[{"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. <i>Nature Cell Biology</i>. 2021;23:733–744. doi:<a href=\"https://doi.org/10.1038/s41556-021-00700-2\">10.1038/s41556-021-00700-2</a>","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","ieee":"Q. Yang <i>et al.</i>, “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” <i>Nature Cell Biology</i>, vol. 23. Springer Nature, pp. 733–744, 2021.","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.” <i>Nature Cell Biology</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41556-021-00700-2\">https://doi.org/10.1038/s41556-021-00700-2</a>.","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.","mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” <i>Nature Cell Biology</i>, vol. 23, Springer Nature, 2021, pp. 733–744, doi:<a href=\"https://doi.org/10.1038/s41556-021-00700-2\">10.1038/s41556-021-00700-2</a>.","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. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-021-00700-2\">https://doi.org/10.1038/s41556-021-00700-2</a>"},"month":"06","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","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."}],"intvolume":"        23","publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"publication_status":"published","title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","oa_version":"Preprint","author":[{"last_name":"Yang","full_name":"Yang, Qiutan","first_name":"Qiutan"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","last_name":"Xue","first_name":"Shi-lei"},{"last_name":"Chan","full_name":"Chan, Chii Jou","first_name":"Chii Jou"},{"last_name":"Rempfler","full_name":"Rempfler, Markus","first_name":"Markus"},{"first_name":"Dario","full_name":"Vischi, Dario","last_name":"Vischi"},{"full_name":"Maurer-Gutierrez, Francisca","last_name":"Maurer-Gutierrez","first_name":"Francisca"},{"full_name":"Hiiragi, Takashi","last_name":"Hiiragi","first_name":"Takashi"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"last_name":"Liberali","full_name":"Liberali, Prisca","first_name":"Prisca"}],"scopus_import":"1","day":"21","article_type":"original","date_created":"2021-07-04T22:01:25Z","volume":23,"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","call_identifier":"FWF","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"}],"status":"public","publication":"Nature Cell Biology","acknowledgement":"We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).","date_published":"2021-06-21T00:00:00Z","pmid":1,"ec_funded":1,"external_id":{"pmid":["34155381"],"isi":["000664016300003"]},"year":"2021","isi":1,"page":"733–744","quality_controlled":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359","open_access":"1"}],"publisher":"Springer Nature","doi":"10.1038/s41556-021-00700-2","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-10T13:57:36Z","_id":"9629"},{"_id":"9636","date_updated":"2024-02-21T12:36:52Z","date_created":"2021-07-07T20:43:10Z","type":"research_data","article_processing_charge":"No","author":[{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-07-07T20:37:28Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"department":[{"_id":"AnHi"}],"file":[{"relation":"main_file","checksum":"18e90687ec7bbd75f8bfea4d8293fb30","success":1,"file_name":"figures_data.zip","access_level":"open_access","content_type":"application/zip","file_id":"9637","file_size":3345244,"date_created":"2021-07-07T20:37:28Z","creator":"ahigginb","date_updated":"2021-07-07T20:37:28Z"}],"year":"2021","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10029"}]},"citation":{"mla":"Higginbotham, Andrew P. <i>Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.”</i> 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.","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","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.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-01-01T00:00:00Z","oa":1,"status":"public"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>","mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009.","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>."},"issue":"1","language":[{"iso":"eng"}],"oa":1,"article_number":"4009","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2021_NatCoom_Tkadlec.pdf","checksum":"5767418926a7f7fb76151de29473dae0","relation":"main_file","date_updated":"2021-07-19T13:02:20Z","creator":"cziletti","date_created":"2021-07-19T13:02:20Z","file_size":628992,"file_id":"9692"}],"department":[{"_id":"KrCh"}],"month":"06","file_date_updated":"2021-07-19T13:02:20Z","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"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"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        12","has_accepted_license":"1","date_created":"2021-07-11T22:01:15Z","article_type":"original","volume":12,"oa_version":"Published Version","title":"Fast and strong amplifiers of natural selection","scopus_import":"1","day":"29","author":[{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"date_published":"2021-06-29T00:00:00Z","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.","ec_funded":1,"pmid":1,"status":"public","publication":"Nature Communications","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"external_id":{"isi":["000671752100003"],"pmid":["34188036"]},"isi":1,"year":"2021","quality_controlled":"1","ddc":["510"],"type":"journal_article","_id":"9640","date_updated":"2025-07-14T09:10:05Z","publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1038/s41467-021-24271-w"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Fredes, F., &#38; Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>","mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>, vol. 183, 107486, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>.","ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486.","chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>.","ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” <i>Neurobiology of Learning and Memory</i>, vol. 183. Elsevier, 2021.","short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. 2021;183. doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>"},"month":"06","article_number":"107486","file":[{"relation":"main_file","checksum":"8e8298a9e8c7df146ad23f32c2a63929","success":1,"file_name":"2021_NeurobLearnMemory_Fredes.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"9694","date_created":"2021-07-19T13:46:06Z","file_size":1994793,"date_updated":"2021-07-19T13:46:06Z","creator":"cziletti"}],"department":[{"_id":"RySh"}],"tmp":{"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","short":"CC BY-NC-ND (4.0)"},"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."}],"intvolume":"       183","has_accepted_license":"1","publication_status":"published","publication_identifier":{"issn":["10747427"],"eissn":["10959564"]},"file_date_updated":"2021-07-19T13:46:06Z","title":"The role of hippocampal mossy cells in novelty detection","oa_version":"Published Version","author":[{"first_name":"Felipe","last_name":"Fredes","full_name":"Fredes, Felipe"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"}],"scopus_import":"1","day":"30","article_type":"original","date_created":"2021-07-11T22:01:16Z","volume":183,"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Neurobiology of Learning and Memory","acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","date_published":"2021-06-30T00:00:00Z","pmid":1,"ec_funded":1,"external_id":{"pmid":["34214666"],"isi":["000677694900004"]},"isi":1,"year":"2021","ddc":["610"],"quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.nlm.2021.107486","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-10T14:10:37Z","_id":"9641"},{"date_updated":"2023-08-10T14:09:39Z","_id":"9642","type":"journal_article","doi":"10.1016/j.celrep.2021.109313","article_processing_charge":"No","publisher":"Elsevier","quality_controlled":"1","ddc":["570"],"isi":1,"year":"2021","external_id":{"isi":["000670188500004"],"pmid":["34233180"]},"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/","description":"News on IST Homepage"}]},"pmid":1,"ec_funded":1,"acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","date_published":"2021-07-06T00:00:00Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425"}],"publication":"Cell Reports","status":"public","volume":36,"article_type":"original","date_created":"2021-07-11T22:01:16Z","author":[{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","last_name":"Venturino","orcid":"0000-0003-2356-9403","first_name":"Alessandro"},{"first_name":"Rouven","orcid":"0000-0001-5297-733X","full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz"},{"first_name":"Héctor","last_name":"De Jesús-Cortés","full_name":"De Jesús-Cortés, Héctor"},{"first_name":"Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E"},{"first_name":"Balint","last_name":"Nagy","full_name":"Nagy, Balint","id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425"},{"last_name":"Reilly-Andújar","full_name":"Reilly-Andújar, Francis","first_name":"Francis"},{"last_name":"Colombo","full_name":"Colombo, Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","orcid":"0000-0001-9434-8902"},{"last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","first_name":"Ryan J"},{"last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","first_name":"Florianne E"},{"first_name":"Mark F.","last_name":"Bear","full_name":"Bear, Mark F."},{"last_name":"Siegert","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra"}],"scopus_import":"1","day":"06","oa_version":"Published Version","title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","publication_identifier":{"eissn":["22111247"]},"publication_status":"published","file_date_updated":"2021-07-19T13:32:17Z","has_accepted_license":"1","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."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        36","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"department":[{"_id":"SaSi"}],"article_number":"109313","file":[{"checksum":"f056255f6d01fd9a86b5387635928173","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2021_CellReports_Venturino.pdf","success":1,"file_id":"9693","creator":"cziletti","date_updated":"2021-07-19T13:32:17Z","file_size":56388540,"date_created":"2021-07-19T13:32:17Z"}],"month":"07","issue":"1","citation":{"ieee":"A. Venturino <i>et al.</i>, “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” <i>Cell Reports</i>, vol. 36, no. 1. Elsevier, 2021.","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. 2021;36(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>, vol. 36, no. 1, 109313, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>.","ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.","chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}]},{"date_created":"2021-07-11T22:01:17Z","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady","first_name":"Ehsan Kafshdar"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr","last_name":"Novotný"},{"last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","first_name":"Dorde"}],"day":"01","scopus_import":"1","title":"Proving non-termination by program reversal","oa_version":"Preprint","publication_status":"published","publication_identifier":{"isbn":["9781450383912"]},"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"}],"department":[{"_id":"KrCh"}],"arxiv":1,"month":"06","citation":{"ama":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination by program reversal. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1033-1048. doi:<a href=\"https://doi.org/10.1145/3453483.3454093\">10.1145/3453483.3454093</a>","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination by program reversal,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1033–1048.","short":"K. Chatterjee, E.K. Goharshady, P. Novotný, 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.","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde Zikelic. “Proving Non-Termination by Program Reversal.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1033–48. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454093\">https://doi.org/10.1145/3453483.3454093</a>.","ista":"Chatterjee K, Goharshady EK, Novotný 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.","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., &#38; Zikelic, D. (2021). Proving non-termination by program reversal. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1033–1048). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454093\">https://doi.org/10.1145/3453483.3454093</a>","mla":"Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1033–48, doi:<a href=\"https://doi.org/10.1145/3453483.3454093\">10.1145/3453483.3454093</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-07-14T09:10:06Z","_id":"9644","type":"conference","doi":"10.1145/3453483.3454093","article_processing_charge":"No","publisher":"Association for Computing Machinery","main_file_link":[{"url":"https://arxiv.org/abs/2104.01189","open_access":"1"}],"quality_controlled":"1","page":"1033-1048","year":"2021","isi":1,"external_id":{"arxiv":["2104.01189"],"isi":["000723661700067"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14539"}]},"ec_funded":1,"conference":{"name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","end_date":"2021-06-26","location":"Online"},"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.","date_published":"2021-06-01T00:00:00Z","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"status":"public","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation"},{"page":"772-787","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03183862/","open_access":"1"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1145/3453483.3454076","publisher":"Association for Computing Machinery","_id":"9645","date_updated":"2025-07-14T09:10:06Z","type":"conference","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","status":"public","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"ec_funded":1,"date_published":"2021-06-01T00:00:00Z","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).","conference":{"location":"Online","name":" PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","end_date":"2021-06-26"},"isi":1,"year":"2021","external_id":{"isi":["000723661700050"]},"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"}],"publication_status":"published","publication_identifier":{"isbn":["9781450383912"]},"scopus_import":"1","day":"01","author":[{"first_name":"Ali","last_name":"Asadi","full_name":"Asadi, Ali"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady"},{"first_name":"Mohammad","full_name":"Mahdavi, Mohammad","last_name":"Mahdavi"}],"title":"Polynomial reachability witnesses via Stellensätze","oa_version":"Submitted Version","date_created":"2021-07-11T22:01:17Z","oa":1,"language":[{"iso":"eng"}],"citation":{"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.","ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 772–787.","ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:772-787. doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>","mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 772–87, doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>.","apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., &#38; Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 772–787). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 772–87. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>.","ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation.  PLDI: Programming Language Design and Implementation, 772–787."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"06","department":[{"_id":"KrCh"}]},{"status":"public","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"conference":{"location":"Online","name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","end_date":"2021-06-26"},"date_published":"2021-06-01T00:00:00Z","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).","year":"2021","isi":1,"external_id":{"isi":["000723661700076"],"arxiv":["2011.14617"]},"page":"1171-1186","main_file_link":[{"url":"https://arxiv.org/abs/2011.14617","open_access":"1"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1145/3453483.3454102","publisher":"Association for Computing Machinery","_id":"9646","date_updated":"2025-07-14T09:10:06Z","type":"conference","oa":1,"language":[{"iso":"eng"}],"citation":{"mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1171–86, doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>.","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1171–1186). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>","ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186.","chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1171–86. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>.","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1171–1186.","ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1171-1186. doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","arxiv":1,"month":"06","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","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."}],"publication_status":"published","publication_identifier":{"isbn":["9781450383912"]},"day":"01","scopus_import":"1","author":[{"first_name":"Jinyi","full_name":"Wang, Jinyi","last_name":"Wang"},{"last_name":"Sun","full_name":"Sun, Yican","first_name":"Yican"},{"last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584"}],"oa_version":"Preprint","title":"Quantitative analysis of assertion violations in probabilistic programs","date_created":"2021-07-11T22:01:18Z"},{"quality_controlled":"1","ddc":["004"],"page":"1-16","type":"journal_article","_id":"9647","date_updated":"2023-08-10T14:11:19Z","publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.tcs.2021.05.023","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).","date_published":"2021-06-04T00:00:00Z","publication":"Theoretical Computer Science","status":"public","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"external_id":{"isi":["000710180500002"]},"year":"2021","isi":1,"file_date_updated":"2022-05-12T12:13:27Z","publication_status":"published","publication_identifier":{"issn":["0304-3975"]},"tmp":{"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","short":"CC BY-NC-ND (4.0)"},"intvolume":"       893","abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"has_accepted_license":"1","date_created":"2021-07-11T22:01:18Z","article_type":"original","volume":893,"oa_version":"Published Version","title":"Long lived transients in gene regulation","day":"04","scopus_import":"1","author":[{"last_name":"Petrov","full_name":"Petrov, Tatjana","first_name":"Tatjana"},{"first_name":"Claudia","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler"},{"first_name":"Ali","last_name":"Sezgin","full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. 2021;893:1-16. doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” <i>Theoretical Computer Science</i>, vol. 893. Elsevier, pp. 1–16, 2021.","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.” <i>Theoretical Computer Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>.","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., &#38; Guet, C. C. (2021). Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>","mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>, vol. 893, Elsevier, 2021, pp. 1–16, doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>."},"language":[{"iso":"eng"}],"oa":1,"file":[{"creator":"dernst","date_updated":"2022-05-12T12:13:27Z","date_created":"2022-05-12T12:13:27Z","file_size":2566504,"file_id":"11364","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2021_TheoreticalComputerScience_Petrov.pdf","checksum":"d3aef34cfb13e53bba4cf44d01680793","relation":"main_file"}],"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"month":"06"},{"author":[{"first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","first_name":"Maciek"},{"last_name":"Qi","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin","first_name":"Linlin","orcid":"0000-0001-5187-8401"},{"first_name":"SS","last_name":"Alotaibi","full_name":"Alotaibi, SS"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"day":"01","scopus_import":"1","title":"PIN-mediated polar auxin transport regulations in plant tropic responses","oa_version":"Published Version","volume":232,"article_type":"original","date_created":"2021-07-14T15:29:14Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment."}],"intvolume":"       232","publication_status":"published","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"file_date_updated":"2021-10-07T13:42:47Z","month":"10","department":[{"_id":"JiFr"}],"file":[{"file_id":"10105","creator":"kschuh","date_updated":"2021-10-07T13:42:47Z","file_size":1939800,"date_created":"2021-10-07T13:42:47Z","checksum":"6422a6eb329b52d96279daaee0fcf189","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2021_NewPhytologist_Han.pdf","success":1}],"oa":1,"language":[{"iso":"eng"}],"issue":"2","citation":{"short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” <i>New Phytologist</i>, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. 2021;232(2):510-522. doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>.","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., &#38; Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1111/nph.17617","article_processing_charge":"Yes (via OA deal)","publisher":"Wiley","date_updated":"2023-08-10T14:02:41Z","_id":"9656","type":"journal_article","page":"510-522","ddc":["580"],"quality_controlled":"1","isi":1,"year":"2021","external_id":{"isi":["000680587100001"],"pmid":["34254313"]},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"publication":"New Phytologist","status":"public","pmid":1,"ec_funded":1,"acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","date_published":"2021-10-01T00:00:00Z"},{"publication":"Plant Cell","status":"public","date_published":"2021-07-07T00:00:00Z","pmid":1,"external_id":{"pmid":["34240197"],"isi":["000702165300012"]},"year":"2021","isi":1,"ddc":["580"],"page":"2981–3003","quality_controlled":"1","publisher":"American Society of Plant Biologists","doi":"10.1093/plcell/koab183","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-10T14:01:41Z","_id":"9657","language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","citation":{"chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","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. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>.","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. 2021;33(9):2981–3003. doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>","ieee":"Z. Gao <i>et al.</i>, “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” <i>Plant Cell</i>, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003."},"month":"07","file":[{"relation":"main_file","checksum":"6715712ec306c321f0204c817b7f8ae7","file_name":"2021_PlantCell_Gao.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"9691","date_created":"2021-07-19T12:13:34Z","file_size":10566921,"creator":"cziletti","date_updated":"2021-07-19T12:13:34Z"}],"department":[{"_id":"JiFr"}],"tmp":{"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","short":"CC BY-NC-ND (4.0)"},"intvolume":"        33","abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"publication_status":"published","file_date_updated":"2021-07-19T12:13:34Z","title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","oa_version":"Published Version","author":[{"full_name":"Gao, Z","last_name":"Gao","first_name":"Z"},{"last_name":"Chen","full_name":"Chen, Z","first_name":"Z"},{"first_name":"Y","last_name":"Cui","full_name":"Cui, Y"},{"last_name":"Ke","full_name":"Ke, M","first_name":"M"},{"full_name":"Xu, H","last_name":"Xu","first_name":"H"},{"first_name":"Q","full_name":"Xu, Q","last_name":"Xu"},{"last_name":"Chen","full_name":"Chen, J","first_name":"J"},{"first_name":"Y","last_name":"Li","full_name":"Li, Y"},{"first_name":"L","last_name":"Huang","full_name":"Huang, L"},{"first_name":"H","full_name":"Zhao, H","last_name":"Zhao"},{"first_name":"D","full_name":"Huang, D","last_name":"Huang"},{"full_name":"Mai, S","last_name":"Mai","first_name":"S"},{"first_name":"T","last_name":"Xu","full_name":"Xu, T"},{"full_name":"Liu, X","last_name":"Liu","first_name":"X"},{"last_name":"Li","full_name":"Li, S","first_name":"S"},{"first_name":"Y","last_name":"Guan","full_name":"Guan, Y"},{"last_name":"Yang","full_name":"Yang, W","first_name":"W"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"J","last_name":"Petrášek","full_name":"Petrášek, J"},{"first_name":"J","last_name":"Zhang","full_name":"Zhang, J"},{"first_name":"X","last_name":"Chen","full_name":"Chen, X"}],"day":"07","article_type":"original","date_created":"2021-07-14T15:32:43Z","volume":33},{"page":"129-139","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.07761"}],"doi":"10.1145/3409964.3461785","article_processing_charge":"No","type":"conference","date_updated":"2024-03-05T07:13:12Z","_id":"9678","project":[{"grant_number":"840605","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","status":"public","acknowledgement":"We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.","conference":{"end_date":"2021-07-08","start_date":"2021-07-06","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures ","location":" Virtual Event, United States"},"date_published":"2021-07-06T00:00:00Z","ec_funded":1,"external_id":{"arxiv":["2005.07761"]},"related_material":{"record":[{"id":"15074","relation":"earlier_version","status":"public"}]},"year":"2021","abstract":[{"text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.","lang":"eng"}],"publication_identifier":{"isbn":["9781450380706"]},"publication_status":"published","title":"Efficient load-balancing through distributed token dropping","oa_version":"Preprint","author":[{"first_name":"Sebastian","full_name":"Brandt, Sebastian","last_name":"Brandt"},{"last_name":"Keller","full_name":"Keller, Barbara","first_name":"Barbara"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646"},{"last_name":"Suomela","full_name":"Suomela, Jukka","first_name":"Jukka"},{"last_name":"Uitto","full_name":"Uitto, Jara","first_name":"Jara"}],"scopus_import":"1","day":"06","date_created":"2021-07-18T22:01:22Z","language":[{"iso":"eng"}],"oa":1,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing through distributed token dropping,” in <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>,  Virtual Event, United States, 2021, pp. 129–139.","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–139.","ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing through distributed token dropping. In: <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>. ; 2021:129-139. doi:<a href=\"https://doi.org/10.1145/3409964.3461785\">10.1145/3409964.3461785</a>","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., &#38; Uitto, J. (2021). Efficient load-balancing through distributed token dropping. In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 129–139).  Virtual Event, United States. <a href=\"https://doi.org/10.1145/3409964.3461785\">https://doi.org/10.1145/3409964.3461785</a>","mla":"Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token Dropping.” <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, 2021, pp. 129–39, doi:<a href=\"https://doi.org/10.1145/3409964.3461785\">10.1145/3409964.3461785</a>.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures , 129–139.","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, 129–39, 2021. <a href=\"https://doi.org/10.1145/3409964.3461785\">https://doi.org/10.1145/3409964.3461785</a>."},"arxiv":1,"month":"07","department":[{"_id":"DaAl"}]},{"quality_controlled":"1","ddc":["530"],"_id":"9679","date_updated":"2023-08-10T13:58:09Z","type":"journal_article","article_processing_charge":"Yes","doi":"10.1088/1367-2630/ac0576","publisher":"IOP Publishing","ec_funded":1,"acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","date_published":"2021-06-23T00:00:00Z","publication":"New Journal of Physics","status":"public","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"year":"2021","external_id":{"isi":["000664736300001"],"arxiv":["2102.04961"]},"file_date_updated":"2021-07-19T11:47:16Z","publication_status":"published","publication_identifier":{"eissn":["13672630"]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        23","abstract":[{"lang":"eng","text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment."}],"volume":23,"date_created":"2021-07-18T22:01:22Z","article_type":"original","scopus_import":"1","day":"23","author":[{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"first_name":"Oleksandr V.","last_name":"Marchukov","full_name":"Marchukov, Oleksandr V."},{"full_name":"Hammer, Hans Werner","last_name":"Hammer","first_name":"Hans Werner"},{"last_name":"Volosniev","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","orcid":"0000-0003-0393-5525"}],"title":"Morphology of three-body quantum states from machine learning","oa_version":"Published Version","citation":{"apa":"Huber, D., Marchukov, O. V., Hammer, H. W., &#38; Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>.","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>.","ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” <i>New Journal of Physics</i>, vol. 23, no. 6. IOP Publishing, 2021.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. 2021;23(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>"},"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"file":[{"creator":"cziletti","date_updated":"2021-07-19T11:47:16Z","date_created":"2021-07-19T11:47:16Z","file_size":3868445,"file_id":"9690","content_type":"application/pdf","access_level":"open_access","file_name":"2021_NewJPhys_Huber.pdf","success":1,"checksum":"e39164ce7ea228d287cf8924e1a0f9fe","relation":"main_file"}],"article_number":"065009","arxiv":1,"month":"06"},{"issue":"10","citation":{"ama":"Schmitt HM, Fehrman RL, Maes ME, et al. Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. <i>Investigative Ophthalmology and Visual Science</i>. 2021;62(10). doi:<a href=\"https://doi.org/10.1167/IOVS.62.10.14\">10.1167/IOVS.62.10.14</a>","ieee":"H. M. Schmitt <i>et al.</i>, “Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression,” <i>Investigative Ophthalmology and Visual Science</i>, vol. 62, no. 10. Association for Research in Vision and Ophthalmology, 2021.","short":"H.M. Schmitt, R.L. Fehrman, M.E. Maes, H. Yang, L.W. Guo, C.L. Schlamp, H.R. Pelzel, R.W. Nickells, Investigative Ophthalmology and Visual Science 62 (2021).","chicago":"Schmitt, Heather M., Rachel L. Fehrman, Margaret E Maes, Huan Yang, Lian Wang Guo, Cassandra L. Schlamp, Heather R. Pelzel, and Robert W. Nickells. “Increased Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.” <i>Investigative Ophthalmology and Visual Science</i>. Association for Research in Vision and Ophthalmology, 2021. <a href=\"https://doi.org/10.1167/IOVS.62.10.14\">https://doi.org/10.1167/IOVS.62.10.14</a>.","ista":"Schmitt HM, Fehrman RL, Maes ME, Yang H, Guo LW, Schlamp CL, Pelzel HR, Nickells RW. 2021. Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 62(10), 14.","apa":"Schmitt, H. M., Fehrman, R. L., Maes, M. E., Yang, H., Guo, L. W., Schlamp, C. L., … Nickells, R. W. (2021). Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression. <i>Investigative Ophthalmology and Visual Science</i>. Association for Research in Vision and Ophthalmology. <a href=\"https://doi.org/10.1167/IOVS.62.10.14\">https://doi.org/10.1167/IOVS.62.10.14</a>","mla":"Schmitt, Heather M., et al. “Increased Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.” <i>Investigative Ophthalmology and Visual Science</i>, vol. 62, no. 10, 14, Association for Research in Vision and Ophthalmology, 2021, doi:<a href=\"https://doi.org/10.1167/IOVS.62.10.14\">10.1167/IOVS.62.10.14</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"SaSi"}],"file":[{"date_updated":"2022-05-13T07:40:15Z","creator":"dernst","date_created":"2022-05-13T07:40:15Z","file_size":19707796,"file_id":"11369","content_type":"application/pdf","access_level":"open_access","file_name":"2021_IOVS_Schmitt.pdf","success":1,"checksum":"c430967746f653aa1ae84ee617f62b73","relation":"main_file"}],"article_number":"14","month":"08","publication_status":"published","publication_identifier":{"eissn":["1552-5783"],"issn":["0146-0404"]},"file_date_updated":"2022-05-13T07:40:15Z","has_accepted_license":"1","tmp":{"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","short":"CC BY-NC-ND (4.0)"},"abstract":[{"lang":"eng","text":"Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs) after acute optic nerve damage. Consistent with this, induced HDAC3 expression in cultured cells shows selective toxicity to neurons. Despite an established role for HDAC3 in neuronal pathology, little is known regarding the mechanism of this pathology."}],"intvolume":"        62","volume":62,"article_type":"original","date_created":"2021-09-12T22:01:23Z","author":[{"last_name":"Schmitt","full_name":"Schmitt, Heather M.","first_name":"Heather M."},{"last_name":"Fehrman","full_name":"Fehrman, Rachel L.","first_name":"Rachel L."},{"orcid":"0000-0001-9642-1085","first_name":"Margaret E","last_name":"Maes","full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yang, Huan","last_name":"Yang","first_name":"Huan"},{"first_name":"Lian Wang","full_name":"Guo, Lian Wang","last_name":"Guo"},{"full_name":"Schlamp, Cassandra L.","last_name":"Schlamp","first_name":"Cassandra L."},{"first_name":"Heather R.","full_name":"Pelzel, Heather R.","last_name":"Pelzel"},{"last_name":"Nickells","full_name":"Nickells, Robert W.","first_name":"Robert W."}],"day":"16","scopus_import":"1","oa_version":"Published Version","title":"Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression","pmid":1,"date_published":"2021-08-16T00:00:00Z","acknowledgement":"The authors thank Joel Dietz for maintaining the mice used in this study, Satoshi Kinoshita and the Translational Research Initiative in Pathology Laboratory at the University of Wisconsin-Madison for cutting retinal sections analyzed in this study, and Mark Banghart for statistical review of the data analysis. Supported by National Eye Institute Grants R01 EY012223 (RWN), R01 EY030123 (RWN), R01 EY029809 (LWG), R01 EY029809 (LWG) and a Vision Research CORE grant P30 EY016665, NRSA grant T32 GM081061, by an unrestricted research grant from Research to Prevent Blindness, Inc., and by a University of Wisconsin-Madison Vilas Life Cycle award and the Frederick A. Davis Research Chair (RWN). ","status":"public","publication":"Investigative Ophthalmology and Visual Science","isi":1,"year":"2021","external_id":{"isi":["000695230000014"],"pmid":["34398198"]},"quality_controlled":"1","ddc":["570"],"date_updated":"2023-08-14T06:35:17Z","_id":"10000","type":"journal_article","doi":"10.1167/IOVS.62.10.14","article_processing_charge":"Yes","publisher":"Association for Research in Vision and Ophthalmology"},{"citation":{"apa":"Chatterjee, K., Dvorak, W., Henzinger, M. H., &#38; Svozil, A. (2021). Symbolic time and space tradeoffs for probabilistic verification. In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470739\">https://doi.org/10.1109/LICS52264.2021.9470739</a>","mla":"Chatterjee, Krishnendu, et al. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13, doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470739\">10.1109/LICS52264.2021.9470739</a>.","ista":"Chatterjee K, Dvorak W, Henzinger MH, Svozil A. 2021. Symbolic time and space tradeoffs for probabilistic verification. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorak, Monika H Henzinger, and Alexander Svozil. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 1–13. Institute of Electrical and Electronics Engineers, 2021. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470739\">https://doi.org/10.1109/LICS52264.2021.9470739</a>.","ieee":"K. Chatterjee, W. Dvorak, M. H. Henzinger, and A. Svozil, “Symbolic time and space tradeoffs for probabilistic verification,” in <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Rome, Italy, 2021, pp. 1–13.","short":"K. Chatterjee, W. Dvorak, M.H. Henzinger, A. Svozil, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13.","ama":"Chatterjee K, Dvorak W, Henzinger MH, Svozil A. Symbolic time and space tradeoffs for probabilistic verification. In: <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Institute of Electrical and Electronics Engineers; 2021:1-13. doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470739\">10.1109/LICS52264.2021.9470739</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"arxiv":1,"month":"07","publication_status":"published","publication_identifier":{"eisbn":["978-1-6654-4895-6"],"issn":["1043-6871"],"isbn":["978-1-6654-4896-3"]},"abstract":[{"text":"We present a faster symbolic algorithm for the following central problem in probabilistic verification: Compute the maximal end-component (MEC) decomposition of Markov decision processes (MDPs). This problem generalizes the SCC decomposition problem of graphs and closed recurrent sets of Markov chains. The model of symbolic algorithms is widely used in formal verification and model-checking, where access to the input model is restricted to only symbolic operations (e.g., basic set operations and computation of one-step neighborhood). For an input MDP with  n  vertices and  m  edges, the classical symbolic algorithm from the 1990s for the MEC decomposition requires  O(n2)  symbolic operations and  O(1)  symbolic space. The only other symbolic algorithm for the MEC decomposition requires  O(nm−−√)  symbolic operations and  O(m−−√)  symbolic space. A main open question is whether the worst-case  O(n2)  bound for symbolic operations can be beaten. We present a symbolic algorithm that requires  O˜(n1.5)  symbolic operations and  O˜(n−−√)  symbolic space. Moreover, the parametrization of our algorithm provides a trade-off between symbolic operations and symbolic space: for all  0<ϵ≤1/2  the symbolic algorithm requires  O˜(n2−ϵ)  symbolic operations and  O˜(nϵ)  symbolic space ( O˜  hides poly-logarithmic factors). Using our techniques we present faster algorithms for computing the almost-sure winning regions of  ω -regular objectives for MDPs. We consider the canonical parity objectives for  ω -regular objectives, and for parity objectives with  d -priorities we present an algorithm that computes the almost-sure winning region with  O˜(n2−ϵ)  symbolic operations and  O˜(nϵ)  symbolic space, for all  0<ϵ≤1/2 .","lang":"eng"}],"date_created":"2021-09-12T22:01:24Z","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Wolfgang","last_name":"Dvorak","full_name":"Dvorak, Wolfgang"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}],"day":"07","scopus_import":"1","oa_version":"Preprint","title":"Symbolic time and space tradeoffs for probabilistic verification","ec_funded":1,"conference":{"location":"Rome, Italy","end_date":"2021-07-02","start_date":"2021-06-29","name":"LICS: Symposium on Logic in Computer Science"},"acknowledgement":"The authors are grateful to the anonymous referees for their valuable comments. A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15–003. K. C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and by the ERC CoG 863818 (ForM-SMArt). For M. H. the research leading to these results has received funding from the European Research Council under the European Unions Seventh Framework Programme (FP/2007–2013) / ERC Grant Agreement no. 340506.","date_published":"2021-07-07T00:00:00Z","project":[{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"status":"public","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","keyword":["Computer science","Computational modeling","Markov processes","Probabilistic logic","Formal verification","Game Theory"],"year":"2021","isi":1,"external_id":{"arxiv":["2104.07466"],"isi":["000947350400089"]},"main_file_link":[{"url":"https://arxiv.org/abs/2104.07466","open_access":"1"}],"quality_controlled":"1","page":"1-13","date_updated":"2025-07-14T09:10:07Z","_id":"10002","type":"conference","doi":"10.1109/LICS52264.2021.9470739","article_processing_charge":"No","publisher":"Institute of Electrical and Electronics Engineers"},{"department":[{"_id":"KrCh"}],"month":"07","arxiv":1,"citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13, doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470595\">10.1109/LICS52264.2021.9470595</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2021). Stochastic processes with expected stopping time. In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470595\">https://doi.org/10.1109/LICS52264.2021.9470595</a>","ista":"Chatterjee K, Doyen L. 2021. Stochastic processes with expected stopping time. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 1–13. Institute of Electrical and Electronics Engineers, 2021. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470595\">https://doi.org/10.1109/LICS52264.2021.9470595</a>.","short":"K. Chatterjee, L. Doyen, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021, pp. 1–13.","ieee":"K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,” in <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Rome, Italy, 2021, pp. 1–13.","ama":"Chatterjee K, Doyen L. Stochastic processes with expected stopping time. In: <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Institute of Electrical and Electronics Engineers; 2021:1-13. doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470595\">10.1109/LICS52264.2021.9470595</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"date_created":"2021-09-12T22:01:25Z","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"scopus_import":"1","day":"07","title":"Stochastic processes with expected stopping time","oa_version":"Preprint","publication_status":"published","publication_identifier":{"issn":["1043-6871"],"isbn":["978-1-6654-4896-3"],"eisbn":["978-1-6654-4895-6"]},"abstract":[{"lang":"eng","text":"Markov chains are the de facto finite-state model for stochastic dynamical systems, and Markov decision processes (MDPs) extend Markov chains by incorporating non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization criterion is the maximal expected total reward where the MDP stops after T steps, which can be computed by a simple dynamic programming algorithm. We consider a natural generalization of the problem where the stopping times can be chosen according to a probability distribution, such that the expected stopping time is T, to optimize the expected total reward. Quite surprisingly we establish inter-reducibility of the expected stopping-time problem for Markov chains with the Positivity problem (which is related to the well-known Skolem problem), for which establishing either decidability or undecidability would be a major breakthrough. Given the hardness of the exact problem, we consider the approximate version of the problem: we show that it can be solved in exponential time for Markov chains and in exponential space for MDPs."}],"keyword":["Computer science","Heuristic algorithms","Memory management","Automata","Markov processes","Probability distribution","Complexity theory"],"year":"2021","isi":1,"external_id":{"isi":["000947350400036"],"arxiv":["2104.07278"]},"ec_funded":1,"conference":{"name":"LICS: Symposium on Logic in Computer Science","end_date":"2021-07-02","start_date":"2021-06-29","location":"Rome, Italy"},"date_published":"2021-07-07T00:00:00Z","acknowledgement":"We are grateful to the anonymous reviewers of LICS 2021 and of a previous version of this paper for insightful comments that helped improving the presentation. This research was partially supported by the grant ERC CoG 863818 (ForM-SMArt).","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"status":"public","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","date_updated":"2025-07-14T09:10:08Z","_id":"10004","type":"conference","doi":"10.1109/LICS52264.2021.9470595","article_processing_charge":"No","publisher":"Institute of Electrical and Electronics Engineers","main_file_link":[{"url":"https://arxiv.org/abs/2104.07278","open_access":"1"}],"quality_controlled":"1","page":"1-13"},{"keyword":["Nonlinear parabolic systems","implicit constitutive theory","weak solutions","existence","uniqueness"],"external_id":{"isi":["000722222900004"],"arxiv":["2009.06917"]},"isi":1,"year":"2021","date_published":"2021-08-25T00:00:00Z","acknowledgement":"M. Bulíček and J. Málek acknowledge the support of the project No. 18-12719S financed by the Czech\r\nScience foundation (GAČR). E. Maringová acknowledges support from Charles University Research program \r\nUNCE/SCI/023, the grant SVV-2020-260583 by the Ministry of Education, Youth and Sports, Czech Republic\r\nand from the Austrian Science Fund (FWF), grants P30000, W1245, and F65. M. Bulíček and J. Málek are\r\nmembers of the Nečas Center for Mathematical Modelling.\r\n","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"publication":"Mathematical Models and Methods in Applied Sciences","status":"public","type":"journal_article","date_updated":"2023-09-04T11:43:45Z","_id":"10005","publisher":"World Scientific","doi":"10.1142/S0218202521500457","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2009.06917","open_access":"1"}],"department":[{"_id":"JuFi"}],"month":"08","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"09","citation":{"ama":"Bulíček M, Maringová E, Málek J. On nonlinear problems of parabolic type with implicit constitutive equations involving flux. <i>Mathematical Models and Methods in Applied Sciences</i>. 2021;31(09). doi:<a href=\"https://doi.org/10.1142/S0218202521500457\">10.1142/S0218202521500457</a>","short":"M. Bulíček, E. Maringová, J. Málek, Mathematical Models and Methods in Applied Sciences 31 (2021).","ieee":"M. Bulíček, E. Maringová, and J. Málek, “On nonlinear problems of parabolic type with implicit constitutive equations involving flux,” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 31, no. 09. World Scientific, 2021.","chicago":"Bulíček, Miroslav, Erika Maringová, and Josef Málek. “On Nonlinear Problems of Parabolic Type with Implicit Constitutive Equations Involving Flux.” <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific, 2021. <a href=\"https://doi.org/10.1142/S0218202521500457\">https://doi.org/10.1142/S0218202521500457</a>.","ista":"Bulíček M, Maringová E, Málek J. 2021. On nonlinear problems of parabolic type with implicit constitutive equations involving flux. Mathematical Models and Methods in Applied Sciences. 31(09).","mla":"Bulíček, Miroslav, et al. “On Nonlinear Problems of Parabolic Type with Implicit Constitutive Equations Involving Flux.” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 31, no. 09, World Scientific, 2021, doi:<a href=\"https://doi.org/10.1142/S0218202521500457\">10.1142/S0218202521500457</a>.","apa":"Bulíček, M., Maringová, E., &#38; Málek, J. (2021). On nonlinear problems of parabolic type with implicit constitutive equations involving flux. <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific. <a href=\"https://doi.org/10.1142/S0218202521500457\">https://doi.org/10.1142/S0218202521500457</a>"},"language":[{"iso":"eng"}],"oa":1,"article_type":"original","date_created":"2021-09-12T22:01:25Z","volume":31,"title":"On nonlinear problems of parabolic type with implicit constitutive equations involving flux","oa_version":"Preprint","author":[{"first_name":"Miroslav","full_name":"Bulíček, Miroslav","last_name":"Bulíček"},{"first_name":"Erika","last_name":"Maringová","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","full_name":"Maringová, Erika"},{"first_name":"Josef","full_name":"Málek, Josef","last_name":"Málek"}],"scopus_import":"1","day":"25","publication_identifier":{"eissn":["1793-6314"],"issn":["0218-2025"]},"publication_status":"published","abstract":[{"text":"We study systems of nonlinear partial differential equations of parabolic type, in which the elliptic operator is replaced by the first-order divergence operator acting on a flux function, which is related to the spatial gradient of the unknown through an additional implicit equation. This setting, broad enough in terms of applications, significantly expands the paradigm of nonlinear parabolic problems. Formulating four conditions concerning the form of the implicit equation, we first show that these conditions describe a maximal monotone p-coercive graph. We then establish the global-in-time and large-data existence of a (weak) solution and its uniqueness. To this end, we adopt and significantly generalize Minty’s method of monotone mappings. A unified theory, containing several novel tools, is developed in a way to be tractable from the point of view of numerical approximations.","lang":"eng"}],"intvolume":"        31"},{"page":"300","ddc":["515"],"date_updated":"2023-09-07T13:30:45Z","_id":"10007","type":"dissertation","doi":"10.15479/at:ista:10007","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","ec_funded":1,"date_published":"2021-09-14T00:00:00Z","degree_awarded":"PhD","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"status":"public","year":"2021","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10012"},{"id":"10013","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7489"}]},"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2021-09-15T14:37:30Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis."}],"date_created":"2021-09-13T11:12:34Z","author":[{"last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","full_name":"Hensel, Sebastian","first_name":"Sebastian","orcid":"0000-0001-7252-8072"}],"day":"14","oa_version":"Published Version","title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","citation":{"apa":"Hensel, S. (2021). <i>Curvature driven interface evolution: Uniqueness properties of weak solution concepts</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10007\">https://doi.org/10.15479/at:ista:10007</a>","mla":"Hensel, Sebastian. <i>Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10007\">10.15479/at:ista:10007</a>.","chicago":"Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10007\">https://doi.org/10.15479/at:ista:10007</a>.","ista":"Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria.","ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021.","short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.","ama":"Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10007\">10.15479/at:ista:10007</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JuFi"}],"file":[{"creator":"shensel","date_updated":"2021-09-15T14:37:30Z","date_created":"2021-09-13T11:03:24Z","file_size":15022154,"file_id":"10008","content_type":"application/x-zip-compressed","access_level":"closed","file_name":"thesis_final_Hensel.zip","checksum":"c8475faaf0b680b4971f638f1db16347","relation":"source_file"},{"creator":"shensel","date_updated":"2021-09-14T09:52:47Z","date_created":"2021-09-13T14:18:56Z","file_size":6583638,"file_id":"10014","content_type":"application/pdf","access_level":"open_access","file_name":"thesis_final_Hensel.pdf","checksum":"1a609937aa5275452822f45f2da17f07","relation":"main_file"}],"supervisor":[{"last_name":"Fischer","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L"}],"month":"09"},{"oa":1,"project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"publication":"arXiv","status":"public","citation":{"apa":"Hensel, S., &#38; Laux, T. (n.d.). A new varifold solution concept for mean curvature flow: Convergence of  the Allen-Cahn equation and weak-strong uniqueness. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2109.04233\">https://doi.org/10.48550/arXiv.2109.04233</a>","mla":"Hensel, Sebastian, and Tim Laux. “A New Varifold Solution Concept for Mean Curvature Flow: Convergence of  the Allen-Cahn Equation and Weak-Strong Uniqueness.” <i>ArXiv</i>, 2109.04233, doi:<a href=\"https://doi.org/10.48550/arXiv.2109.04233\">10.48550/arXiv.2109.04233</a>.","ista":"Hensel S, Laux T. A new varifold solution concept for mean curvature flow: Convergence of  the Allen-Cahn equation and weak-strong uniqueness. arXiv, 2109.04233.","chicago":"Hensel, Sebastian, and Tim Laux. “A New Varifold Solution Concept for Mean Curvature Flow: Convergence of  the Allen-Cahn Equation and Weak-Strong Uniqueness.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2109.04233\">https://doi.org/10.48550/arXiv.2109.04233</a>.","ieee":"S. Hensel and T. Laux, “A new varifold solution concept for mean curvature flow: Convergence of  the Allen-Cahn equation and weak-strong uniqueness,” <i>arXiv</i>. .","short":"S. Hensel, T. Laux, ArXiv (n.d.).","ama":"Hensel S, Laux T. A new varifold solution concept for mean curvature flow: Convergence of  the Allen-Cahn equation and weak-strong uniqueness. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2109.04233\">10.48550/arXiv.2109.04233</a>"},"ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819), and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813. The content of this paper was developed and parts of it were written during a visit of the first author to the Hausdorff Center of Mathematics (HCM), University of Bonn. The hospitality and the support of HCM are gratefully acknowledged.","date_published":"2021-09-09T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","external_id":{"arxiv":["2109.04233"]},"month":"09","arxiv":1,"department":[{"_id":"JuFi"}],"keyword":["Mean curvature flow","gradient flows","varifolds","weak solutions","weak-strong uniqueness","calibrated geometry","gradient-flow calibrations"],"article_number":"2109.04233","abstract":[{"text":"We propose a new weak solution concept for (two-phase) mean curvature flow which enjoys both (unconditional) existence and (weak-strong) uniqueness properties. These solutions are evolving varifolds, just as in Brakke's formulation, but are coupled to the phase volumes by a simple transport equation. First, we show that, in the exact same setup as in Ilmanen's proof [J. Differential Geom. 38, 417-461, (1993)], any limit point of solutions to the Allen-Cahn equation is a varifold solution in our sense. Second, we prove that any calibrated flow in the sense of Fischer et al. [arXiv:2003.05478] - and hence any classical solution to mean curvature flow - is unique in the class of our new varifold solutions. This is in sharp contrast to the case of Brakke flows, which a priori may disappear at any given time and are therefore fatally non-unique. Finally, we propose an extension of the solution concept to the multi-phase case which is at least guaranteed to satisfy a weak-strong uniqueness principle.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2109.04233"}],"publication_status":"submitted","doi":"10.48550/arXiv.2109.04233","author":[{"first_name":"Sebastian","orcid":"0000-0001-7252-8072","last_name":"Hensel","full_name":"Hensel, Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tim","full_name":"Laux, Tim","last_name":"Laux"}],"article_processing_charge":"No","day":"09","title":"A new varifold solution concept for mean curvature flow: Convergence of  the Allen-Cahn equation and weak-strong uniqueness","oa_version":"Preprint","date_updated":"2023-05-03T10:34:38Z","_id":"10011","type":"preprint","date_created":"2021-09-13T12:17:10Z"},{"doi":"10.48550/arXiv.2108.01733","author":[{"orcid":"0000-0001-7252-8072","first_name":"Sebastian","full_name":"Hensel, Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","last_name":"Hensel"},{"first_name":"Tim","full_name":"Laux, Tim","last_name":"Laux"}],"article_processing_charge":"No","day":"03","title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","oa_version":"Preprint","date_updated":"2023-09-07T13:30:45Z","_id":"10013","type":"preprint","date_created":"2021-09-13T12:17:11Z","abstract":[{"lang":"eng","text":"We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction of a gradient-flow calibration in the sense of the recent work of Fischer et al. [arXiv:2003.05478] for any such cluster. This extends the two-dimensional construction to the three-dimensional case of surfaces meeting along triple junctions."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.01733"}],"publication_status":"submitted","year":"2021","external_id":{"arxiv":["2108.01733"]},"arxiv":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"13043"},{"id":"10007","relation":"dissertation_contains","status":"public"}]},"month":"08","department":[{"_id":"JuFi"}],"article_number":"2108.01733","oa":1,"project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"status":"public","language":[{"iso":"eng"}],"publication":"arXiv","ec_funded":1,"citation":{"ama":"Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2108.01733\">10.48550/arXiv.2108.01733</a>","ieee":"S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow of double bubbles,” <i>arXiv</i>. .","short":"S. Hensel, T. Laux, ArXiv (n.d.).","chicago":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2108.01733\">https://doi.org/10.48550/arXiv.2108.01733</a>.","ista":"Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. arXiv, 2108.01733.","apa":"Hensel, S., &#38; Laux, T. (n.d.). Weak-strong uniqueness for the mean curvature flow of double bubbles. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2108.01733\">https://doi.org/10.48550/arXiv.2108.01733</a>","mla":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” <i>ArXiv</i>, 2108.01733, doi:<a href=\"https://doi.org/10.48550/arXiv.2108.01733\">10.48550/arXiv.2108.01733</a>."},"date_published":"2021-08-03T00:00:00Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819), and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]