209-021-02695-w","date_published":"2021-03-05T00:00:00Z","date_created":"2021-03-21T23:01:21Z","page":"1071–1101"},{"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.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2021","isi":1,"publication":"Nature Methods","day":"01","page":"226-228","date_created":"2021-03-21T23:01:20Z","date_published":"2021-03-01T00:00:00Z","doi":"10.1038/s41592-021-01087-6","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000625600600007"],"pmid":["33674797"]},"author":[{"first_name":"Henry","last_name":"Pinkard","full_name":"Pinkard, Henry"},{"last_name":"Stuurman","full_name":"Stuurman, Nico","first_name":"Nico"},{"first_name":"Ivan E.","last_name":"Ivanov","full_name":"Ivanov, Ivan E."},{"last_name":"Anthony","full_name":"Anthony, Nicholas M.","first_name":"Nicholas M."},{"first_name":"Wei","last_name":"Ouyang","full_name":"Ouyang, Wei"},{"first_name":"Bin","full_name":"Li, Bin","last_name":"Li"},{"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"},{"first_name":"Grace","last_name":"Zhang","full_name":"Zhang, Grace"},{"first_name":"Ryan","full_name":"Mei, Ryan","last_name":"Mei"},{"full_name":"Anderson, Michael","last_name":"Anderson","first_name":"Michael"},{"last_name":"Shepherd","full_name":"Shepherd, Douglas P.","first_name":"Douglas P."},{"first_name":"Ian","full_name":"Hunt-Isaak, Ian","last_name":"Hunt-Isaak"},{"first_name":"Raymond L.","full_name":"Dunn, Raymond L.","last_name":"Dunn"},{"full_name":"Jahr, Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke"},{"last_name":"Kato","full_name":"Kato, Saul","first_name":"Saul"},{"first_name":"Loïc A.","last_name":"Royer","full_name":"Royer, Loïc A."},{"first_name":"Jay R.","last_name":"Thiagarajah","full_name":"Thiagarajah, Jay R."},{"first_name":"Kevin W.","last_name":"Eliceiri","full_name":"Eliceiri, Kevin W."},{"last_name":"Lundberg","full_name":"Lundberg, Emma","first_name":"Emma"},{"last_name":"Mehta","full_name":"Mehta, Shalin B.","first_name":"Shalin B."},{"full_name":"Waller, Laura","last_name":"Waller","first_name":"Laura"}],"title":"Pycro-Manager: Open-source software for customized and reproducible microscope control","oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41592-021-01087-6","open_access":"1"}],"scopus_import":"1","intvolume":" 18","month":"03","publication_status":"published","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"language":[{"iso":"eng"}],"volume":18,"issue":"3","_id":"9258","type":"journal_article","article_type":"letter_note","status":"public","date_updated":"2023-08-07T14:19:08Z","department":[{"_id":"JoDa"}]},{"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.","oa":1,"publisher":"Rockefeller University Press","quality_controlled":"1","publication":"Journal of Cell Biology","day":"19","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-04-04T22:01:21Z","date_published":"2021-03-19T00:00:00Z","doi":"10.1083/jcb.202003052","article_number":"e202003052","project":[{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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.","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.","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."},"title":"Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation","article_processing_charge":"No","external_id":{"pmid":["33740033"],"isi":["000663160600002"]},"author":[{"first_name":"Ulrich","full_name":"Dobramysl, Ulrich","last_name":"Dobramysl"},{"first_name":"Iris Katharina","full_name":"Jarsch, Iris Katharina","last_name":"Jarsch"},{"last_name":"Inoue","full_name":"Inoue, Yoshiko","first_name":"Yoshiko"},{"first_name":"Hanae","full_name":"Shimo, Hanae","last_name":"Shimo"},{"first_name":"Benjamin","full_name":"Richier, Benjamin","last_name":"Richier"},{"full_name":"Gadsby, Jonathan R.","last_name":"Gadsby","first_name":"Jonathan R."},{"first_name":"Julia","last_name":"Mason","full_name":"Mason, Julia"},{"first_name":"Alicja","last_name":"Szałapak","full_name":"Szałapak, Alicja"},{"first_name":"Pantelis Savvas","last_name":"Ioannou","full_name":"Ioannou, Pantelis Savvas"},{"last_name":"Correia","full_name":"Correia, Guilherme Pereira","first_name":"Guilherme Pereira"},{"last_name":"Walrant","full_name":"Walrant, Astrid","first_name":"Astrid"},{"last_name":"Butler","full_name":"Butler, Richard","first_name":"Richard"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Simons","full_name":"Simons, Benjamin D.","first_name":"Benjamin D."},{"first_name":"Jennifer L.","full_name":"Gallop, Jennifer L.","last_name":"Gallop"}],"pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 220","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":9019720,"date_updated":"2021-04-06T10:39:08Z","file_name":"2021_JCB_Dobramysl.pdf","date_created":"2021-04-06T10:39:08Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9310","checksum":"4739ffd90f2c7e05ac5b00f057c58aa2"}],"publication_status":"published","publication_identifier":{"eissn":["15408140"]},"issue":"4","volume":220,"_id":"9306","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":["576"],"date_updated":"2023-08-07T14:32:28Z","department":[{"_id":"EdHa"}],"file_date_updated":"2021-04-06T10:39:08Z"},{"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":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9309","checksum":"6529b609c9209861720ffa4685111bc6","success":1,"date_updated":"2021-04-06T09:31:28Z","file_size":727005,"creator":"dernst","date_created":"2021-04-06T09:31:28Z","file_name":"2021_StochPartDiffEquation_Hensel.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2194-0401"],"eissn":["2194-041X"]},"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","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","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"publication":"Stochastics and Partial Differential Equations: Analysis and Computations","day":"21","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-04-04T22:01:21Z","doi":"10.1007/s40072-021-00188-9","date_published":"2021-03-21T00:00:00Z","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,"publisher":"Springer Nature","quality_controlled":"1"},{"title":"Decay of streaks and rolls in plane Couette-Poiseuille flow","author":[{"full_name":"Liu, T.","last_name":"Liu","first_name":"T."},{"first_name":"B.","last_name":"Semin","full_name":"Semin, B."},{"id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","first_name":"Lukasz","last_name":"Klotz","full_name":"Klotz, Lukasz","orcid":"0000-0003-1740-7635"},{"first_name":"R.","full_name":"Godoy-Diana, R.","last_name":"Godoy-Diana"},{"full_name":"Wesfreid, J. E.","last_name":"Wesfreid","first_name":"J. E."},{"full_name":"Mullin, T.","last_name":"Mullin","first_name":"T."}],"external_id":{"arxiv":["2008.08851"],"isi":["000629677500001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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","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."},"article_number":"A65","doi":"10.1017/jfm.2021.89","date_published":"2021-03-17T00:00:00Z","date_created":"2021-03-28T22:01:42Z","day":"17","publication":"Journal of Fluid Mechanics","isi":1,"year":"2021","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"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.","department":[{"_id":"BjHo"}],"date_updated":"2023-08-07T14:30:11Z","status":"public","type":"journal_article","article_type":"original","_id":"9297","volume":915,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"publication_status":"published","month":"03","intvolume":" 915","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2008.08851","open_access":"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."}]},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.02287"}],"scopus_import":"1","intvolume":" 97","month":"03","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."}],"oa_version":"Preprint","ec_funded":1,"volume":97,"issue":"3","publication_status":"published","publication_identifier":{"issn":["0364-9024"],"eissn":["1097-0118"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"9295","department":[{"_id":"UlWa"}],"date_updated":"2023-08-07T14:26:15Z","oa":1,"publisher":"Wiley","quality_controlled":"1","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.","page":"426-440","date_created":"2021-03-28T22:01:41Z","date_published":"2021-03-23T00:00:00Z","doi":"10.1002/jgt.22665","year":"2021","isi":1,"publication":"Journal of Graph Theory","day":"23","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_processing_charge":"No","external_id":{"arxiv":["2002.02287"],"isi":["000631693200001"]},"author":[{"last_name":"Arroyo Guevara","orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M"},{"first_name":"Dan","full_name":"Mcquillan, Dan","last_name":"Mcquillan"},{"last_name":"Richter","full_name":"Richter, R. Bruce","first_name":"R. Bruce"},{"last_name":"Salazar","full_name":"Salazar, Gelasio","first_name":"Gelasio"},{"full_name":"Sullivan, Matthew","last_name":"Sullivan","first_name":"Matthew"}],"title":"Drawings of complete graphs in the projective plane","citation":{"chicago":"Arroyo Guevara, Alan M, Dan Mcquillan, R. Bruce Richter, Gelasio Salazar, and Matthew Sullivan. “Drawings of Complete Graphs in the Projective Plane.” Journal of Graph Theory. Wiley, 2021. https://doi.org/10.1002/jgt.22665.","ista":"Arroyo Guevara AM, Mcquillan D, Richter RB, Salazar G, Sullivan M. 2021. Drawings of complete graphs in the projective plane. Journal of Graph Theory. 97(3), 426–440.","mla":"Arroyo Guevara, Alan M., et al. “Drawings of Complete Graphs in the Projective Plane.” Journal of Graph Theory, vol. 97, no. 3, Wiley, 2021, pp. 426–40, doi:10.1002/jgt.22665.","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.","apa":"Arroyo Guevara, A. M., Mcquillan, D., Richter, R. B., Salazar, G., & Sullivan, M. (2021). Drawings of complete graphs in the projective plane. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22665","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"title":"Engaging the front wheels to drive through fibrous terrain","article_processing_charge":"No","external_id":{"isi":["000631681200004"],"pmid":["33756118"]},"author":[{"full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Gärtner, F. R., & Sixt, M. K. (2021). Engaging the front wheels to drive through fibrous terrain. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2021.03.002","ama":"Gärtner FR, Sixt MK. Engaging the front wheels to drive through fibrous terrain. Developmental Cell. 2021;56(6):723-725. doi:10.1016/j.devcel.2021.03.002","ieee":"F. R. Gärtner and M. K. Sixt, “Engaging the front wheels to drive through fibrous terrain,” Developmental Cell, vol. 56, no. 6. Elsevier, pp. 723–725, 2021.","short":"F.R. Gärtner, M.K. Sixt, Developmental Cell 56 (2021) 723–725.","mla":"Gärtner, Florian R., and Michael K. Sixt. “Engaging the Front Wheels to Drive through Fibrous Terrain.” Developmental Cell, vol. 56, no. 6, Elsevier, 2021, pp. 723–25, doi:10.1016/j.devcel.2021.03.002.","ista":"Gärtner FR, Sixt MK. 2021. Engaging the front wheels to drive through fibrous terrain. Developmental Cell. 56(6), 723–725.","chicago":"Gärtner, Florian R, and Michael K Sixt. “Engaging the Front Wheels to Drive through Fibrous Terrain.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2021.03.002."},"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2021-03-28T22:01:41Z","date_published":"2021-03-22T00:00:00Z","doi":"10.1016/j.devcel.2021.03.002","page":"723-725","publication":"Developmental Cell","day":"22","year":"2021","isi":1,"status":"public","type":"journal_article","article_type":"original","_id":"9294","department":[{"_id":"MiSi"}],"date_updated":"2023-08-07T14:26:47Z","intvolume":" 56","month":"03","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2021.03.002","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"issue":"6","volume":56,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["15345807"],"eissn":["18781551"]}},{"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"file_date_updated":"2021-04-19T08:30:22Z","date_updated":"2023-08-07T14:36:14Z","ddc":["570"],"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":"9329","issue":"6","volume":357,"ec_funded":1,"publication_identifier":{"issn":["0165-0270"],"eissn":["1872-678X"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9339","checksum":"2a5800d91b96d08b525e17319dcd5e44","success":1,"date_updated":"2021-04-19T08:30:22Z","file_size":6924738,"creator":"dernst","date_created":"2021-04-19T08:30:22Z","file_name":"2021_JourNeuroscienceMeth_Zhang.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 357","acknowledged_ssus":[{"_id":"SSU"}],"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."}],"oa_version":"Published Version","author":[{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"external_id":{"isi":["000661088500005"]},"article_processing_charge":"Yes (via OA deal)","title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","citation":{"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.","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.","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","short":"X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"}],"article_number":"109125","doi":"10.1016/j.jneumeth.2021.109125","date_published":"2021-03-09T00:00:00Z","date_created":"2021-04-18T22:01:39Z","isi":1,"has_accepted_license":"1","year":"2021","day":"09","publication":"Journal of Neuroscience Methods","quality_controlled":"1","publisher":"Elsevier","oa":1,"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."},{"article_processing_charge":"No","external_id":{"isi":["000636734000022"],"pmid":["33730596"]},"author":[{"last_name":"Petridou","orcid":"0000-0002-8451-1195","full_name":"Petridou, Nicoletta","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Nicoletta"},{"first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"title":"Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions","citation":{"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.","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.","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","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","short":"N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell 184 (2021) 1914–1928.e19.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"grant_number":"V00736","name":"Tissue material properties in embryonic development","call_identifier":"FWF","_id":"2693FD8C-B435-11E9-9278-68D0E5697425"}],"page":"1914-1928.e19","date_created":"2021-04-11T22:01:14Z","doi":"10.1016/j.cell.2021.02.017","date_published":"2021-04-01T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"Cell","day":"01","oa":1,"quality_controlled":"1","publisher":"Elsevier","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.).","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"file_date_updated":"2021-06-08T10:04:10Z","date_updated":"2023-08-07T14:33:59Z","ddc":["570"],"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","status":"public","_id":"9316","ec_funded":1,"issue":"7","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/","relation":"press_release"}]},"volume":184,"publication_status":"published","publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"1e5295fbd9c2a459173ec45a0e8a7c2e","file_id":"9534","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_Cell_Petridou.pdf","date_created":"2021-06-08T10:04:10Z","file_size":11405875,"date_updated":"2021-06-08T10:04:10Z","creator":"cziletti"}],"scopus_import":"1","intvolume":" 184","month":"04","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"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"pmid":1,"oa_version":"Published Version"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"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).","date_published":"2021-03-31T00:00:00Z","doi":"10.1007/s00454-021-00281-9","date_created":"2021-04-11T22:01:15Z","page":"1296–1313","day":"31","publication":"Discrete and Computational Geometry","isi":1,"has_accepted_license":"1","year":"2021","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"The multi-cover persistence of Euclidean balls","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","last_name":"Osang"}],"external_id":{"isi":["000635460400001"]},"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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."},"month":"03","intvolume":" 65","scopus_import":"1","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."}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"187"}]},"volume":65,"ec_funded":1,"file":[{"success":1,"file_id":"10394","checksum":"59b4e1e827e494209bcb4aae22e1d347","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"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"publication_status":"published","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":"9317","file_date_updated":"2021-12-01T10:56:53Z","department":[{"_id":"HeEd"}],"ddc":["516"],"date_updated":"2023-08-07T14:35:44Z"},{"volume":9,"ec_funded":1,"publication_identifier":{"eissn":["20505094"]},"publication_status":"published","file":[{"date_updated":"2021-04-12T07:15:58Z","file_size":883851,"creator":"dernst","date_created":"2021-04-12T07:15:58Z","file_name":"2021_ForumMath_Bossmann.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"17a3e6786d1e930cf0c14a880a6d7e92","file_id":"9319","success":1}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 9","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","file_date_updated":"2021-04-12T07:15:58Z","department":[{"_id":"RoSe"}],"date_updated":"2023-08-07T14:35:06Z","ddc":["510"],"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":"9318","doi":"10.1017/fms.2021.22","date_published":"2021-03-26T00:00:00Z","date_created":"2021-04-11T22:01:15Z","has_accepted_license":"1","isi":1,"year":"2021","day":"26","publication":"Forum of Mathematics, Sigma","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"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).","author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343","last_name":"Bossmann"},{"orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P","last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000634006900001"]},"title":"Asymptotic expansion of low-energy excitations for weakly interacting bosons","citation":{"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.","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.","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","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.","ista":"Bossmann L, Petrat SP, Seiringer R. 2021. Asymptotic expansion of low-energy excitations for weakly interacting bosons. Forum of Mathematics, Sigma. 9, e28."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"article_number":"e28"},{"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","quality_controlled":"1","publisher":"AIP Publishing","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.","author":[{"last_name":"Szigeti","full_name":"Szigeti, Stuart S.","first_name":"Stuart S."},{"orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"},{"first_name":"Simon A.","full_name":"Haine, Simon A.","last_name":"Haine"}],"article_processing_charge":"No","external_id":{"arxiv":["2010.09168"],"isi":["000637702100001"]},"title":"Improving cold-atom sensors with quantum entanglement: Prospects and challenges","citation":{"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.","ista":"Szigeti SS, Hosten O, Haine SA. 2021. Improving cold-atom sensors with quantum entanglement: Prospects and challenges. Applied Physics Letters. 118(14), 140501.","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.","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).","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"140501","volume":118,"issue":"14","publication_identifier":{"issn":["00036951"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2010.09168"}],"month":"04","intvolume":" 118","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","department":[{"_id":"OnHo"}],"date_updated":"2023-08-07T14:36:42Z","article_type":"original","type":"journal_article","status":"public","_id":"9331"},{"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","external_id":{"isi":["000637398300002"]},"author":[{"full_name":"Schöpf, Clemens L.","last_name":"Schöpf","first_name":"Clemens L."},{"full_name":"Ablinger, Cornelia","last_name":"Ablinger","first_name":"Cornelia"},{"last_name":"Geisler","full_name":"Geisler, Stefanie M.","first_name":"Stefanie M."},{"full_name":"Stanika, Ruslan I.","last_name":"Stanika","first_name":"Ruslan I."},{"first_name":"Marta","full_name":"Campiglio, Marta","last_name":"Campiglio"},{"last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nimmervoll, Benedikt","last_name":"Nimmervoll","first_name":"Benedikt"},{"full_name":"Schlick, Bettina","last_name":"Schlick","first_name":"Bettina"},{"last_name":"Brockhaus","full_name":"Brockhaus, Johannes","first_name":"Johannes"},{"first_name":"Markus","full_name":"Missler, Markus","last_name":"Missler"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gerald J.","full_name":"Obermair, Gerald J.","last_name":"Obermair"}],"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.","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.","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).","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","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","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","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","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","ec_funded":1,"volume":118,"issue":"14","publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_PNAS_Schoepf.pdf","date_created":"2021-04-19T10:10:56Z","creator":"dernst","file_size":2603911,"date_updated":"2021-04-19T10:10:56Z","success":1,"file_id":"9340","checksum":"dd014f68ae9d7d8d8fc4139a24e04506","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}]},{"date_created":"2021-04-18T22:01:41Z","date_published":"2021-04-08T00:00:00Z","doi":"10.3390/ijms22083862","publication":"International Journal of Molecular Sciences","day":"08","year":"2021","has_accepted_license":"1","isi":1,"oa":1,"publisher":"MDPI","quality_controlled":"1","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.","title":"Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis","article_processing_charge":"No","external_id":{"isi":["000644394800001"]},"author":[{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina"},{"first_name":"Pál","last_name":"Miskolczi","full_name":"Miskolczi, Pál"},{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavý","orcid":"0000-0001-5227-5741","full_name":"Marhavý, Peter"},{"full_name":"Cruz-Ramírez, Alfredo","last_name":"Cruz-Ramírez","first_name":"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","last_name":"Robert","full_name":"Robert, Stéphanie"},{"first_name":"László","last_name":"Bakó","full_name":"Bakó, László"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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","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","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.","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."},"article_number":"3862","issue":"8","volume":22,"language":[{"iso":"eng"}],"file":[{"date_created":"2021-04-19T10:54:55Z","file_name":"2021_JourMolecularScience_Oetvoes.pdf","date_updated":"2021-04-19T10:54:55Z","file_size":2769717,"creator":"dernst","file_id":"9342","checksum":"26ada2531ad1f9c01a1664de0431f1fe","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"intvolume":" 22","month":"04","scopus_import":"1","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."}],"file_date_updated":"2021-04-19T10:54:55Z","department":[{"_id":"EvBe"}],"ddc":["570"],"date_updated":"2023-08-08T13:09:58Z","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":"9332"},{"_id":"9333","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":"2023-08-08T13:09:28Z","ddc":["510"],"department":[{"_id":"RoSe"}],"file_date_updated":"2021-04-19T10:40:01Z","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 111","publication_identifier":{"eissn":["15730530"],"issn":["03779017"]},"publication_status":"published","file":[{"date_updated":"2021-04-19T10:40:01Z","file_size":438084,"creator":"dernst","date_created":"2021-04-19T10:40:01Z","file_name":"2021_LettersMathPhysics_Mitrouskas.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"be56c0845a43c0c5c772ee0b5053f7d7","file_id":"9341","success":1}],"language":[{"iso":"eng"}],"volume":111,"article_number":"45","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.","short":"D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021).","ieee":"D. J. Mitrouskas, “A note on the Fröhlich dynamics in the strong coupling limit,” Letters in Mathematical Physics, vol. 111. Springer Nature, 2021.","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","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","author":[{"first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas"}],"article_processing_charge":"No","external_id":{"isi":["000637359300002"]},"title":"A note on the Fröhlich dynamics in the strong coupling limit","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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"05","publication":"Letters in Mathematical Physics","date_published":"2021-04-05T00:00:00Z","doi":"10.1007/s11005-021-01380-7","date_created":"2021-04-18T22:01:41Z"},{"acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics”.","oa":1,"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","year":"2021","isi":1,"publication":"SIAM Journal on Numerical Analysis","day":"01","page":"60-87","date_created":"2021-04-18T22:01:42Z","doi":"10.1137/19M1300017","date_published":"2021-01-01T00:00:00Z","citation":{"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.","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.","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1911.04185"],"isi":["000625044600003"]},"article_processing_charge":"No","author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer"},{"full_name":"Matthes, Daniel","last_name":"Matthes","first_name":"Daniel"}],"title":"The waiting time phenomenon in spatially discretized porous medium and thin film equations","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."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.04185"}],"scopus_import":"1","intvolume":" 59","month":"01","publication_status":"published","publication_identifier":{"issn":["0036-1429"]},"language":[{"iso":"eng"}],"volume":59,"issue":"1","_id":"9335","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-08T13:10:40Z","department":[{"_id":"JuFi"}]},{"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"article_number":"041501","title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","author":[{"first_name":"Pierre François","last_name":"Lenne","full_name":"Lenne, Pierre François"},{"last_name":"Munro","full_name":"Munro, Edwin","first_name":"Edwin"},{"last_name":"Heemskerk","full_name":"Heemskerk, Idse","first_name":"Idse"},{"first_name":"Aryeh","full_name":"Warmflash, Aryeh","last_name":"Warmflash"},{"full_name":"Bocanegra, Laura","last_name":"Bocanegra","first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi","full_name":"Kishi, Kasumi","last_name":"Kishi"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"first_name":"Yuchen","last_name":"Long","full_name":"Long, Yuchen"},{"first_name":"Antoine","last_name":"Fruleux","full_name":"Fruleux, Antoine"},{"last_name":"Boudaoud","full_name":"Boudaoud, Arezki","first_name":"Arezki"},{"full_name":"Saunders, Timothy E.","last_name":"Saunders","first_name":"Timothy E."},{"first_name":"Paolo","last_name":"Caldarelli","full_name":"Caldarelli, Paolo"},{"first_name":"Arthur","full_name":"Michaut, Arthur","last_name":"Michaut"},{"first_name":"Jerome","last_name":"Gros","full_name":"Gros, Jerome"},{"full_name":"Maroudas-Sacks, Yonit","last_name":"Maroudas-Sacks","first_name":"Yonit"},{"first_name":"Kinneret","full_name":"Keren, Kinneret","last_name":"Keren"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Zev J.","last_name":"Gartner","full_name":"Gartner, Zev J."},{"last_name":"Stormo","full_name":"Stormo, Benjamin","first_name":"Benjamin"},{"first_name":"Amy","full_name":"Gladfelter, Amy","last_name":"Gladfelter"},{"full_name":"Rodrigues, Alan","last_name":"Rodrigues","first_name":"Alan"},{"full_name":"Shyer, Amy","last_name":"Shyer","first_name":"Amy"},{"last_name":"Minc","full_name":"Minc, Nicolas","first_name":"Nicolas"},{"first_name":"Jean Léon","last_name":"Maître","full_name":"Maître, Jean Léon"},{"first_name":"Stefano","last_name":"Di Talia","full_name":"Di Talia, Stefano"},{"first_name":"Bassma","full_name":"Khamaisi, Bassma","last_name":"Khamaisi"},{"first_name":"David","last_name":"Sprinzak","full_name":"Sprinzak, David"},{"last_name":"Tlili","full_name":"Tlili, Sham","first_name":"Sham"}],"article_processing_charge":"No","external_id":{"pmid":["33276350"],"isi":["000640396400001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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","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.","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)."},"publisher":"IOP Publishing","quality_controlled":"1","oa":1,"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).","doi":"10.1088/1478-3975/abd0db","date_published":"2021-04-14T00:00:00Z","date_created":"2021-04-25T22:01:29Z","day":"14","publication":"Physical biology","has_accepted_license":"1","isi":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":"9349","file_date_updated":"2021-04-27T08:38:35Z","department":[{"_id":"AnKi"},{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-08-08T13:15:46Z","month":"04","intvolume":" 18","scopus_import":"1","pmid":1,"oa_version":"Published Version","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."}],"volume":18,"related_material":{"record":[{"relation":"dissertation_contains","id":"13081","status":"public"}]},"issue":"4","ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9355","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","file_size":6296324,"date_updated":"2021-04-27T08:38:35Z","creator":"cziletti","file_name":"2021_PhysBio_Lenne.pdf","date_created":"2021-04-27T08:38:35Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1478-3975"]},"publication_status":"published"},{"type":"journal_article","article_type":"original","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)"},"status":"public","_id":"9334","file_date_updated":"2021-04-19T11:17:29Z","department":[{"_id":"NanoFab"}],"date_updated":"2023-08-08T13:11:31Z","ddc":["530"],"scopus_import":"1","month":"04","intvolume":" 7","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."}],"oa_version":"Published Version","pmid":1,"issue":"14","volume":7,"publication_identifier":{"eissn":["23752548"]},"publication_status":"published","file":[{"file_name":"2021_ScienceAdv_Duan.pdf","date_created":"2021-04-19T11:17:29Z","file_size":717489,"date_updated":"2021-04-19T11:17:29Z","creator":"dernst","success":1,"file_id":"9343","checksum":"4b383d4a1d484a71bbc64ecf401bbdbb","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"article_number":"eabf2690","author":[{"first_name":"J.","last_name":"Duan","full_name":"Duan, J."},{"full_name":"Álvarez-Pérez, G.","last_name":"Álvarez-Pérez","first_name":"G."},{"full_name":"Voronin, K. V.","last_name":"Voronin","first_name":"K. V."},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan"},{"last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, J.","first_name":"J."},{"last_name":"Volkov","full_name":"Volkov, V. S.","first_name":"V. S."},{"last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, J.","first_name":"J."},{"full_name":"Nikitin, A. Y.","last_name":"Nikitin","first_name":"A. Y."},{"full_name":"Alonso-González, P.","last_name":"Alonso-González","first_name":"P."}],"external_id":{"pmid":["33811076"],"isi":["000636455600027"]},"article_processing_charge":"No","title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","citation":{"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.","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.","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"AAAS","quality_controlled":"1","oa":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_published":"2021-04-02T00:00:00Z","doi":"10.1126/sciadv.abf2690","date_created":"2021-04-18T22:01:42Z","has_accepted_license":"1","isi":1,"year":"2021","day":"02","publication":"Science Advances"},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"citation":{"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.","ista":"Kirkpatrick K, Rademacher SAE, Schlein B. 2021. A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. 22, 2595–2618.","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.","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000638022600001"],"arxiv":["2010.13754"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Kay","last_name":"Kirkpatrick","full_name":"Kirkpatrick, Kay"},{"last_name":"Rademacher","full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira"},{"last_name":"Schlein","full_name":"Schlein, Benjamin","first_name":"Benjamin"}],"title":"A large deviation principle in many-body quantum dynamics","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","year":"2021","isi":1,"has_accepted_license":"1","publication":"Annales Henri Poincare","day":"08","page":"2595-2618","date_created":"2021-04-25T22:01:30Z","doi":"10.1007/s00023-021-01044-1","date_published":"2021-04-08T00:00:00Z","_id":"9351","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":"2023-08-08T13:14:40Z","ddc":["530"],"file_date_updated":"2021-10-15T11:15:40Z","department":[{"_id":"RoSe"}],"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. "}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 22","month":"04","publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-10-15T11:15:40Z","file_name":"2021_Annales_Kirkpatrick.pdf","creator":"cchlebak","date_updated":"2021-10-15T11:15:40Z","file_size":522669,"checksum":"1a0fb963f2f415ba470881a794f20eb6","file_id":"10143","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":22},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/febs.15823"}],"alternative_title":["Words of Advice"],"scopus_import":"1","month":"04","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"}],"pmid":1,"oa_version":"Published Version","publication_status":"published","publication_identifier":{"eissn":["1742-4658"],"issn":["1742-464X"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"9336","department":[{"_id":"CaHe"}],"date_updated":"2023-08-08T13:12:55Z","oa":1,"quality_controlled":"1","publisher":"Wiley","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.","date_created":"2021-04-18T22:01:43Z","date_published":"2021-04-05T00:00:00Z","doi":"10.1111/febs.15823","year":"2021","isi":1,"publication":"FEBS Journal","day":"05","article_processing_charge":"No","external_id":{"isi":["000636678800001"],"pmid":["33818917"]},"author":[{"last_name":"Sarabipour","full_name":"Sarabipour, Sarvenaz","first_name":"Sarvenaz"},{"full_name":"Hainer, Sarah J.","last_name":"Hainer","first_name":"Sarah J."},{"full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","last_name":"Arslan","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Charlotte M.","full_name":"De Winde, Charlotte M.","last_name":"De Winde"},{"first_name":"Emily","last_name":"Furlong","full_name":"Furlong, Emily"},{"full_name":"Bielczyk, Natalia","last_name":"Bielczyk","first_name":"Natalia"},{"last_name":"Jadavji","full_name":"Jadavji, Nafisa M.","first_name":"Nafisa M."},{"first_name":"Aparna P.","last_name":"Shah","full_name":"Shah, Aparna P."},{"last_name":"Davla","full_name":"Davla, Sejal","first_name":"Sejal"}],"title":"Building and sustaining mentor interactions as a mentee","citation":{"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.","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.","mla":"Sarabipour, Sarvenaz, et al. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal, Wiley, 2021, doi: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","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","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)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"author":[{"last_name":"Arslan","full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Eckert","full_name":"Eckert, Julia","first_name":"Julia"},{"first_name":"Thomas","last_name":"Schmidt","full_name":"Schmidt, Thomas"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"external_id":{"isi":["000704646900006"],"pmid":["33794149"]},"article_processing_charge":"No","title":"Holding it together: when cadherin meets cadherin","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"4182-4192","doi":"10.1016/j.bpj.2021.03.025","date_published":"2021-10-05T00:00:00Z","date_created":"2021-04-25T22:01:30Z","isi":1,"year":"2021","day":"05","publication":"Biophysical Journal","quality_controlled":"1","publisher":"Biophysical Society","oa":1,"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).","department":[{"_id":"CaHe"}],"date_updated":"2023-08-08T13:14:10Z","article_type":"original","type":"journal_article","status":"public","_id":"9350","related_material":{"record":[{"status":"public","id":"12368","relation":"dissertation_contains"}]},"volume":120,"publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view"}],"month":"10","intvolume":" 120","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version"},{"department":[{"_id":"RoSe"}],"date_updated":"2023-08-08T13:15:11Z","status":"public","article_type":"original","type":"journal_article","_id":"9348","issue":"3","volume":281,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"intvolume":" 281","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1911.03187","open_access":"1"}],"scopus_import":"1","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"}],"title":"Sharp tunneling estimates for a double-well model in infinite dimension","article_processing_charge":"No","external_id":{"isi":["000644702800005"],"arxiv":["1911.03187"]},"author":[{"orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris","last_name":"Brooks","first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"},{"last_name":"Di Gesù","full_name":"Di Gesù, Giacomo","first_name":"Giacomo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021).","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.","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","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."},"article_number":"109029","date_created":"2021-04-25T22:01:29Z","doi":"10.1016/j.jfa.2021.109029","date_published":"2021-04-07T00:00:00Z","publication":"Journal of Functional Analysis","day":"07","year":"2021","isi":1,"oa":1,"quality_controlled":"1","publisher":"Elsevier","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."},{"external_id":{"isi":["000646030400003"],"arxiv":["1912.11646"]},"article_processing_charge":"No","author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"full_name":"Gallistl, Dietmar","last_name":"Gallistl","first_name":"Dietmar"},{"last_name":"Peterseim","full_name":"Peterseim, Dietmar","first_name":"Dietmar"}],"title":"A priori error analysis of a numerical stochastic homogenization method","citation":{"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","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","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.","short":"J.L. Fischer, D. Gallistl, D. Peterseim, SIAM Journal on Numerical Analysis 59 (2021) 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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"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.","page":"660-674","date_created":"2021-04-25T22:01:31Z","doi":"10.1137/19M1308992","date_published":"2021-03-09T00:00:00Z","year":"2021","isi":1,"publication":"SIAM Journal on Numerical Analysis","day":"09","type":"journal_article","article_type":"original","status":"public","_id":"9352","department":[{"_id":"JuFi"}],"date_updated":"2023-08-08T13:13:37Z","main_file_link":[{"url":"https://arxiv.org/abs/1912.11646","open_access":"1"}],"scopus_import":"1","intvolume":" 59","month":"03","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","volume":59,"issue":"2","publication_status":"published","publication_identifier":{"issn":["0036-1429"]},"language":[{"iso":"eng"}]},{"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","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_created":"2021-05-02T22:01:29Z","doi":"10.1371/journal.pgen.1009479","date_published":"2021-04-01T00:00:00Z","page":"e1009479","publication":"PLoS genetics","day":"01","year":"2021","has_accepted_license":"1","isi":1,"title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","article_processing_charge":"No","external_id":{"isi":["000640606700001"]},"author":[{"last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro"},{"last_name":"Furthmann","full_name":"Furthmann, Nikolas","first_name":"Nikolas"},{"first_name":"Samuel H.","last_name":"Crossman","full_name":"Crossman, Samuel H."},{"full_name":"Tichy, Alexandra Madelaine","last_name":"Tichy","first_name":"Alexandra Madelaine"},{"full_name":"Hoyer, Nina","last_name":"Hoyer","first_name":"Nina"},{"full_name":"Petersen, Meike","last_name":"Petersen","first_name":"Meike"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","last_name":"Zheden"},{"full_name":"Bicher, Julia","last_name":"Bicher","first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gschaider-Reichhart","full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1819-198X","full_name":"György, Attila","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus"},{"last_name":"Soba","full_name":"Soba, Peter","first_name":"Peter"},{"last_name":"Winklhofer","full_name":"Winklhofer, Konstanze F.","first_name":"Konstanze F."},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","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.","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.","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."},"intvolume":" 17","month":"04","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."}],"volume":17,"issue":"4","language":[{"iso":"eng"}],"file":[{"file_name":"2021_PLOS_Ingles-Prieto.pdf","date_created":"2021-05-04T09:05:27Z","file_size":3072764,"date_updated":"2021-05-04T09:05:27Z","creator":"kschuh","success":1,"file_id":"9369","checksum":"82a74668f863e8dfb22fdd4f845c92ce","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["15537404"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"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"},{"author":[{"last_name":"Seferbekova","full_name":"Seferbekova, Zaira","first_name":"Zaira"},{"full_name":"Zabelkin, Alexey","last_name":"Zabelkin","first_name":"Alexey"},{"first_name":"Yulia","full_name":"Yakovleva, Yulia","last_name":"Yakovleva"},{"first_name":"Robert","full_name":"Afasizhev, Robert","last_name":"Afasizhev"},{"last_name":"Dranenko","full_name":"Dranenko, Natalia O.","first_name":"Natalia O."},{"first_name":"Nikita","full_name":"Alexeev, Nikita","last_name":"Alexeev"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","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"}],"article_processing_charge":"No","external_id":{"isi":["000643713300001"]},"title":"High rates of genome rearrangements and pathogenicity of Shigella spp","citation":{"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.","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.","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","ieee":"Z. Seferbekova et al., “High rates of genome rearrangements and pathogenicity of Shigella spp,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.","short":"Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N. Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"628622","date_published":"2021-04-12T00:00:00Z","doi":"10.3389/fmicb.2021.628622","date_created":"2021-05-09T22:01:38Z","has_accepted_license":"1","isi":1,"year":"2021","day":"12","publication":"Frontiers in Microbiology","publisher":"Frontiers","quality_controlled":"1","oa":1,"acknowledgement":"We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos.","file_date_updated":"2021-05-11T13:05:52Z","department":[{"_id":"FyKo"}],"date_updated":"2023-08-08T13:30:39Z","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":"9380","volume":12,"ec_funded":1,"publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published","file":[{"checksum":"2f856543add59273a482a7f326fc0400","file_id":"9384","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-05-11T13:05:52Z","file_name":"2021_Frontiers_Microbiology_Seferbekova.pdf","date_updated":"2021-05-11T13:05:52Z","file_size":14362316,"creator":"kschuh"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 12","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version"},{"ec_funded":1,"volume":25,"issue":"2","publication_status":"published","publication_identifier":{"issn":["1364-0380"]},"language":[{"iso":"eng"}],"file":[{"file_name":"densities.pdf","date_created":"2021-05-03T06:54:06Z","creator":"qho","file_size":479268,"date_updated":"2021-05-03T06:54:06Z","success":1,"file_id":"9366","checksum":"643a8d2d6f06f0888dcd7503f55d0920","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"intvolume":" 25","month":"04","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","department":[{"_id":"TaHa"}],"file_date_updated":"2021-05-03T06:54:06Z","date_updated":"2023-08-08T13:28:59Z","ddc":["514","516","512"],"type":"journal_article","article_type":"original","keyword":["Generalized configuration spaces","homological stability","homological densities","chiral algebras","chiral homology","factorization algebras","Koszul duality","Ran space"],"status":"public","_id":"9359","page":"813-912","date_created":"2021-05-02T06:59:33Z","date_published":"2021-04-27T00:00:00Z","doi":"10.2140/gt.2021.25.813","year":"2021","has_accepted_license":"1","isi":1,"publication":"Geometry & Topology","day":"27","oa":1,"quality_controlled":"1","publisher":"Mathematical Sciences Publishers","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.","external_id":{"arxiv":["1802.07948"],"isi":["000682738600005"]},"article_processing_charge":"No","author":[{"last_name":"Ho","full_name":"Ho, Quoc P","first_name":"Quoc P","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87"}],"title":"Homological stability and densities of generalized configuration spaces","citation":{"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","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.","short":"Q.P. Ho, Geometry & Topology 25 (2021) 813–912.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces"},{"name":"Algebro-Geometric Applications of Factorization Homology","grant_number":"M02751","_id":"26B96266-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"date_created":"2021-05-02T22:01:28Z","date_published":"2021-04-14T00:00:00Z","doi":"10.1128/mSphere.01024-20","publication":"mSphere","day":"14","year":"2021","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Society for Microbiology","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","article_processing_charge":"No","external_id":{"isi":["000663823400025"],"pmid":["33853875"]},"author":[{"full_name":"Gast, Matthieu","last_name":"Gast","first_name":"Matthieu"},{"first_name":"Nicole P.","last_name":"Kadzioch","full_name":"Kadzioch, Nicole P."},{"first_name":"Doreen","id":"384050BC-F248-11E8-B48F-1D18A9856A87","full_name":"Milius, Doreen","last_name":"Milius"},{"full_name":"Origgi, Francesco","last_name":"Origgi","first_name":"Francesco"},{"first_name":"Philippe","last_name":"Plattet","full_name":"Plattet, Philippe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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."},"article_number":"e01024-20","volume":6,"issue":"2","language":[{"iso":"eng"}],"file":[{"creator":"kschuh","date_updated":"2021-05-04T12:41:38Z","file_size":3379349,"date_created":"2021-05-04T12:41:38Z","file_name":"2021_mSphere_Gast.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"310748d140c8838335c1314431095898","file_id":"9370","success":1}],"publication_status":"published","publication_identifier":{"eissn":["23795042"]},"intvolume":" 6","month":"04","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"file_date_updated":"2021-05-04T12:41:38Z","department":[{"_id":"Bio"}],"ddc":["570"],"date_updated":"2023-08-08T13:26:12Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"9361"},{"_id":"9376","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","keyword":["multistability","mechanism","computational design","rigidity"],"status":"public","date_updated":"2023-08-08T13:31:38Z","ddc":["000"],"file_date_updated":"2021-12-17T08:13:51Z","department":[{"_id":"BeBi"}],"abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa_version":"Published Version","intvolume":" 40","month":"10","publication_status":"published","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-05-08T17:36:59Z","file_size":18926557,"creator":"bbickel","date_created":"2021-05-08T17:36:59Z","file_name":"Multistable-authorversion.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8564b3118457d4c8939a8ef2b1a2f16c","file_id":"9377"},{"creator":"bbickel","file_size":76542901,"date_updated":"2021-05-08T17:38:22Z","file_name":"multistable-video.mp4","date_created":"2021-05-08T17:38:22Z","relation":"main_file","access_level":"open_access","content_type":"video/mp4","success":1,"checksum":"3b6e874e30bfa1bfc3ad3498710145a1","file_id":"9378"},{"file_size":3367072,"date_updated":"2021-12-17T08:13:51Z","creator":"bbickel","file_name":"multistable-supplementary material.pdf","title":"Supplementary Material for “Computational Design of Planar Multistable Compliant Structures”","date_created":"2021-12-17T08:13:51Z","content_type":"application/pdf","description":"This document provides additional results and analyzes the robustness and limitations of our approach.","relation":"supplementary_material","access_level":"open_access","checksum":"20dc3bc42e1a912a5b0247c116772098","file_id":"10562"}],"ec_funded":1,"issue":"5","volume":40,"article_number":"186","project":[{"grant_number":"642841","name":"Distributed 3D Object Design","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"citation":{"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.","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.","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","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","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.","ista":"Zhang R, Auzinger T, Bickel B. 2021. Computational design of planar multistable compliant structures. ACM Transactions on Graphics. 40(5), 186."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000752079300003"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran","last_name":"Zhang","first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"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).","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","year":"2021","has_accepted_license":"1","isi":1,"publication":"ACM Transactions on Graphics","day":"08","date_created":"2021-05-08T17:37:08Z","doi":"10.1145/3453477","date_published":"2021-10-08T00:00:00Z"},{"publication_status":"published","publication_identifier":{"eissn":["0027-8424"]},"language":[{"iso":"eng"}],"file":[{"file_size":20592929,"date_updated":"2022-03-08T08:18:16Z","creator":"dernst","file_name":"2021_PNAS_Meier.pdf","date_created":"2022-03-08T08:18:16Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"cb30c6166b2132ee60d616b31a1a7c29","file_id":"10835"}],"issue":"25","volume":118,"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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 118","month":"06","date_updated":"2023-08-08T13:33:09Z","ddc":["570"],"department":[{"_id":"NiBa"}],"file_date_updated":"2022-03-08T08:18:16Z","_id":"9375","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","year":"2021","isi":1,"has_accepted_license":"1","publication":"PNAS","day":"21","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","citation":{"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.","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.","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.","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.","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).","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["34155138"],"isi":["000671755600001"]},"article_processing_charge":"No","author":[{"last_name":"Meier","full_name":"Meier, Joana I.","first_name":"Joana I."},{"full_name":"Salazar, Patricio A.","last_name":"Salazar","first_name":"Patricio A."},{"first_name":"Marek","full_name":"Kučka, Marek","last_name":"Kučka"},{"full_name":"Davies, Robert William","last_name":"Davies","first_name":"Robert William"},{"last_name":"Dréau","full_name":"Dréau, Andreea","first_name":"Andreea"},{"full_name":"Aldás, Ismael","last_name":"Aldás","first_name":"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"},{"last_name":"Bridle","full_name":"Bridle, Jon R.","first_name":"Jon R."},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"W. Owen","full_name":"McMillan, W. Owen","last_name":"McMillan"},{"full_name":"Jiggins, Chris D.","last_name":"Jiggins","first_name":"Chris D."},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","article_number":"e2015005118"},{"year":"2021","has_accepted_license":"1","isi":1,"publication":"Evolution Letters","day":"07","page":"196-213","date_created":"2021-05-16T22:01:47Z","date_published":"2021-05-07T00:00:00Z","doi":"10.1002/evl3.227","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. ","oa":1,"quality_controlled":"1","publisher":"Wiley","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.","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","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.","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","external_id":{"isi":["000647846200001"]},"article_processing_charge":"No","author":[{"first_name":"Eva L.","full_name":"Koch, Eva L.","last_name":"Koch"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"first_name":"Jenny","full_name":"Larsson, Jenny","last_name":"Larsson"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Alan R.","full_name":"Lemmon, Alan R.","last_name":"Lemmon"},{"first_name":"E. Moriarty","full_name":"Lemmon, E. Moriarty","last_name":"Lemmon"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"publication_status":"published","publication_identifier":{"eissn":["2056-3744"]},"language":[{"iso":"eng"}],"file":[{"file_size":3021108,"date_updated":"2021-10-15T08:26:02Z","creator":"cchlebak","file_name":"2021_EvolutionLetters_Koch.pdf","date_created":"2021-10-15T08:26:02Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10142","checksum":"023b1608e311f0fda30593ba3d0a4e0b"}],"ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"12987"}]},"issue":"3","volume":5,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 5","month":"05","date_updated":"2023-08-08T13:34:08Z","ddc":["570"],"file_date_updated":"2021-10-15T08:26:02Z","department":[{"_id":"NiBa"}],"_id":"9394","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","status":"public"},{"acknowledgement":"Authors would like to thank Christian Hilbe and Martin Nowak for their inspiring and very helpful feedback on the manuscript.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1008523","date_published":"2021-04-01T00:00:00Z","date_created":"2021-05-09T22:01:38Z","article_number":"e1008523","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"citation":{"short":"M. Kleshnina, S.S. Streipert, J.A. Filar, K. Chatterjee, PLoS Computational Biology 17 (2021).","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.","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","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","author":[{"first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina","full_name":"Kleshnina, Maria"},{"last_name":"Streipert","full_name":"Streipert, Sabrina S.","first_name":"Sabrina S."},{"last_name":"Filar","full_name":"Filar, Jerzy A.","first_name":"Jerzy A."},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"article_processing_charge":"No","external_id":{"isi":["000639711200001"]},"title":"Mistakes can stabilise the dynamics of rock-paper-scissors games","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","scopus_import":"1","month":"04","intvolume":" 17","publication_identifier":{"eissn":["15537358"],"issn":["1553734X"]},"publication_status":"published","file":[{"file_name":"2021_pcbi_Kleshnina.pdf","date_created":"2021-05-11T13:50:06Z","creator":"kschuh","file_size":1323820,"date_updated":"2021-05-11T13:50:06Z","success":1,"checksum":"a94ebe0c4116f5047eaa6029e54d2dac","file_id":"9385","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"4","volume":17,"ec_funded":1,"_id":"9381","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":"2023-08-08T13:31:08Z","ddc":["000"],"file_date_updated":"2021-05-11T13:50:06Z","department":[{"_id":"KrCh"}]},{"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.","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"}],"external_id":{"pmid":["33974865"],"isi":["000654741200004"]},"article_processing_charge":"No","title":"Quantifying the use of species concepts","isi":1,"year":"2021","day":"10","publication":"Current Biology","page":"R428-R429","date_published":"2021-05-10T00:00:00Z","doi":"10.1016/j.cub.2021.03.060","date_created":"2021-05-16T22:01:46Z","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.","publisher":"Cell Press","quality_controlled":"1","oa":1,"date_updated":"2023-08-08T13:34:38Z","department":[{"_id":"NiBa"}],"_id":"9392","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"eissn":["18790445"],"issn":["09609822"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"9","volume":31,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"month":"05","intvolume":" 31"},{"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/477489v1"}],"month":"04","intvolume":" 524","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","volume":524,"publication_identifier":{"issn":["0022-5193"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","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"],"_id":"9387","department":[{"_id":"GradSch"}],"date_updated":"2023-08-08T13:32:40Z","quality_controlled":"1","publisher":"Elsevier ","oa":1,"acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","doi":"10.1016/j.jtbi.2021.110729","date_published":"2021-04-24T00:00:00Z","date_created":"2021-05-12T05:58:42Z","isi":1,"year":"2021","day":"24","publication":"Journal of Theoretical Biology","article_number":"110729","author":[{"full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia"},{"full_name":"Neretina, Tatiana Yu.","last_name":"Neretina","first_name":"Tatiana Yu."},{"first_name":"Alexey S.","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S."}],"article_processing_charge":"No","external_id":{"isi":["000659161500002"]},"title":"Two linked loci under mutation-selection balance and Muller’s ratchet","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.","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.","short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021).","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9394"}]},"doi":"10.5061/DRYAD.ZGMSBCCB4","date_published":"2021-04-10T00:00:00Z","date_created":"2023-05-16T12:34:09Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"10","has_accepted_license":"1","year":"2021","month":"04","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.zgmsbccb4"}],"oa":1,"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."}],"department":[{"_id":"NiBa"}],"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","author":[{"first_name":"Eva","last_name":"Koch","full_name":"Koch, Eva"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"first_name":"Jenny","full_name":"Larsson, Jenny","last_name":"Larsson"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"last_name":"Lemmon","full_name":"Lemmon, E. Moriarty","first_name":"E. Moriarty"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2023-08-08T13:34:07Z","citation":{"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.","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.","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","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.","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."},"status":"public","type":"research_data_reference","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)"},"_id":"12987"},{"publication_identifier":{"eissn":["10772626"],"issn":["19410506"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"a78e6ac94e33ade4ffaea66943d5f7dc","file_id":"9427","file_size":6183002,"date_updated":"2021-05-25T15:08:49Z","creator":"kschuh","file_name":"2021_TVCG_Feng.pdf","date_created":"2021-05-25T15:08:49Z"}],"language":[{"iso":"eng"}],"issue":"6","volume":27,"ec_funded":1,"abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 27","date_updated":"2023-08-08T13:45:46Z","ddc":["000"],"file_date_updated":"2021-05-25T15:08:49Z","department":[{"_id":"BeBi"}],"_id":"9408","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","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"IEEE Transactions on Visualization and Computer Graphics","doi":"10.1109/TVCG.2019.2957218","date_published":"2021-06-01T00:00:00Z","date_created":"2021-05-23T22:01:42Z","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).","publisher":"IEEE","quality_controlled":"1","oa":1,"citation":{"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.","ieee":"X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021.","short":"X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021).","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Feng","full_name":"Feng, Xudong","first_name":"Xudong"},{"first_name":"Jiafeng","full_name":"Liu, Jiafeng","last_name":"Liu"},{"last_name":"Wang","full_name":"Wang, Huamin","first_name":"Huamin"},{"first_name":"Yin","last_name":"Yang","full_name":"Yang, Yin"},{"first_name":"Hujun","last_name":"Bao","full_name":"Bao, Hujun"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xu","full_name":"Xu, Weiwei","first_name":"Weiwei"}],"external_id":{"pmid":["31804937"],"isi":["000649620700009"]},"article_processing_charge":"No","title":"Computational design of skinned Quad-Robots","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"}]},{"scopus_import":"1","month":"05","intvolume":" 17","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","pmid":1,"volume":17,"issue":"5","ec_funded":1,"publication_identifier":{"eissn":["1744957X"]},"publication_status":"published","file":[{"file_id":"9425","checksum":"9c13c1f5af7609c97c741f11d293188a","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-05-25T14:09:03Z","file_name":"2021_BiologyLetters_Lagator.pdf","creator":"kschuh","date_updated":"2021-05-25T14:09:03Z","file_size":726759}],"language":[{"iso":"eng"}],"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":"9410","file_date_updated":"2021-05-25T14:09:03Z","department":[{"_id":"NiBa"}],"date_updated":"2023-08-08T13:44:35Z","ddc":["570"],"quality_controlled":"1","publisher":"Royal Society of London","oa":1,"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.","date_published":"2021-05-12T00:00:00Z","doi":"10.1098/rsbl.2020.0913","date_created":"2021-05-23T22:01:43Z","isi":1,"has_accepted_license":"1","year":"2021","day":"12","publication":"Biology letters","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"article_number":"20200913","author":[{"last_name":"Lagator","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard"},{"last_name":"Neve","full_name":"Neve, Paul","first_name":"Paul"}],"external_id":{"pmid":[" 33975485"],"isi":["000651501400001"]},"article_processing_charge":"No","title":"Adaptation at different points along antibiotic concentration gradients","citation":{"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.","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publication_identifier":{"eissn":["10836489"]},"publication_status":"published","file":[{"success":1,"file_id":"9423","checksum":"864ab003ad4cffea783f65aa8c2ba69f","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_EJP_Cipolloni.pdf","date_created":"2021-05-25T13:24:19Z","creator":"kschuh","file_size":865148,"date_updated":"2021-05-25T13:24:19Z"}],"language":[{"iso":"eng"}],"volume":26,"ec_funded":1,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 26","date_updated":"2023-08-08T13:39:19Z","ddc":["510"],"department":[{"_id":"LaEr"}],"file_date_updated":"2021-05-25T13:24:19Z","_id":"9412","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","isi":1,"has_accepted_license":"1","year":"2021","day":"23","publication":"Electronic Journal of Probability","doi":"10.1214/21-EJP591","date_published":"2021-03-23T00:00:00Z","date_created":"2021-05-23T22:01:44Z","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"citation":{"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.","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.","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","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder"}],"external_id":{"arxiv":["2002.02438"],"isi":["000641855600001"]},"article_processing_charge":"No","title":"Fluctuation around the circular law for random matrices with real entries","article_number":"24","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}]},{"article_number":"2586","article_processing_charge":"No","external_id":{"isi":["000687305500044"]},"author":[{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide","last_name":"Scarselli","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271"},{"last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"first_name":"Marc","full_name":"Timme, Marc","last_name":"Timme"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"title":"Discontinuous epidemic transition due to limited testing","citation":{"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.","short":"D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021).","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.","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","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","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.","ista":"Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Springer Nature","quality_controlled":"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.","date_created":"2021-05-23T22:01:42Z","date_published":"2021-05-10T00:00:00Z","doi":"10.1038/s41467-021-22725-9","year":"2021","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"10","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","status":"public","_id":"9407","file_date_updated":"2021-05-25T14:18:40Z","department":[{"_id":"BjHo"}],"date_updated":"2023-08-08T13:45:13Z","ddc":["570"],"scopus_import":"1","intvolume":" 12","month":"05","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."}],"oa_version":"Published Version","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/smashing-the-covid-curve/","relation":"press_release"}]},"issue":"1","volume":12,"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"file_size":1176573,"date_updated":"2021-05-25T14:18:40Z","creator":"kschuh","file_name":"2021_NatureCommunications_Scarselli.pdf","date_created":"2021-05-25T14:18:40Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9426","checksum":"fe26c1b8a7da1ae07a6c03f80ff06ea1"}]},{"ddc":["530"],"date_updated":"2023-08-08T13:36:28Z","department":[{"_id":"ScWa"}],"file_date_updated":"2021-05-25T11:32:14Z","_id":"9411","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)"},"file":[{"file_size":2507870,"date_updated":"2021-05-25T11:32:14Z","creator":"kschuh","file_name":"2021_EPJE_Sukhov.pdf","date_created":"2021-05-25T11:32:14Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9422","checksum":"0ef342d011afbe3c5cb058fda9a3f395"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1292895X"],"issn":["12928941"]},"publication_status":"published","issue":"4","volume":44,"oa_version":"Published Version","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."}],"month":"04","intvolume":" 44","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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).","ieee":"A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,” European Physical Journal E, vol. 44, no. 4. Springer, 2021."},"title":"Regimes of motion of magnetocapillary swimmers","author":[{"first_name":"Alexander","full_name":"Sukhov, Alexander","last_name":"Sukhov"},{"first_name":"Maxime","full_name":"Hubert, Maxime","last_name":"Hubert"},{"orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M","last_name":"Grosjean","first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425"},{"last_name":"Trosman","full_name":"Trosman, Oleg","first_name":"Oleg"},{"first_name":"Sebastian","last_name":"Ziegler","full_name":"Ziegler, Sebastian"},{"first_name":"Ylona","full_name":"Collard, Ylona","last_name":"Collard"},{"full_name":"Vandewalle, Nicolas","last_name":"Vandewalle","first_name":"Nicolas"},{"first_name":"Ana Sunčana","last_name":"Smith","full_name":"Smith, Ana Sunčana"},{"last_name":"Harting","full_name":"Harting, Jens","first_name":"Jens"}],"article_processing_charge":"No","external_id":{"isi":["000643251300001"]},"article_number":"59","day":"24","publication":"European Physical Journal E","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1140/epje/s10189-021-00065-2","date_published":"2021-04-24T00:00:00Z","date_created":"2021-05-23T22:01:44Z","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.","quality_controlled":"1","publisher":"Springer","oa":1},{"publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"9","volume":32,"license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","ec_funded":1,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723"}],"month":"04","intvolume":" 32","date_updated":"2023-08-08T13:36:02Z","department":[{"_id":"MaLo"}],"_id":"9414","article_type":"original","type":"journal_article","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)"},"status":"public","isi":1,"year":"2021","day":"19","publication":"Molecular Biology of the Cell","page":"869-879","doi":"10.1091/MBC.E20-11-0723","date_published":"2021-04-19T00:00:00Z","date_created":"2021-05-23T22:01:45Z","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.","publisher":"American Society for Cell Biology","quality_controlled":"1","oa":1,"citation":{"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.","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.","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Keisuke","last_name":"Ishihara","full_name":"Ishihara, Keisuke"},{"first_name":"Franziska","full_name":"Decker, Franziska","last_name":"Decker"},{"last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R"},{"first_name":"James F.","last_name":"Pelletier","full_name":"Pelletier, James F."},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"},{"full_name":"Brugués, Jan","last_name":"Brugués","first_name":"Jan"},{"last_name":"Mitchison","full_name":"Mitchison, Timothy J.","first_name":"Timothy J."}],"article_processing_charge":"No","external_id":{"isi":["000641574700005"]},"title":"Spatial variation of microtubule depolymerization in large asters","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","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."},"title":"Quantitative and approximate monitoring","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"article_processing_charge":"No","external_id":{"isi":["000947350400021"],"arxiv":["2105.08353"]},"article_number":"9470547","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"day":"29","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-06-29T00:00:00Z","doi":"10.1109/LICS52264.2021.9470547","date_created":"2021-04-30T17:30:47Z","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).","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","oa":1,"ddc":["000"],"date_updated":"2023-08-08T13:52:56Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2021-06-16T08:23:54Z","_id":"9356","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"},"file":[{"success":1,"file_id":"9557","checksum":"6e4cba3f72775f479c5b1b75d1a4a0c4","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"qam.pdf","date_created":"2021-06-16T08:23:54Z","creator":"esarac","file_size":641990,"date_updated":"2021-06-16T08:23:54Z"}],"language":[{"iso":"eng"}],"publication_status":"published","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"}],"month":"06","scopus_import":"1"},{"_id":"9439","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-08T13:51:14Z","department":[{"_id":"GaTk"}],"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."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/669200 ","open_access":"1"}],"month":"05","intvolume":" 24","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":24,"ec_funded":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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.","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi: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","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.","ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hermundstad, Ann M.","last_name":"Hermundstad","first_name":"Ann M."}],"article_processing_charge":"No","external_id":{"isi":["000652577300003"]},"title":"Efficient and adaptive sensory codes","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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"isi":1,"year":"2021","day":"20","publication":"Nature Neuroscience","page":"998-1009","doi":"10.1038/s41593-021-00846-0","date_published":"2021-05-20T00:00:00Z","date_created":"2021-05-30T22:01:24Z"},{"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","_id":"9443","department":[{"_id":"JiFr"}],"file_date_updated":"2021-10-14T13:36:38Z","date_updated":"2023-08-08T13:54:32Z","ddc":["580"],"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","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,"checksum":"22d596678d00310d793611864a6d0fcd","file_id":"10141","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_processing_charge":"No","external_id":{"isi":["000703938100026"],"pmid":["33944955"]},"author":[{"first_name":"N","full_name":"Ruiz-Lopez, N","last_name":"Ruiz-Lopez"},{"full_name":"Pérez-Sancho, J","last_name":"Pérez-Sancho","first_name":"J"},{"last_name":"Esteban Del Valle","full_name":"Esteban Del Valle, A","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","full_name":"Catalá, R","last_name":"Catalá"},{"last_name":"Perea-Resa","full_name":"Perea-Resa, C","first_name":"C"},{"last_name":"Van Damme","full_name":"Van Damme, D","first_name":"D"},{"last_name":"García-Hernández","full_name":"García-Hernández, S","first_name":"S"},{"last_name":"Albert","full_name":"Albert, A","first_name":"A"},{"first_name":"J","last_name":"Vallarino","full_name":"Vallarino, J"},{"first_name":"J","last_name":"Lin","full_name":"Lin, J"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"AP","last_name":"Macho","full_name":"Macho, AP"},{"last_name":"Salinas","full_name":"Salinas, J","first_name":"J"},{"last_name":"Rosado","full_name":"Rosado, A","first_name":"A"},{"first_name":"JA","full_name":"Napier, JA","last_name":"Napier"},{"full_name":"Amorim-Silva, V","last_name":"Amorim-Silva","first_name":"V"},{"first_name":"MA","full_name":"Botella, MA","last_name":"Botella"}],"title":"Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress","citation":{"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.","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.","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","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","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"}]