[{"isi":1,"page":"443-447","quality_controlled":"1","external_id":{"isi":["000721363700003"],"arxiv":["1912.03670"]},"year":"2021","intvolume":" 64","abstract":[{"lang":"eng","text":"We compute the deficiency spaces of operators of the form đ»đŽâŠ—Ì‚ đŒ+đŒâŠ—Ì‚ đ»đ”, for symmetric đ»đŽ and self-adjoint đ»đ”. This enables us to construct self-adjoint extensions (if they exist) by means of von Neumann's theory. The structure of the deficiency spaces for this case was asserted already in Ibort et al. [Boundary dynamics driven entanglement, J. Phys. A: Math. Theor. 47(38) (2014) 385301], but only proven under the restriction of đ»đ” having discrete, non-degenerate spectrum."}],"day":"01","date_updated":"2026-06-18T19:54:27Z","title":"Self-adjoint extensions of bipartite Hamiltonians","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"journal_article","status":"public","doi":"10.1017/S0013091521000080","date_created":"2021-07-04T22:01:24Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/S0013091521000080"}],"issue":"3","acknowledgement":"M. W. gratefully acknowledges financial support by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes). T.W. thanks PAO Gazprom Neft, the Euler International Mathematical Institute in Saint Petersburg and ORISA GmbH for their financial support in the form of scholarships during his Master's and Bachelor's studies respectively. The authors want to thank Mark Malamud for pointing out the reference [1] to them. This work was supported by the Ministry of Science and Higher Education of the Russian Federation, agreement No 075-15-2019-1619.","author":[{"full_name":"Lenz, Daniel","first_name":"Daniel","last_name":"Lenz"},{"first_name":"Timon","last_name":"Weinmann","full_name":"Weinmann, Timon"},{"full_name":"Wirth, Melchior","orcid":"0000-0002-0519-4241","last_name":"Wirth","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"ddc":["500"],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","date_published":"2021-08-01T00:00:00Z","publication_status":"published","month":"08","volume":64,"citation":{"short":"D. Lenz, T. Weinmann, M. Wirth, Proceedings of the Edinburgh Mathematical Society 64 (2021) 443–447.","mla":"Lenz, Daniel, et al. “Self-Adjoint Extensions of Bipartite Hamiltonians.” Proceedings of the Edinburgh Mathematical Society, vol. 64, no. 3, Cambridge University Press, 2021, pp. 443–47, doi:10.1017/S0013091521000080.","apa":"Lenz, D., Weinmann, T., & Wirth, M. (2021). Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. Cambridge University Press. https://doi.org/10.1017/S0013091521000080","ista":"Lenz D, Weinmann T, Wirth M. 2021. Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. 64(3), 443–447.","ieee":"D. Lenz, T. Weinmann, and M. Wirth, “Self-adjoint extensions of bipartite Hamiltonians,” Proceedings of the Edinburgh Mathematical Society, vol. 64, no. 3. Cambridge University Press, pp. 443–447, 2021.","chicago":"Lenz, Daniel, Timon Weinmann, and Melchior Wirth. “Self-Adjoint Extensions of Bipartite Hamiltonians.” Proceedings of the Edinburgh Mathematical Society. Cambridge University Press, 2021. https://doi.org/10.1017/S0013091521000080.","ama":"Lenz D, Weinmann T, Wirth M. Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. 2021;64(3):443-447. doi:10.1017/S0013091521000080"},"article_processing_charge":"No","department":[{"_id":"JaMa"}],"oa":1,"arxiv":1,"publication":"Proceedings of the Edinburgh Mathematical Society","_id":"9627","publication_identifier":{"eissn":["1464-3839"],"issn":["0013-0915"]},"fulldoi":"https://doi.org/10.1017/S0013091521000080","publisher":"Cambridge University Press","scopus_import":"1"},{"intvolume":" 23","abstract":[{"text":"Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis.","lang":"eng"}],"date_updated":"2025-04-14T07:52:26Z","title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","day":"21","language":[{"iso":"eng"}],"oa_version":"Preprint","page":"733–744","isi":1,"quality_controlled":"1","external_id":{"pmid":["34155381"],"isi":["000664016300003"]},"year":"2021","date_created":"2021-07-04T22:01:25Z","acknowledgement":"We acknowledge the members of the Lennon-DumĂ©nil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359","open_access":"1"}],"author":[{"full_name":"Yang, Qiutan","first_name":"Qiutan","last_name":"Yang"},{"first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","last_name":"Xue","full_name":"Xue, Shi-lei"},{"last_name":"Chan","first_name":"Chii Jou","full_name":"Chan, Chii Jou"},{"full_name":"Rempfler, Markus","first_name":"Markus","last_name":"Rempfler"},{"full_name":"Vischi, Dario","last_name":"Vischi","first_name":"Dario"},{"last_name":"Maurer-Gutierrez","first_name":"Francisca","full_name":"Maurer-Gutierrez, Francisca"},{"last_name":"Hiiragi","first_name":"Takashi","full_name":"Hiiragi, Takashi"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"full_name":"Liberali, Prisca","first_name":"Prisca","last_name":"Liberali"}],"corr_author":"1","type":"journal_article","status":"public","doi":"10.1038/s41556-021-00700-2","volume":23,"citation":{"ieee":"Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744, 2021.","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021, pp. 733–744, doi:10.1038/s41556-021-00700-2.","ista":"Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744.","apa":"Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., 
 Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2","chicago":"Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2.","ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2"},"ec_funded":1,"department":[{"_id":"EdHa"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","date_published":"2021-06-21T00:00:00Z","publication_status":"published","month":"06","publication":"Nature Cell Biology","pmid":1,"_id":"9629","publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"fulldoi":"https://doi.org/10.1038/s41556-021-00700-2","scopus_import":"1","publisher":"Springer Nature","oa":1,"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF"}]},{"related_material":{"record":[{"status":"public","id":"10029","relation":"used_in_publication"}]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","date_published":"2021-01-01T00:00:00Z","file":[{"file_name":"figures_data.zip","date_updated":"2021-07-07T20:37:28Z","access_level":"open_access","file_id":"9637","content_type":"application/zip","checksum":"18e90687ec7bbd75f8bfea4d8293fb30","success":1,"creator":"ahigginb","date_created":"2021-07-07T20:37:28Z","file_size":3345244,"relation":"main_file"}],"citation":{"mla":"Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology Austria, 2021.","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.","short":"A.P. Higginbotham, (2021).","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021.","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021."},"oa_version":"Submitted Version","title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","date_updated":"2025-04-15T06:54:43Z","department":[{"_id":"AnHi"}],"article_processing_charge":"No","has_accepted_license":"1","oa":1,"file_date_updated":"2021-07-07T20:37:28Z","status":"public","type":"research_data","_id":"9636","date_created":"2021-07-07T20:43:10Z","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"}]},{"type":"journal_article","status":"public","file_date_updated":"2021-07-19T13:02:20Z","doi":"10.1038/s41467-021-24271-w","ddc":["510"],"author":[{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2021-07-11T22:01:15Z","issue":"1","acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","external_id":{"isi":["000671752100003"],"pmid":["34188036"]},"year":"2021","isi":1,"quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","title":"Fast and strong amplifiers of natural selection","date_updated":"2026-04-02T14:04:10Z","day":"29","language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":" 12","file":[{"relation":"main_file","file_size":628992,"date_created":"2021-07-19T13:02:20Z","file_id":"9692","content_type":"application/pdf","success":1,"checksum":"5767418926a7f7fb76151de29473dae0","creator":"cziletti","file_name":"2021_NatCoom_Tkadlec.pdf","date_updated":"2021-07-19T13:02:20Z","access_level":"open_access"}],"abstract":[{"text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.","lang":"eng"}],"article_number":"4009","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"oa":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1038/s41467-021-24271-w","scopus_import":"1","publisher":"Springer Nature","publication":"Nature Communications","pmid":1,"_id":"9640","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","date_published":"2021-06-29T00:00:00Z","month":"06","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_type":"original","department":[{"_id":"KrCh"}],"article_processing_charge":"No","volume":12,"citation":{"chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-24271-w","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009."},"ec_funded":1},{"acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","date_created":"2021-07-11T22:01:16Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"},"author":[{"first_name":"Felipe","last_name":"Fredes","full_name":"Fredes, Felipe"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"ddc":["610"],"file_date_updated":"2021-07-19T13:46:06Z","doi":"10.1016/j.nlm.2021.107486","status":"public","type":"journal_article","article_number":"107486","abstract":[{"lang":"eng","text":"At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation."}],"file":[{"file_size":1994793,"relation":"main_file","date_updated":"2021-07-19T13:46:06Z","file_name":"2021_NeurobLearnMemory_Fredes.pdf","access_level":"open_access","file_id":"9694","content_type":"application/pdf","checksum":"8e8298a9e8c7df146ad23f32c2a63929","creator":"cziletti","success":1,"date_created":"2021-07-19T13:46:06Z"}],"intvolume":" 183","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"30","title":"The role of hippocampal mossy cells in novelty detection","date_updated":"2025-07-10T12:02:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","quality_controlled":"1","isi":1,"year":"2021","external_id":{"pmid":["34214666"],"isi":["000677694900004"]},"pmid":1,"_id":"9641","publication_identifier":{"eissn":["1095-9564"],"issn":["1074-7427"]},"publication":"Neurobiology of Learning and Memory","scopus_import":"1","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.nlm.2021.107486","has_accepted_license":"1","oa":1,"project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"citation":{"ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021.","apa":"Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486","ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486.","mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486, Elsevier, 2021, doi:10.1016/j.nlm.2021.107486.","short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021. https://doi.org/10.1016/j.nlm.2021.107486.","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486"},"volume":183,"article_processing_charge":"No","department":[{"_id":"RySh"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","date_published":"2021-06-30T00:00:00Z","publication_status":"published"},{"type":"journal_article","file_date_updated":"2021-07-19T13:32:17Z","doi":"10.1016/j.celrep.2021.109313","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"ddc":["570"],"author":[{"full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro"},{"full_name":"Schulz, Rouven","last_name":"Schulz","orcid":"0000-0001-5297-733X","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De JesĂșs-CortĂ©s, HĂ©ctor","last_name":"De JesĂșs-CortĂ©s","first_name":"HĂ©ctor"},{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","last_name":"Maes","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E"},{"full_name":"Nagy, Balint","first_name":"Balint","id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425","last_name":"Nagy"},{"last_name":"Reilly-AndĂșjar","first_name":"Francis","full_name":"Reilly-AndĂșjar, Francis"},{"orcid":"0000-0001-9434-8902","last_name":"Colombo","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria"},{"full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero","first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","last_name":"Schoot Uiterkamp"},{"first_name":"Mark F.","last_name":"Bear","full_name":"Bear, Mark F."},{"full_name":"Siegert, Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2021-07-11T22:01:16Z","issue":"1","acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; JĂŒrgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie SkƂodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","external_id":{"isi":["000670188500004"],"pmid":["34233180"]},"year":"2021","isi":1,"quality_controlled":"1","date_updated":"2026-04-03T09:46:05Z","title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","day":"06","oa_version":"Published Version","language":[{"iso":"eng"}],"intvolume":" 36","file":[{"date_created":"2021-07-19T13:32:17Z","checksum":"f056255f6d01fd9a86b5387635928173","creator":"cziletti","success":1,"content_type":"application/pdf","file_id":"9693","access_level":"open_access","date_updated":"2021-07-19T13:32:17Z","file_name":"2021_CellReports_Venturino.pdf","relation":"main_file","file_size":56388540}],"abstract":[{"lang":"eng","text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain."}],"article_number":"109313","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"oa":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1016/j.celrep.2021.109313","scopus_import":"1","publisher":"Elsevier","publication":"Cell Reports","pmid":1,"_id":"9642","publication_identifier":{"eissn":["2211-1247"]},"date_published":"2021-07-06T00:00:00Z","publication_status":"published","month":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/","relation":"press_release"}]},"article_type":"original","department":[{"_id":"SaSi"}],"article_processing_charge":"No","volume":36,"citation":{"ieee":"A. Venturino et al., “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” Cell Reports, vol. 36, no. 1. Elsevier, 2021.","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313.","apa":"Venturino, A., Schulz, R., De JesĂșs-CortĂ©s, H., Maes, M. E., Nagy, B., Reilly-AndĂșjar, F., 
 Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313","ista":"Venturino A, Schulz R, De JesĂșs-CortĂ©s H, Maes ME, Nagy B, Reilly-AndĂșjar F, Colombo G, Cubero RJ, Miteva FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.","short":"A. Venturino, R. Schulz, H. De JesĂșs-CortĂ©s, M.E. Maes, B. Nagy, F. Reilly-AndĂșjar, G. Colombo, R.J. Cubero, F.E. Miteva, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","ama":"Venturino A, Schulz R, De JesĂșs-CortĂ©s H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313","chicago":"Venturino, Alessandro, Rouven Schulz, HĂ©ctor De JesĂșs-CortĂ©s, Margaret E Maes, Balint Nagy, Francis Reilly-AndĂșjar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier, 2021. https://doi.org/10.1016/j.celrep.2021.109313."},"ec_funded":1},{"department":[{"_id":"KrCh"}],"article_processing_charge":"No","ec_funded":1,"citation":{"ama":"Chatterjee K, Goharshady EK, NovotnĂœ P, Zikelic D. Proving non-termination by program reversal. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1033-1048. doi:10.1145/3453483.3454093","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr NovotnĂœ, and Dorde Zikelic. “Proving Non-Termination by Program Reversal.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1033–48. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454093.","apa":"Chatterjee, K., Goharshady, E. K., NovotnĂœ, P., & Zikelic, D. (2021). Proving non-termination by program reversal. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1033–1048). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454093","ista":"Chatterjee K, Goharshady EK, NovotnĂœ P, Zikelic D. 2021. Proving non-termination by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1033–1048.","mla":"Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–48, doi:10.1145/3453483.3454093.","short":"K. Chatterjee, E.K. Goharshady, P. NovotnĂœ, D. Zikelic, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048.","ieee":"K. Chatterjee, E. K. Goharshady, P. NovotnĂœ, and D. Zikelic, “Proving non-termination by program reversal,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1033–1048."},"publication_status":"published","date_published":"2021-06-01T00:00:00Z","month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"relation":"research_data","id":"15284","status":"public"},{"id":"14539","status":"public","relation":"dissertation_contains"}]},"fulldoi":"https://doi.org/10.1145/3453483.3454093","publisher":"Association for Computing Machinery","scopus_import":"1","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","publication_identifier":{"isbn":["9781450383912"]},"_id":"9644","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"arxiv":1,"oa":1,"day":"01","title":"Proving non-termination by program reversal","date_updated":"2026-04-07T13:27:55Z","oa_version":"Preprint","language":[{"iso":"eng"}],"abstract":[{"text":"We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters.","lang":"eng"}],"external_id":{"isi":["000723661700067"],"arxiv":["2104.01189"]},"year":"2021","isi":1,"page":"1033-1048","quality_controlled":"1","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Ehsan Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar"},{"full_name":"NovotnĂœ, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"NovotnĂœ"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"}],"date_created":"2021-07-11T22:01:17Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.01189"}],"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech Science Foundation grant No. GJ19-15134Y.","type":"conference","status":"public","doi":"10.1145/3453483.3454093","conference":{"name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","location":"Online","end_date":"2021-06-26"}},{"author":[{"full_name":"Asadi, Ali","first_name":"Ali","last_name":"Asadi"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mahdavi","first_name":"Mohammad","full_name":"Mahdavi, Mohammad"}],"date_created":"2021-07-11T22:01:17Z","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03183862/","open_access":"1"}],"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).","type":"conference","doi":"10.1145/3453483.3454076","status":"public","conference":{"end_date":"2021-06-26","start_date":"2021-06-20","name":"PLDI: Programming Language Design and Implementation","location":"Online"},"day":"01","date_updated":"2025-07-10T12:02:00Z","title":"Polynomial reachability witnesses via StellensĂ€tze","oa_version":"Submitted Version","language":[{"iso":"eng"}],"abstract":[{"text":"We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods.","lang":"eng"}],"external_id":{"isi":["000723661700050"]},"year":"2021","isi":1,"page":"772-787","quality_controlled":"1","fulldoi":"https://doi.org/10.1145/3453483.3454076","scopus_import":"1","publisher":"Association for Computing Machinery","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","_id":"9645","publication_identifier":{"isbn":["9781450383912"]},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"}],"oa":1,"article_processing_charge":"No","department":[{"_id":"KrCh"}],"ec_funded":1,"citation":{"ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via StellensĂ€tze. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via StellensĂ€tze.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 772–87. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454076.","short":"A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787.","apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021). Polynomial reachability witnesses via StellensĂ€tze. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076","ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via StellensĂ€tze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.","mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via StellensĂ€tze.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–87, doi:10.1145/3453483.3454076.","ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via StellensĂ€tze,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 772–787."},"publication_status":"published","date_published":"2021-06-01T00:00:00Z","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"conference":{"end_date":"2021-06-26","name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","location":"Online"},"status":"public","doi":"10.1145/3453483.3454102","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/2011.14617","open_access":"1"}],"acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).","date_created":"2021-07-11T22:01:18Z","author":[{"full_name":"Wang, Jinyi","first_name":"Jinyi","last_name":"Wang"},{"last_name":"Sun","first_name":"Yican","full_name":"Sun, Yican"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584"}],"quality_controlled":"1","isi":1,"page":"1171-1186","year":"2021","external_id":{"arxiv":["2011.14617"],"isi":["000723661700076"]},"abstract":[{"text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude.","lang":"eng"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"day":"01","title":"Quantitative analysis of assertion violations in probabilistic programs","date_updated":"2025-04-15T07:55:05Z","oa":1,"arxiv":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"}],"publication_identifier":{"isbn":["9781450383912"]},"_id":"9646","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","scopus_import":"1","publisher":"Association for Computing Machinery","fulldoi":"https://doi.org/10.1145/3453483.3454102","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"06","date_published":"2021-06-01T00:00:00Z","publication_status":"published","ec_funded":1,"citation":{"ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102","chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1171–86. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454102.","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186.","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1171–1186). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454102","mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1171–1186."},"article_processing_charge":"No","department":[{"_id":"KrCh"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","publication_status":"published","date_published":"2021-06-04T00:00:00Z","month":"06","volume":893,"citation":{"ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” Theoretical Computer Science, vol. 893. Elsevier, pp. 1–16, 2021.","mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023.","ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16.","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021). Long lived transients in gene regulation. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023"},"article_processing_charge":"No","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"oa":1,"has_accepted_license":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"publication":"Theoretical Computer Science","publication_identifier":{"issn":["0304-3975"]},"_id":"9647","fulldoi":"https://doi.org/10.1016/j.tcs.2021.05.023","publisher":"Elsevier","scopus_import":"1","isi":1,"page":"1-16","quality_controlled":"1","external_id":{"isi":["000710180500002"]},"year":"2021","intvolume":" 893","abstract":[{"lang":"eng","text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof."}],"file":[{"creator":"dernst","success":1,"checksum":"d3aef34cfb13e53bba4cf44d01680793","content_type":"application/pdf","file_id":"11364","date_created":"2022-05-12T12:13:27Z","access_level":"open_access","file_name":"2021_TheoreticalComputerScience_Petrov.pdf","date_updated":"2022-05-12T12:13:27Z","relation":"main_file","file_size":2566504}],"day":"04","title":"Long lived transients in gene regulation","date_updated":"2025-04-15T06:25:56Z","oa_version":"Published Version","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2022-05-12T12:13:27Z","status":"public","doi":"10.1016/j.tcs.2021.05.023","date_created":"2021-07-11T22:01:18Z","acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","author":[{"full_name":"Petrov, Tatjana","last_name":"Petrov","first_name":"Tatjana"},{"full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"ddc":["004"],"corr_author":"1","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"}},{"isi":1,"page":"510-522","quality_controlled":"1","external_id":{"isi":["000680587100001"],"pmid":["34254313"]},"year":"2021","intvolume":" 232","abstract":[{"text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.","lang":"eng"}],"file":[{"file_size":1939800,"relation":"main_file","access_level":"open_access","date_updated":"2021-10-07T13:42:47Z","file_name":"2021_NewPhytologist_Han.pdf","content_type":"application/pdf","checksum":"6422a6eb329b52d96279daaee0fcf189","success":1,"creator":"kschuh","file_id":"10105","date_created":"2021-10-07T13:42:47Z"}],"day":"01","title":"PIN-mediated polar auxin transport regulations in plant tropic responses","date_updated":"2025-04-14T07:45:00Z","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"journal_article","doi":"10.1111/nph.17617","status":"public","file_date_updated":"2021-10-07T13:42:47Z","date_created":"2021-07-14T15:29:14Z","acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","issue":"2","author":[{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"id":"44B04502-A9ED-11E9-B6FC-583AE6697425","first_name":"Linlin","last_name":"Qi","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin"},{"full_name":"Alotaibi, SS","first_name":"SS","last_name":"Alotaibi"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiƙí","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiƙí"}],"ddc":["580"],"corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","date_published":"2021-10-01T00:00:00Z","publication_status":"published","month":"10","volume":232,"ec_funded":1,"citation":{"chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiƙí Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617.","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522. doi:10.1111/nph.17617","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” New Phytologist, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:10.1111/nph.17617.","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. Wiley. https://doi.org/10.1111/nph.17617"},"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"JiFr"}],"oa":1,"has_accepted_license":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"}],"publication":"New Phytologist","pmid":1,"_id":"9656","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"fulldoi":"https://doi.org/10.1111/nph.17617","scopus_import":"1","publisher":"Wiley"},{"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"},"author":[{"full_name":"Gao, Z","first_name":"Z","last_name":"Gao"},{"first_name":"Z","last_name":"Chen","full_name":"Chen, Z"},{"full_name":"Cui, Y","last_name":"Cui","first_name":"Y"},{"full_name":"Ke, M","first_name":"M","last_name":"Ke"},{"first_name":"H","last_name":"Xu","full_name":"Xu, H"},{"last_name":"Xu","first_name":"Q","full_name":"Xu, Q"},{"last_name":"Chen","first_name":"J","full_name":"Chen, J"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"full_name":"Huang, L","first_name":"L","last_name":"Huang"},{"last_name":"Zhao","first_name":"H","full_name":"Zhao, H"},{"full_name":"Huang, D","first_name":"D","last_name":"Huang"},{"last_name":"Mai","first_name":"S","full_name":"Mai, S"},{"full_name":"Xu, T","first_name":"T","last_name":"Xu"},{"first_name":"X","last_name":"Liu","full_name":"Liu, X"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"last_name":"Guan","first_name":"Y","full_name":"Guan, Y"},{"first_name":"W","last_name":"Yang","full_name":"Yang, W"},{"full_name":"Friml, Jiƙí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiƙí"},{"full_name":"PetrĂĄĆĄek, J","last_name":"PetrĂĄĆĄek","first_name":"J"},{"full_name":"Zhang, J","last_name":"Zhang","first_name":"J"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"}],"ddc":["580"],"issue":"9","date_created":"2021-07-14T15:32:43Z","file_date_updated":"2021-07-19T12:13:34Z","status":"public","doi":"10.1093/plcell/koab183","type":"journal_article","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"07","date_updated":"2024-10-21T06:02:03Z","title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","abstract":[{"lang":"eng","text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia."}],"file":[{"file_size":10566921,"relation":"main_file","file_name":"2021_PlantCell_Gao.pdf","date_updated":"2021-07-19T12:13:34Z","access_level":"open_access","file_id":"9691","content_type":"application/pdf","checksum":"6715712ec306c321f0204c817b7f8ae7","success":1,"creator":"cziletti","date_created":"2021-07-19T12:13:34Z"}],"intvolume":" 33","year":"2021","external_id":{"isi":["000702165300012"],"pmid":["34240197"]},"quality_controlled":"1","isi":1,"page":"2981–3003","scopus_import":"1","publisher":"American Society of Plant Biologists","fulldoi":"https://doi.org/10.1093/plcell/koab183","_id":"9657","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"pmid":1,"publication":"Plant Cell","has_accepted_license":"1","oa":1,"article_processing_charge":"No","department":[{"_id":"JiFr"}],"citation":{"ieee":"Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, PetrĂĄĆĄek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., 
 Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. PetrĂĄĆĄek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183","chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183."},"volume":33,"month":"07","publication_status":"published","date_published":"2021-07-07T00:00:00Z","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_type":"original","date_published":"2021-01-26T00:00:00Z","publication_status":"published","month":"01","volume":12,"citation":{"ama":"Reinhardt A, Cheng B. Quantum-mechanical exploration of the phase diagram of water. Nature Communications. 2021;12(1). doi:10.1038/s41467-020-20821-w","chicago":"Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of the Phase Diagram of Water.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-020-20821-w.","short":"A. Reinhardt, B. Cheng, Nature Communications 12 (2021).","apa":"Reinhardt, A., & Cheng, B. (2021). Quantum-mechanical exploration of the phase diagram of water. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20821-w","ista":"Reinhardt A, Cheng B. 2021. Quantum-mechanical exploration of the phase diagram of water. Nature Communications. 12(1), 588.","mla":"Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of the Phase Diagram of Water.” Nature Communications, vol. 12, no. 1, 588, Springer Nature, 2021, doi:10.1038/s41467-020-20821-w.","ieee":"A. Reinhardt and B. Cheng, “Quantum-mechanical exploration of the phase diagram of water,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021."},"article_processing_charge":"No","oa":1,"has_accepted_license":"1","extern":"1","arxiv":1,"publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"_id":"9669","pmid":1,"fulldoi":"https://doi.org/10.1038/s41467-020-20821-w","publisher":"Springer Nature","scopus_import":"1","quality_controlled":"1","external_id":{"arxiv":["2010.13729"],"pmid":["33500405"]},"year":"2021","intvolume":" 12","article_number":"588","abstract":[{"lang":"eng","text":"The set of known stable phases of water may not be complete, and some of the phase boundaries between them are fuzzy. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the phase diagram at three hybrid density-functional-theory levels of approximation, accounting for thermal and nuclear fluctuations as well as proton disorder. Such calculations are only made tractable because we combine machine-learning methods and advanced free-energy techniques. The computed phase diagram is in qualitative agreement with experiment, particularly at pressures â‰Č 8000 bar, and the discrepancy in chemical potential is comparable with the subtle uncertainties introduced by proton disorder and the spread between the three hybrid functionals. None of the hypothetical ice phases considered is thermodynamically stable in our calculations, suggesting the completeness of the experimental water phase diagram in the region considered. Our work demonstrates the feasibility of predicting the phase diagram of a polymorphic system from first principles and provides a thermodynamic way of testing the limits of quantum-mechanical calculations."}],"file":[{"file_id":"9670","content_type":"application/pdf","success":1,"creator":"asandaue","checksum":"8b5e1fbe2f1ab936047008043150e894","date_created":"2021-07-15T13:55:46Z","file_name":"2021_NatureCommunications_Reinhardt.pdf","date_updated":"2021-07-15T13:55:46Z","access_level":"open_access","relation":"main_file","file_size":1180227}],"day":"26","date_updated":"2023-02-23T14:04:20Z","title":"Quantum-mechanical exploration of the phase diagram of water","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"journal_article","doi":"10.1038/s41467-020-20821-w","status":"public","file_date_updated":"2021-07-15T13:55:46Z","date_created":"2021-07-15T13:48:13Z","issue":"1","author":[{"full_name":"Reinhardt, Aleks","last_name":"Reinhardt","first_name":"Aleks"},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632"}],"ddc":["530","540"],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"publication":"New Journal of Physics","publication_identifier":{"eissn":["1367-2630"]},"_id":"9679","fulldoi":"https://doi.org/10.1088/1367-2630/ac0576","scopus_import":"1","publisher":"IOP Publishing","oa":1,"has_accepted_license":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"volume":23,"ec_funded":1,"citation":{"ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. New Journal of Physics. 2021;23(6). doi:10.1088/1367-2630/ac0576","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac0576.","ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” New Journal of Physics, vol. 23, no. 6. IOP Publishing, 2021.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:10.1088/1367-2630/ac0576.","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., & Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac0576"},"department":[{"_id":"MiLe"}],"article_processing_charge":"Yes","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_type":"original","publication_status":"published","date_published":"2021-06-23T00:00:00Z","month":"06","date_created":"2021-07-18T22:01:22Z","issue":"6","acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie SkƂodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium fĂŒr Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische UniversitĂ€t Darmstadt.","author":[{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"full_name":"Marchukov, Oleksandr V.","last_name":"Marchukov","first_name":"Oleksandr V."},{"first_name":"Hans Werner","last_name":"Hammer","full_name":"Hammer, Hans Werner"},{"full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525"}],"ddc":["530"],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","doi":"10.1088/1367-2630/ac0576","status":"public","file_date_updated":"2021-07-19T11:47:16Z","intvolume":" 23","abstract":[{"text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio Îș of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/Îș ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/Îș = 1 and 1/Îș = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.","lang":"eng"}],"article_number":"065009","file":[{"date_updated":"2021-07-19T11:47:16Z","file_name":"2021_NewJPhys_Huber.pdf","access_level":"open_access","file_id":"9690","checksum":"e39164ce7ea228d287cf8924e1a0f9fe","creator":"cziletti","content_type":"application/pdf","success":1,"date_created":"2021-07-19T11:47:16Z","file_size":3868445,"relation":"main_file"}],"day":"23","title":"Morphology of three-body quantum states from machine learning","date_updated":"2026-04-02T14:01:49Z","oa_version":"Published Version","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000664736300001"],"arxiv":["2102.04961"]},"year":"2021"},{"year":"2021","month":"03","external_id":{"arxiv":["2103.09035"]},"publication_status":"submitted","date_published":"2021-03-16T00:00:00Z","related_material":{"record":[{"status":"public","id":"19909","relation":"later_version"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa_version":"Preprint","date_updated":"2025-06-26T11:49:07Z","title":"Predicting the phase behaviors of superionic water at planetary conditions","day":"16","article_processing_charge":"No","citation":{"chicago":"Cheng, Bingqing, Mandy Bethkenhagen, Chris J. Pickard, and Sebastien Hamel. “Predicting the Phase Behaviors of Superionic Water at Planetary Conditions.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2103.09035.","ama":"Cheng B, Bethkenhagen M, Pickard CJ, Hamel S. Predicting the phase behaviors of superionic water at planetary conditions. arXiv. doi:10.48550/arXiv.2103.09035","short":"B. Cheng, M. Bethkenhagen, C.J. Pickard, S. Hamel, ArXiv (n.d.).","mla":"Cheng, Bingqing, et al. “Predicting the Phase Behaviors of Superionic Water at Planetary Conditions.” ArXiv, 2103.09035, doi:10.48550/arXiv.2103.09035.","apa":"Cheng, B., Bethkenhagen, M., Pickard, C. J., & Hamel, S. (n.d.). Predicting the phase behaviors of superionic water at planetary conditions. arXiv. https://doi.org/10.48550/arXiv.2103.09035","ista":"Cheng B, Bethkenhagen M, Pickard CJ, Hamel S. Predicting the phase behaviors of superionic water at planetary conditions. arXiv, 2103.09035.","ieee":"B. Cheng, M. Bethkenhagen, C. J. Pickard, and S. Hamel, “Predicting the phase behaviors of superionic water at planetary conditions,” arXiv. ."},"article_number":"2103.09035","abstract":[{"text":"Most water in the universe may be superionic, and its thermodynamic and transport properties are crucial for planetary science but difficult to probe experimentally or theoretically. We use machine learning and free energy methods to overcome the limitations of quantum mechanical simulations, and characterize hydrogen diffusion, superionic transitions, and phase behaviors of water at extreme conditions. We predict that a close-packed superionic phase with mixed stacking is stable over a wide temperature and pressure range, while a body-centered cubic phase is only thermodynamically stable in a small window but is kinetically favored. Our phase boundaries, which are consistent with the existing-albeit scarce-experimental observations, help resolve the fractions of insulating ice, different superionic phases, and liquid water inside of ice giants.","lang":"eng"}],"arxiv":1,"doi":"10.48550/arXiv.2103.09035","status":"public","type":"preprint","extern":"1","oa":1,"fulldoi":"https://doi.org/10.48550/arXiv.2103.09035","author":[{"full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"Mandy","last_name":"Bethkenhagen","full_name":"Bethkenhagen, Mandy"},{"full_name":"Pickard, Chris J.","first_name":"Chris J.","last_name":"Pickard"},{"full_name":"Hamel, Sebastien","first_name":"Sebastien","last_name":"Hamel"}],"_id":"9696","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.09035"}],"date_created":"2021-07-20T06:42:29Z","publication":"arXiv"},{"extern":"1","oa":1,"arxiv":1,"publication_identifier":{"issn":["0009-2665"],"eissn":["1520-6890"]},"_id":"9698","publication":"Chemical Reviews","publisher":"American Chemical Society","scopus_import":"1","fulldoi":"https://doi.org/10.1021/acs.chemrev.1c00107","article_type":"review","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","publication_status":"published","date_published":"2021-07-07T00:00:00Z","citation":{"ieee":"J. A. Keith et al., “Combining machine learning and computational chemistry for predictive insights into chemical systems,” Chemical Reviews, vol. 121, no. 16. American Chemical Society, pp. 9816–9872, 2021.","apa":"Keith, J. A., Valentin Vassilev-Galindo, V., Cheng, B., Chmiela, S., Gastegger, M., MĂŒller, K.-R., & Tkatchenko, A. (2021). Combining machine learning and computational chemistry for predictive insights into chemical systems. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.1c00107","ista":"Keith JA, Valentin Vassilev-Galindo V, Cheng B, Chmiela S, Gastegger M, MĂŒller K-R, Tkatchenko A. 2021. Combining machine learning and computational chemistry for predictive insights into chemical systems. Chemical Reviews. 121(16), 9816–9872.","mla":"Keith, John A., et al. “Combining Machine Learning and Computational Chemistry for Predictive Insights into Chemical Systems.” Chemical Reviews, vol. 121, no. 16, American Chemical Society, 2021, pp. 9816–72, doi:10.1021/acs.chemrev.1c00107.","short":"J.A. Keith, V. Valentin Vassilev-Galindo, B. Cheng, S. Chmiela, M. Gastegger, K.-R. MĂŒller, A. Tkatchenko, Chemical Reviews 121 (2021) 9816–9872.","chicago":"Keith, John A., Valentin Valentin Vassilev-Galindo, Bingqing Cheng, Stefan Chmiela, Michael Gastegger, Klaus-Robert MĂŒller, and Alexandre Tkatchenko. “Combining Machine Learning and Computational Chemistry for Predictive Insights into Chemical Systems.” Chemical Reviews. American Chemical Society, 2021. https://doi.org/10.1021/acs.chemrev.1c00107.","ama":"Keith JA, Valentin Vassilev-Galindo V, Cheng B, et al. Combining machine learning and computational chemistry for predictive insights into chemical systems. Chemical Reviews. 2021;121(16):9816-9872. doi:10.1021/acs.chemrev.1c00107"},"volume":121,"article_processing_charge":"No","doi":"10.1021/acs.chemrev.1c00107","status":"public","type":"journal_article","issue":"16","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.chemrev.1c00107"}],"date_created":"2021-07-20T11:18:37Z","author":[{"first_name":"John A.","last_name":"Keith","full_name":"Keith, John A."},{"last_name":"Valentin Vassilev-Galindo","first_name":"Valentin","full_name":"Valentin Vassilev-Galindo, Valentin"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"},{"full_name":"Chmiela, Stefan","last_name":"Chmiela","first_name":"Stefan"},{"last_name":"Gastegger","first_name":"Michael","full_name":"Gastegger, Michael"},{"first_name":"Klaus-Robert","last_name":"MĂŒller","full_name":"MĂŒller, Klaus-Robert"},{"full_name":"Tkatchenko, Alexandre","last_name":"Tkatchenko","first_name":"Alexandre"}],"quality_controlled":"1","page":"9816-9872","year":"2021","external_id":{"arxiv":["2102.06321"]},"abstract":[{"lang":"eng","text":"Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We then follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design."}],"intvolume":" 121","oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2023-05-08T11:31:03Z","title":"Combining machine learning and computational chemistry for predictive insights into chemical systems","day":"07"},{"oa":1,"_id":"9746","pmid":1,"publication_identifier":{"eissn":["2050-084X"]},"publication":"eLife","publisher":"eLife Sciences Publications","scopus_import":"1","fulldoi":"https://doi.org/10.7554/elife.68876","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","date_published":"2021-07-28T00:00:00Z","publication_status":"published","citation":{"ieee":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876","ista":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876.","mla":"Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021, doi:10.7554/elife.68876.","short":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021).","chicago":"Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876.","ama":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 2021;10. doi:10.7554/elife.68876"},"volume":10,"department":[{"_id":"CaGu"}],"article_processing_charge":"No","status":"public","doi":"10.7554/elife.68876","type":"journal_article","acknowledgement":"We would like to thank Leif Tueffers and JoĂŁo Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel).","main_file_link":[{"url":"https://doi.org/10.7554/eLife.68876","open_access":"1"}],"date_created":"2021-07-28T13:36:57Z","ddc":["570"],"author":[{"full_name":"Batra, Aditi","first_name":"Aditi","last_name":"Batra"},{"full_name":"Römhild, Roderich","last_name":"Römhild","orcid":"0000-0001-9480-5261","first_name":"Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E"},{"first_name":"Emilie","last_name":"Rousseau","full_name":"Rousseau, Emilie"},{"first_name":"Sören","last_name":"Franzenburg","full_name":"Franzenburg, Sören"},{"full_name":"Niemann, Stefan","first_name":"Stefan","last_name":"Niemann"},{"last_name":"Schulenburg","first_name":"Hinrich","full_name":"Schulenburg, Hinrich"}],"quality_controlled":"1","isi":1,"year":"2021","external_id":{"pmid":["34318749"],"isi":["000692027800001"]},"abstract":[{"lang":"eng","text":"Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only ÎČ-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs."}],"article_number":"e68876","intvolume":" 10","language":[{"iso":"eng"}],"oa_version":"Published Version","title":"High potency of sequential therapy with only beta-lactam antibiotics","date_updated":"2026-06-18T19:56:55Z","day":"28"},{"file":[{"date_created":"2021-08-05T12:06:49Z","content_type":"application/pdf","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","creator":"cchlebak","file_id":"9771","access_level":"open_access","date_updated":"2021-08-05T12:06:49Z","file_name":"2021_PlosCompBio_Bartlett.pdf","relation":"main_file","file_size":693633}],"article_number":"e1009124","intvolume":" 17","oa_version":"Published Version","language":[{"iso":"eng"}],"title":"Ten simple rules to improve academic work- life balance","date_updated":"2025-07-10T12:02:02Z","day":"15","isi":1,"year":"2021","external_id":{"isi":["000677713500008"],"pmid":["34264932"]},"issue":"7","acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","date_created":"2021-08-01T22:01:21Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["613"],"author":[{"first_name":"Michael John","last_name":"Bartlett","full_name":"Bartlett, Michael John"},{"full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","last_name":"Arslan","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N"},{"last_name":"Bankston","first_name":"Adriana","full_name":"Bankston, Adriana"},{"full_name":"Sarabipour, Sarvenaz","first_name":"Sarvenaz","last_name":"Sarabipour"}],"doi":"10.1371/journal.pcbi.1009124","status":"public","file_date_updated":"2021-08-05T12:06:49Z","type":"journal_article","citation":{"ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” PLoS Computational Biology, vol. 17, no. 7. Public Library of Science, 2021.","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124","ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009124.","ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124","chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124."},"volume":17,"department":[{"_id":"CaHe"}],"article_processing_charge":"Yes","article_type":"letter_note","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","date_published":"2021-07-15T00:00:00Z","publication_status":"published","_id":"9759","pmid":1,"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"publication":"PLoS Computational Biology","scopus_import":"1","publisher":"Public Library of Science","fulldoi":"https://doi.org/10.1371/journal.pcbi.1009124","has_accepted_license":"1","oa":1},{"citation":{"ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593","chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071593.","ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells, vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593.","ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593"},"volume":10,"article_processing_charge":"Yes","department":[{"_id":"SaSi"}],"article_type":"original","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"06","date_published":"2021-06-25T00:00:00Z","publication_status":"published","_id":"9761","publication_identifier":{"eissn":["2073-4409"]},"pmid":1,"publication":"Cells","scopus_import":"1","publisher":"MDPI","fulldoi":"https://doi.org/10.3390/cells10071593","has_accepted_license":"1","oa":1,"file":[{"file_name":"2021_Cells_Muench.pdf","date_updated":"2021-08-04T14:01:30Z","access_level":"open_access","date_created":"2021-08-04T14:01:30Z","file_id":"9768","checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","content_type":"application/pdf","creator":"cziletti","success":1,"file_size":4555611,"relation":"main_file"}],"abstract":[{"text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. ","lang":"eng"}],"article_number":"1593","intvolume":" 10","language":[{"iso":"eng"}],"oa_version":"Published Version","title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","date_updated":"2026-04-02T13:56:24Z","day":"25","quality_controlled":"1","isi":1,"year":"2021","external_id":{"pmid":["34201955"],"isi":["000678193300001"]},"acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","issue":"7","date_created":"2021-08-01T22:01:22Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"author":[{"full_name":"Muench, Nicole A.","first_name":"Nicole A.","last_name":"Muench"},{"full_name":"Patel, Sonia","first_name":"Sonia","last_name":"Patel"},{"full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes"},{"full_name":"Donahue, Ryan J.","first_name":"Ryan J.","last_name":"Donahue"},{"first_name":"Akihiro","last_name":"Ikeda","full_name":"Ikeda, Akihiro"},{"last_name":"Nickells","first_name":"Robert W.","full_name":"Nickells, Robert W."}],"file_date_updated":"2021-08-04T14:01:30Z","doi":"10.3390/cells10071593","status":"public","type":"journal_article"},{"volume":11,"citation":{"short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021).","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost Foundation, 2021, doi:10.21468/scipostphys.11.1.008.","ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.","apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.11.1.008","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” SciPost Physics, vol. 11, no. 1. SciPost Foundation, 2021.","ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008","chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics. SciPost Foundation, 2021. https://doi.org/10.21468/scipostphys.11.1.008."},"ec_funded":1,"department":[{"_id":"MiLe"}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","date_published":"2021-07-13T00:00:00Z","publication_status":"published","month":"07","publication":"SciPost Physics","publication_identifier":{"eissn":["2542-4653"]},"_id":"9769","fulldoi":"https://doi.org/10.21468/scipostphys.11.1.008","scopus_import":"1","publisher":"SciPost Foundation","oa":1,"has_accepted_license":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"intvolume":" 11","file":[{"relation":"main_file","file_size":1085300,"success":1,"creator":"asandaue","checksum":"eaa847346b1a023d97bbb291779610ed","content_type":"application/pdf","file_id":"9875","date_created":"2021-08-10T11:44:59Z","access_level":"open_access","date_updated":"2021-08-10T11:44:59Z","file_name":"2021_SciPostPhysics_Brauneis.pdf"}],"abstract":[{"text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak.","lang":"eng"}],"article_number":"008","title":"Impurities in a one-dimensional Bose gas: The flow equation approach","date_updated":"2025-05-14T10:51:56Z","day":"13","oa_version":"Published Version","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000680039500013"],"arxiv":["2101.10958"]},"year":"2021","date_created":"2021-08-04T15:00:55Z","issue":"1","acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie SkƂodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","ddc":["530"],"author":[{"first_name":"Fabian","last_name":"Brauneis","full_name":"Brauneis, Fabian"},{"full_name":"Hammer, Hans-Werner","last_name":"Hammer","first_name":"Hans-Werner"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","doi":"10.21468/scipostphys.11.1.008","status":"public","file_date_updated":"2021-08-10T11:44:59Z"}]