[{"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":"9332","file_date_updated":"2021-04-19T10:54:55Z","department":[{"_id":"EvBe"}],"date_updated":"2023-08-08T13:09:58Z","ddc":["570"],"scopus_import":"1","month":"04","intvolume":" 22","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","issue":"8","volume":22,"publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"26ada2531ad1f9c01a1664de0431f1fe","file_id":"9342","creator":"dernst","file_size":2769717,"date_updated":"2021-04-19T10:54:55Z","file_name":"2021_JourMolecularScience_Oetvoes.pdf","date_created":"2021-04-19T10:54:55Z"}],"language":[{"iso":"eng"}],"article_number":"3862","author":[{"last_name":"Ötvös","orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina"},{"full_name":"Miskolczi, Pál","last_name":"Miskolczi","first_name":"Pál"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Marhavý, Peter","orcid":"0000-0001-5227-5741","last_name":"Marhavý"},{"first_name":"Alfredo","last_name":"Cruz-Ramírez","full_name":"Cruz-Ramírez, Alfredo"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"last_name":"Bakó","full_name":"Bakó, László","first_name":"László"}],"external_id":{"isi":["000644394800001"]},"article_processing_charge":"No","title":"Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis","citation":{"ista":"Ötvös K, Miskolczi P, Marhavý P, Cruz-Ramírez A, Benková E, Robert S, Bakó L. 2021. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. 22(8), 3862.","chicago":"Ötvös, Krisztina, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva Benková, Stéphanie Robert, and László Bakó. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22083862.","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","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).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"MDPI","quality_controlled":"1","oa":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.","doi":"10.3390/ijms22083862","date_published":"2021-04-08T00:00:00Z","date_created":"2021-04-18T22:01:41Z","isi":1,"has_accepted_license":"1","year":"2021","day":"08","publication":"International Journal of Molecular Sciences"},{"intvolume":" 111","month":"04","scopus_import":"1","oa_version":"Published Version","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."}],"volume":111,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9341","checksum":"be56c0845a43c0c5c772ee0b5053f7d7","success":1,"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"}],"publication_status":"published","publication_identifier":{"eissn":["15730530"],"issn":["03779017"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"9333","department":[{"_id":"RoSe"}],"file_date_updated":"2021-04-19T10:40:01Z","ddc":["510"],"date_updated":"2023-08-08T13:09:28Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"I thank Marcel Griesemer for many interesting discussions about the Fröhlich polaron and also for valuable comments on this manuscript. Helpful discussions with Nikolai Leopold and Robert Seiringer are also gratefully acknowledged. This work was partially supported by the Deutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral Theory and Dynamics of Quantum Systems. Open Access funding enabled and organized by Projekt DEAL.","date_created":"2021-04-18T22:01:41Z","doi":"10.1007/s11005-021-01380-7","date_published":"2021-04-05T00:00:00Z","publication":"Letters in Mathematical Physics","day":"05","year":"2021","isi":1,"has_accepted_license":"1","article_number":"45","title":"A note on the Fröhlich dynamics in the strong coupling limit","external_id":{"isi":["000637359300002"]},"article_processing_charge":"No","author":[{"first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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.","ista":"Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 111, 45.","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."}},{"external_id":{"arxiv":["1911.04185"],"isi":["000625044600003"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","full_name":"Matthes, Daniel","last_name":"Matthes"}],"title":"The waiting time phenomenon in spatially discretized porous medium and thin film equations","citation":{"short":"J.L. Fischer, D. Matthes, SIAM Journal on Numerical Analysis 59 (2021) 60–87.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics”.","page":"60-87","date_created":"2021-04-18T22:01:42Z","doi":"10.1137/19M1300017","date_published":"2021-01-01T00:00:00Z","year":"2021","isi":1,"publication":"SIAM Journal on Numerical Analysis","day":"01","article_type":"original","type":"journal_article","status":"public","_id":"9335","department":[{"_id":"JuFi"}],"date_updated":"2023-08-08T13:10:40Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.04185"}],"scopus_import":"1","intvolume":" 59","month":"01","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","issue":"1","volume":59,"publication_status":"published","publication_identifier":{"issn":["0036-1429"]},"language":[{"iso":"eng"}]},{"volume":18,"issue":"4","related_material":{"record":[{"relation":"dissertation_contains","id":"13081","status":"public"}]},"ec_funded":1,"publication_identifier":{"eissn":["1478-3975"]},"publication_status":"published","file":[{"success":1,"file_id":"9355","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_PhysBio_Lenne.pdf","date_created":"2021-04-27T08:38:35Z","file_size":6296324,"date_updated":"2021-04-27T08:38:35Z","creator":"cziletti"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 18","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"AnKi"},{"_id":"EdHa"}],"file_date_updated":"2021-04-27T08:38:35Z","date_updated":"2023-08-08T13:15:46Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9349","date_published":"2021-04-14T00:00:00Z","doi":"10.1088/1478-3975/abd0db","date_created":"2021-04-25T22:01:29Z","isi":1,"has_accepted_license":"1","year":"2021","day":"14","publication":"Physical biology","quality_controlled":"1","publisher":"IOP Publishing","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).","author":[{"last_name":"Lenne","full_name":"Lenne, Pierre François","first_name":"Pierre François"},{"first_name":"Edwin","last_name":"Munro","full_name":"Munro, Edwin"},{"first_name":"Idse","last_name":"Heemskerk","full_name":"Heemskerk, Idse"},{"last_name":"Warmflash","full_name":"Warmflash, Aryeh","first_name":"Aryeh"},{"full_name":"Bocanegra, Laura","last_name":"Bocanegra","first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kishi, Kasumi","last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"},{"last_name":"Long","full_name":"Long, Yuchen","first_name":"Yuchen"},{"full_name":"Fruleux, Antoine","last_name":"Fruleux","first_name":"Antoine"},{"first_name":"Arezki","full_name":"Boudaoud, Arezki","last_name":"Boudaoud"},{"full_name":"Saunders, Timothy E.","last_name":"Saunders","first_name":"Timothy E."},{"full_name":"Caldarelli, Paolo","last_name":"Caldarelli","first_name":"Paolo"},{"last_name":"Michaut","full_name":"Michaut, Arthur","first_name":"Arthur"},{"full_name":"Gros, Jerome","last_name":"Gros","first_name":"Jerome"},{"full_name":"Maroudas-Sacks, Yonit","last_name":"Maroudas-Sacks","first_name":"Yonit"},{"first_name":"Kinneret","full_name":"Keren, Kinneret","last_name":"Keren"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, 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","last_name":"Gladfelter","full_name":"Gladfelter, Amy"},{"first_name":"Alan","last_name":"Rodrigues","full_name":"Rodrigues, Alan"},{"last_name":"Shyer","full_name":"Shyer, Amy","first_name":"Amy"},{"last_name":"Minc","full_name":"Minc, Nicolas","first_name":"Nicolas"},{"first_name":"Jean Léon","full_name":"Maître, Jean Léon","last_name":"Maître"},{"full_name":"Di Talia, Stefano","last_name":"Di Talia","first_name":"Stefano"},{"full_name":"Khamaisi, Bassma","last_name":"Khamaisi","first_name":"Bassma"},{"last_name":"Sprinzak","full_name":"Sprinzak, David","first_name":"David"},{"first_name":"Sham","last_name":"Tlili","full_name":"Tlili, Sham"}],"article_processing_charge":"No","external_id":{"isi":["000640396400001"],"pmid":["33276350"]},"title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","citation":{"ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 2021;18(4). doi:10.1088/1478-3975/abd0db","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abd0db","short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).","ieee":"P. F. Lenne et al., “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” Physical biology, vol. 18, no. 4. IOP Publishing, 2021.","mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” Physical Biology, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:10.1088/1478-3975/abd0db.","ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501.","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” Physical Biology. IOP Publishing, 2021. https://doi.org/10.1088/1478-3975/abd0db."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}],"article_number":"041501"},{"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"04","intvolume":" 7","publication_identifier":{"eissn":["23752548"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"4b383d4a1d484a71bbc64ecf401bbdbb","file_id":"9343","creator":"dernst","file_size":717489,"date_updated":"2021-04-19T11:17:29Z","file_name":"2021_ScienceAdv_Duan.pdf","date_created":"2021-04-19T11:17:29Z"}],"language":[{"iso":"eng"}],"issue":"14","volume":7,"_id":"9334","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","date_updated":"2023-08-08T13:11:31Z","ddc":["530"],"file_date_updated":"2021-04-19T11:17:29Z","department":[{"_id":"NanoFab"}],"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. ","publisher":"AAAS","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"02","publication":"Science Advances","doi":"10.1126/sciadv.abf2690","date_published":"2021-04-02T00:00:00Z","date_created":"2021-04-18T22:01:42Z","article_number":"eabf2690","citation":{"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.","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.","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.","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).","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Duan","full_name":"Duan, J.","first_name":"J."},{"first_name":"G.","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, G."},{"first_name":"K. V.","last_name":"Voronin","full_name":"Voronin, 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."},{"first_name":"A. Y.","last_name":"Nikitin","full_name":"Nikitin, A. Y."},{"first_name":"P.","full_name":"Alonso-González, P.","last_name":"Alonso-González"}],"external_id":{"pmid":["33811076"],"isi":["000636455600027"]},"article_processing_charge":"No","title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition"},{"citation":{"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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2010.13754"],"isi":["000638022600001"]},"title":"A large deviation principle in many-body quantum dynamics","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"has_accepted_license":"1","year":"2021","day":"08","publication":"Annales Henri Poincare","page":"2595-2618","doi":"10.1007/s00023-021-01044-1","date_published":"2021-04-08T00:00:00Z","date_created":"2021-04-25T22:01:30Z","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).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"date_updated":"2023-08-08T13:14:40Z","ddc":["530"],"department":[{"_id":"RoSe"}],"file_date_updated":"2021-10-15T11:15:40Z","_id":"9351","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","publication_identifier":{"issn":["1424-0637"]},"publication_status":"published","file":[{"success":1,"checksum":"1a0fb963f2f415ba470881a794f20eb6","file_id":"10143","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_Annales_Kirkpatrick.pdf","date_created":"2021-10-15T11:15:40Z","file_size":522669,"date_updated":"2021-10-15T11:15:40Z","creator":"cchlebak"}],"language":[{"iso":"eng"}],"volume":22,"ec_funded":1,"abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 22"},{"isi":1,"year":"2021","day":"05","publication":"FEBS Journal","date_published":"2021-04-05T00:00:00Z","doi":"10.1111/febs.15823","date_created":"2021-04-18T22:01:43Z","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.","publisher":"Wiley","quality_controlled":"1","oa":1,"citation":{"ista":"Sarabipour S, Hainer SJ, Arslan FN, De Winde CM, Furlong E, Bielczyk N, Jadavji NM, Shah AP, Davla S. 2021. Building and sustaining mentor interactions as a mentee. FEBS Journal.","chicago":"Sarabipour, Sarvenaz, Sarah J. Hainer, Feyza N Arslan, Charlotte M. De Winde, Emily Furlong, Natalia Bielczyk, Nafisa M. Jadavji, Aparna P. Shah, and Sejal Davla. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal. Wiley, 2021. https://doi.org/10.1111/febs.15823.","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).","ieee":"S. Sarabipour et al., “Building and sustaining mentor interactions as a mentee,” FEBS Journal. Wiley, 2021.","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","mla":"Sarabipour, Sarvenaz, et al. “Building and Sustaining Mentor Interactions as a Mentee.” FEBS Journal, Wiley, 2021, doi:10.1111/febs.15823."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Sarvenaz","last_name":"Sarabipour","full_name":"Sarabipour, Sarvenaz"},{"full_name":"Hainer, Sarah J.","last_name":"Hainer","first_name":"Sarah J."},{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","last_name":"Arslan"},{"last_name":"De Winde","full_name":"De Winde, Charlotte M.","first_name":"Charlotte M."},{"full_name":"Furlong, Emily","last_name":"Furlong","first_name":"Emily"},{"first_name":"Natalia","full_name":"Bielczyk, Natalia","last_name":"Bielczyk"},{"full_name":"Jadavji, Nafisa M.","last_name":"Jadavji","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"}],"article_processing_charge":"No","external_id":{"pmid":["33818917"],"isi":["000636678800001"]},"title":"Building and sustaining mentor interactions as a mentee","publication_identifier":{"eissn":["1742-4658"],"issn":["1742-464X"]},"publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","alternative_title":["Words of Advice"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/febs.15823"}],"month":"04","date_updated":"2023-08-08T13:12:55Z","department":[{"_id":"CaHe"}],"_id":"9336","article_type":"original","type":"journal_article","status":"public"},{"citation":{"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.","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","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.","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.","ista":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together: when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Arslan","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N"},{"first_name":"Julia","last_name":"Eckert","full_name":"Eckert, Julia"},{"last_name":"Schmidt","full_name":"Schmidt, Thomas","first_name":"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"}],"article_processing_charge":"No","external_id":{"pmid":["33794149"],"isi":["000704646900006"]},"title":"Holding it together: when cadherin meets cadherin","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).","quality_controlled":"1","publisher":"Biophysical Society","oa":1,"isi":1,"year":"2021","day":"05","publication":"Biophysical Journal","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","_id":"9350","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-08T13:14:10Z","department":[{"_id":"CaHe"}],"abstract":[{"lang":"eng","text":"Intercellular adhesion is the key to multicellularity, and its malfunction plays an important role in various developmental and disease-related processes. Although it has been intensively studied by both biologists and physicists, a commonly accepted definition of cell-cell adhesion is still being debated. Cell-cell adhesion has been described at the molecular scale as a function of adhesion receptors controlling binding affinity, at the cellular scale as resistance to detachment forces or modulation of surface tension, and at the tissue scale as a regulator of cellular rearrangements and morphogenesis. In this review, we aim to summarize and discuss recent advances in the molecular, cellular, and theoretical description of cell-cell adhesion, ranging from biomimetic models to the complexity of cells and tissues in an organismal context. In particular, we will focus on cadherin-mediated cell-cell adhesion and the role of adhesion signaling and mechanosensation therein, two processes central for understanding the biological and physical basis of cell-cell adhesion."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view","open_access":"1"}],"month":"10","intvolume":" 120","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":120,"related_material":{"record":[{"status":"public","id":"12368","relation":"dissertation_contains"}]}},{"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.","ieee":"M. Brooks and G. Di Gesù, “Sharp tunneling estimates for a double-well model in infinite dimension,” Journal of Functional Analysis, vol. 281, no. 3. Elsevier, 2021.","short":"M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021).","apa":"Brooks, M., & Di Gesù, G. (2021). Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109029","ama":"Brooks M, Di Gesù G. Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. 2021;281(3). doi:10.1016/j.jfa.2021.109029","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."},"title":"Sharp tunneling estimates for a double-well model in infinite dimension","author":[{"first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","last_name":"Brooks","orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris"},{"first_name":"Giacomo","full_name":"Di Gesù, Giacomo","last_name":"Di Gesù"}],"external_id":{"arxiv":["1911.03187"],"isi":["000644702800005"]},"article_processing_charge":"No","article_number":"109029","day":"07","publication":"Journal of Functional Analysis","isi":1,"year":"2021","date_published":"2021-04-07T00:00:00Z","doi":"10.1016/j.jfa.2021.109029","date_created":"2021-04-25T22:01:29Z","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.","quality_controlled":"1","publisher":"Elsevier","oa":1,"date_updated":"2023-08-08T13:15:11Z","department":[{"_id":"RoSe"}],"_id":"9348","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"publication_status":"published","issue":"3","volume":281,"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"month":"04","intvolume":" 281","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1911.03187","open_access":"1"}]},{"title":"A priori error analysis of a numerical stochastic homogenization method","external_id":{"isi":["000646030400003"],"arxiv":["1912.11646"]},"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"},{"last_name":"Gallistl","full_name":"Gallistl, Dietmar","first_name":"Dietmar"},{"full_name":"Peterseim, Dietmar","last_name":"Peterseim","first_name":"Dietmar"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Fischer, Julian L, Dietmar Gallistl, and Dietmar Peterseim. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/19M1308992.","ista":"Fischer JL, Gallistl D, Peterseim D. 2021. A priori error analysis of a numerical stochastic homogenization method. SIAM Journal on Numerical Analysis. 59(2), 660–674.","mla":"Fischer, Julian L., et al. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” SIAM Journal on Numerical Analysis, vol. 59, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 660–74, doi:10.1137/19M1308992.","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.","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"},"date_created":"2021-04-25T22:01:31Z","doi":"10.1137/19M1308992","date_published":"2021-03-09T00:00:00Z","page":"660-674","publication":"SIAM Journal on Numerical Analysis","day":"09","year":"2021","isi":1,"oa":1,"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","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.","department":[{"_id":"JuFi"}],"date_updated":"2023-08-08T13:13:37Z","status":"public","type":"journal_article","article_type":"original","_id":"9352","volume":59,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0036-1429"]},"intvolume":" 59","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.11646"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","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."}]},{"volume":17,"issue":"4","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"82a74668f863e8dfb22fdd4f845c92ce","file_id":"9369","success":1,"date_updated":"2021-05-04T09:05:27Z","file_size":3072764,"creator":"kschuh","date_created":"2021-05-04T09:05:27Z","file_name":"2021_PLOS_Ingles-Prieto.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["15537404"]},"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."}],"file_date_updated":"2021-05-04T09:05:27Z","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"ddc":["570"],"date_updated":"2023-08-08T13:17:47Z","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","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","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","acknowledgement":"We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice, S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for help with statistical analysis.","title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","external_id":{"isi":["000640606700001"]},"article_processing_charge":"No","author":[{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571"},{"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"},{"first_name":"Nina","full_name":"Hoyer, Nina","last_name":"Hoyer"},{"last_name":"Petersen","full_name":"Petersen, Meike","first_name":"Meike"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Zheden, Vanessa","last_name":"Zheden"},{"id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Bicher","full_name":"Bicher, Julia"},{"first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart"},{"full_name":"György, Attila","orcid":"0000-0002-1819-198X","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"full_name":"Soba, Peter","last_name":"Soba","first_name":"Peter"},{"full_name":"Winklhofer, Konstanze F.","last_name":"Winklhofer","first_name":"Konstanze F."},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M, Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 17(4), e1009479.","chicago":"Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS Genetics. Public Library of Science, 2021. https://doi.org/10.1371/journal.pgen.1009479.","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","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.","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.","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."}},{"author":[{"first_name":"Zaira","full_name":"Seferbekova, Zaira","last_name":"Seferbekova"},{"full_name":"Zabelkin, Alexey","last_name":"Zabelkin","first_name":"Alexey"},{"full_name":"Yakovleva, Yulia","last_name":"Yakovleva","first_name":"Yulia"},{"first_name":"Robert","last_name":"Afasizhev","full_name":"Afasizhev, Robert"},{"first_name":"Natalia O.","last_name":"Dranenko","full_name":"Dranenko, Natalia O."},{"first_name":"Nikita","last_name":"Alexeev","full_name":"Alexeev, Nikita"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."},{"first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"}],"external_id":{"isi":["000643713300001"]},"article_processing_charge":"No","title":"High rates of genome rearrangements and pathogenicity of Shigella spp","citation":{"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.","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).","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","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","chicago":"Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.628622.","ista":"Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 12, 628622."},"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","doi":"10.3389/fmicb.2021.628622","date_published":"2021-04-12T00:00:00Z","date_created":"2021-05-09T22:01:38Z","has_accepted_license":"1","isi":1,"year":"2021","day":"12","publication":"Frontiers in Microbiology","quality_controlled":"1","publisher":"Frontiers","oa":1,"acknowledgement":"We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos.","department":[{"_id":"FyKo"}],"file_date_updated":"2021-05-11T13:05:52Z","date_updated":"2023-08-08T13:30:39Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9380","volume":12,"ec_funded":1,"publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published","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","checksum":"2f856543add59273a482a7f326fc0400","file_id":"9384","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"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"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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","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","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."},"title":"Homological stability and densities of generalized configuration spaces","article_processing_charge":"No","external_id":{"arxiv":["1802.07948"],"isi":["000682738600005"]},"author":[{"full_name":"Ho, Quoc P","last_name":"Ho","first_name":"Quoc P","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"26B96266-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02751","name":"Algebro-Geometric Applications of Factorization Homology"}],"publication":"Geometry & Topology","day":"27","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-05-02T06:59:33Z","date_published":"2021-04-27T00:00:00Z","doi":"10.2140/gt.2021.25.813","page":"813-912","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.","oa":1,"publisher":"Mathematical Sciences Publishers","quality_controlled":"1","ddc":["514","516","512"],"date_updated":"2023-08-08T13:28:59Z","department":[{"_id":"TaHa"}],"file_date_updated":"2021-05-03T06:54:06Z","_id":"9359","keyword":["Generalized configuration spaces","homological stability","homological densities","chiral algebras","chiral homology","factorization algebras","Koszul duality","Ran space"],"status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"checksum":"643a8d2d6f06f0888dcd7503f55d0920","file_id":"9366","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-05-03T06:54:06Z","file_name":"densities.pdf","creator":"qho","date_updated":"2021-05-03T06:54:06Z","file_size":479268}],"publication_status":"published","publication_identifier":{"issn":["1364-0380"]},"ec_funded":1,"volume":25,"issue":"2","oa_version":"Submitted Version","abstract":[{"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","lang":"eng"}],"intvolume":" 25","month":"04"},{"day":"14","publication":"mSphere","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1128/mSphere.01024-20","date_published":"2021-04-14T00:00:00Z","date_created":"2021-05-02T22:01:28Z","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","publisher":"American Society for Microbiology","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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.","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","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","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"},"title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","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"},{"last_name":"Origgi","full_name":"Origgi, Francesco","first_name":"Francesco"},{"full_name":"Plattet, Philippe","last_name":"Plattet","first_name":"Philippe"}],"article_processing_charge":"No","external_id":{"pmid":["33853875"],"isi":["000663823400025"]},"article_number":"e01024-20","file":[{"creator":"kschuh","file_size":3379349,"date_updated":"2021-05-04T12:41:38Z","file_name":"2021_mSphere_Gast.pdf","date_created":"2021-05-04T12:41:38Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9370","checksum":"310748d140c8838335c1314431095898"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23795042"]},"publication_status":"published","volume":6,"issue":"2","oa_version":"Published Version","pmid":1,"abstract":[{"text":"The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM.","lang":"eng"}],"month":"04","intvolume":" 6","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-08T13:26:12Z","department":[{"_id":"Bio"}],"file_date_updated":"2021-05-04T12:41:38Z","_id":"9361","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"_id":"9376","status":"public","keyword":["multistability","mechanism","computational design","rigidity"],"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)"},"ddc":["000"],"date_updated":"2023-08-08T13:31:38Z","file_date_updated":"2021-12-17T08:13:51Z","department":[{"_id":"BeBi"}],"oa_version":"Published Version","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"}],"month":"10","intvolume":" 40","file":[{"file_name":"Multistable-authorversion.pdf","date_created":"2021-05-08T17:36:59Z","creator":"bbickel","file_size":18926557,"date_updated":"2021-05-08T17:36:59Z","file_id":"9377","checksum":"8564b3118457d4c8939a8ef2b1a2f16c","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"date_updated":"2021-05-08T17:38:22Z","file_size":76542901,"creator":"bbickel","date_created":"2021-05-08T17:38:22Z","file_name":"multistable-video.mp4","content_type":"video/mp4","access_level":"open_access","relation":"main_file","checksum":"3b6e874e30bfa1bfc3ad3498710145a1","file_id":"9378","success":1},{"checksum":"20dc3bc42e1a912a5b0247c116772098","file_id":"10562","relation":"supplementary_material","access_level":"open_access","description":"This document provides additional results and analyzes the robustness and limitations of our approach.","content_type":"application/pdf","file_name":"multistable-supplementary material.pdf","title":"Supplementary Material for “Computational Design of Planar Multistable Compliant Structures”","date_created":"2021-12-17T08:13:51Z","creator":"bbickel","file_size":3367072,"date_updated":"2021-12-17T08:13:51Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"publication_status":"published","issue":"5","volume":40,"ec_funded":1,"article_number":"186","project":[{"name":"Distributed 3D Object Design","grant_number":"642841","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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.","short":"R. Zhang, T. Auzinger, B. Bickel, ACM Transactions on Graphics 40 (2021).","ama":"Zhang R, Auzinger T, Bickel B. Computational design of planar multistable compliant structures. ACM Transactions on Graphics. 2021;40(5). doi:10.1145/3453477","apa":"Zhang, R., Auzinger, T., & Bickel, B. (2021). Computational design of planar multistable compliant structures. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3453477","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."},"title":"Computational design of planar multistable compliant structures","author":[{"last_name":"Zhang","orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran","first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"external_id":{"isi":["000752079300003"]},"article_processing_charge":"No","acknowledgement":"We would like to thank everyone who contributed to this paper, the authors of artworks for all the examples, including @macrovec-tor_official and Wikimedia for the FLAG semaphore, and @pikisuper-star for the FIGURINE. The photos of iconic poses in the teaser were supplied by (from left to right): Mike Hewitt/Olympics Day 8 - Athletics/Gettty Images, Oneinchpunch/Basketball player training on acourt in New york city/Shutterstock, and Andrew Redington/TigerWoods/Getty Images. We also want to express our gratitude to Christian Hafner for insightful discussions, the IST Austria machine shop SSU, all proof-readers, and anonymous reviewers. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"day":"08","publication":"ACM Transactions on Graphics","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1145/3453477","date_published":"2021-10-08T00:00:00Z","date_created":"2021-05-08T17:37:08Z"},{"department":[{"_id":"NiBa"}],"file_date_updated":"2022-03-08T08:18:16Z","date_updated":"2023-08-08T13:33:09Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"9375","volume":118,"issue":"25","publication_identifier":{"eissn":["0027-8424"]},"publication_status":"published","file":[{"success":1,"checksum":"cb30c6166b2132ee60d616b31a1a7c29","file_id":"10835","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_PNAS_Meier.pdf","date_created":"2022-03-08T08:18:16Z","file_size":20592929,"date_updated":"2022-03-08T08:18:16Z","creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 118","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"author":[{"first_name":"Joana I.","last_name":"Meier","full_name":"Meier, Joana I."},{"last_name":"Salazar","full_name":"Salazar, Patricio A.","first_name":"Patricio A."},{"full_name":"Kučka, Marek","last_name":"Kučka","first_name":"Marek"},{"full_name":"Davies, Robert William","last_name":"Davies","first_name":"Robert William"},{"first_name":"Andreea","full_name":"Dréau, Andreea","last_name":"Dréau"},{"first_name":"Ismael","last_name":"Aldás","full_name":"Aldás, Ismael"},{"first_name":"Olivia Box","full_name":"Power, Olivia Box","last_name":"Power"},{"full_name":"Nadeau, Nicola J.","last_name":"Nadeau","first_name":"Nicola J."},{"last_name":"Bridle","full_name":"Bridle, Jon R.","first_name":"Jon R."},{"last_name":"Rolian","full_name":"Rolian, Campbell","first_name":"Campbell"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"McMillan","full_name":"McMillan, W. Owen","first_name":"W. Owen"},{"full_name":"Jiggins, Chris D.","last_name":"Jiggins","first_name":"Chris D."},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"}],"article_processing_charge":"No","external_id":{"pmid":["34155138"],"isi":["000671755600001"]},"title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","citation":{"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.","short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, PNAS 118 (2021).","ieee":"J. I. Meier et al., “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings of the National Academy of Sciences, 2021.","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2015005118","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e2015005118","doi":"10.1073/pnas.2015005118","date_published":"2021-06-21T00:00:00Z","date_created":"2021-05-07T17:10:21Z","isi":1,"has_accepted_license":"1","year":"2021","day":"21","publication":"PNAS","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"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”)."},{"project":[{"grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","apa":"Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.227","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 2021;5(3):196-213. doi:10.1002/evl3.227","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227.","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."},"title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","author":[{"first_name":"Eva L.","full_name":"Koch, Eva L.","last_name":"Koch"},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Alan R.","full_name":"Lemmon, Alan R.","last_name":"Lemmon"},{"first_name":"E. Moriarty","last_name":"Lemmon","full_name":"Lemmon, E. Moriarty"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"external_id":{"isi":["000647846200001"]},"article_processing_charge":"No","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. ","quality_controlled":"1","publisher":"Wiley","oa":1,"day":"07","publication":"Evolution Letters","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1002/evl3.227","date_published":"2021-05-07T00:00:00Z","date_created":"2021-05-16T22:01:47Z","page":"196-213","_id":"9394","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)"},"ddc":["570"],"date_updated":"2023-08-08T13:34:08Z","department":[{"_id":"NiBa"}],"file_date_updated":"2021-10-15T08:26:02Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow."}],"month":"05","intvolume":" 5","scopus_import":"1","file":[{"file_name":"2021_EvolutionLetters_Koch.pdf","date_created":"2021-10-15T08:26:02Z","file_size":3021108,"date_updated":"2021-10-15T08:26:02Z","creator":"cchlebak","success":1,"checksum":"023b1608e311f0fda30593ba3d0a4e0b","file_id":"10142","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2056-3744"]},"publication_status":"published","issue":"3","volume":5,"related_material":{"record":[{"id":"12987","status":"public","relation":"research_data"}]},"ec_funded":1},{"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 17","publication_identifier":{"issn":["1553734X"],"eissn":["15537358"]},"publication_status":"published","file":[{"file_name":"2021_pcbi_Kleshnina.pdf","date_created":"2021-05-11T13:50:06Z","file_size":1323820,"date_updated":"2021-05-11T13:50:06Z","creator":"kschuh","success":1,"checksum":"a94ebe0c4116f5047eaa6029e54d2dac","file_id":"9385","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"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"}],"acknowledgement":"Authors would like to thank Christian Hilbe and Martin Nowak for their inspiring and very helpful feedback on the manuscript.","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"isi":1,"has_accepted_license":"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":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"citation":{"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.","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.","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Kleshnina","full_name":"Kleshnina, Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"full_name":"Streipert, Sabrina S.","last_name":"Streipert","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","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"external_id":{"isi":["000639711200001"]},"article_processing_charge":"No","title":"Mistakes can stabilise the dynamics of rock-paper-scissors games"},{"day":"10","publication":"Current Biology","isi":1,"year":"2021","date_published":"2021-05-10T00:00:00Z","doi":"10.1016/j.cub.2021.03.060","date_created":"2021-05-16T22:01:46Z","page":"R428-R429","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,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","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.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), 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."},"title":"Quantifying the use of species concepts","author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"article_processing_charge":"No","external_id":{"pmid":["33974865"],"isi":["000654741200004"]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["18790445"],"issn":["09609822"]},"publication_status":"published","volume":31,"issue":"9","oa_version":"Published Version","pmid":1,"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"}],"month":"05","intvolume":" 31","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2021.03.060"}],"date_updated":"2023-08-08T13:34:38Z","department":[{"_id":"NiBa"}],"_id":"9392","status":"public","article_type":"original","type":"journal_article"},{"department":[{"_id":"GradSch"}],"date_updated":"2023-08-08T13:32:40Z","type":"journal_article","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"status":"public","_id":"9387","volume":524,"publication_status":"published","publication_identifier":{"issn":["0022-5193"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/477489v1"}],"intvolume":" 524","month":"04","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","article_processing_charge":"No","external_id":{"isi":["000659161500002"]},"author":[{"orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia"},{"last_name":"Neretina","full_name":"Neretina, Tatiana Yu.","first_name":"Tatiana Yu."},{"full_name":"Kondrashov, Alexey S.","last_name":"Kondrashov","first_name":"Alexey S."}],"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.","ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524. doi:10.1016/j.jtbi.2021.110729","apa":"Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729","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).","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","article_number":"110729","date_created":"2021-05-12T05:58:42Z","date_published":"2021-04-24T00:00:00Z","doi":"10.1016/j.jtbi.2021.110729","year":"2021","isi":1,"publication":"Journal of Theoretical Biology","day":"24","oa":1,"publisher":"Elsevier ","quality_controlled":"1","acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173."}]