[{"date_updated":"2026-04-03T09:30:47Z","title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","author":[{"first_name":"Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"full_name":"Di Donato, Martin","first_name":"Martin","last_name":"Di Donato"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","orcid":"0000-0003-0619-7783","first_name":"Matous"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","last_name":"Zhang","orcid":"0000-0001-7048-4627"},{"first_name":"Petr","last_name":"Klíma","full_name":"Klíma, Petr"},{"full_name":"Liu, Jie","last_name":"Liu","first_name":"Jie"},{"first_name":"Aurélien","last_name":"Bailly","full_name":"Bailly, Aurélien"},{"full_name":"Ferro, Noel","first_name":"Noel","last_name":"Ferro"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"external_id":{"isi":["000595658100018"],"pmid":["33264621"]},"license":"https://creativecommons.org/licenses/by/4.0/","acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","publication_identifier":{"eissn":["2211-1247"]},"file_date_updated":"2020-12-14T07:33:39Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/plants-on-aspirin/","relation":"press_release","description":"News on IST Homepage"}]},"article_type":"original","day":"01","oa_version":"Published Version","quality_controlled":"1","_id":"8943","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.celrep.2020.108463","citation":{"short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>.","apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>","ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. 2020;33(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>","ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","ieee":"S. Tan <i>et al.</i>, “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” <i>Cell Reports</i>, vol. 33, no. 9. Elsevier, 2020.","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>, vol. 33, no. 9, 108463, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>."},"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis"}],"volume":33,"scopus_import":"1","department":[{"_id":"JiFr"}],"date_published":"2020-12-01T00:00:00Z","article_number":"108463","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_size":8056434,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-12-14T07:33:39Z","checksum":"ed18cba0fb48ed2e789381a54cc21904","creator":"dernst","file_name":"2020_CellReports_Tan.pdf","date_updated":"2020-12-14T07:33:39Z","success":1,"file_id":"8948"}],"year":"2020","article_processing_charge":"Yes","publication_status":"published","oa":1,"type":"journal_article","ec_funded":1,"isi":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"status":"public","month":"12","corr_author":"1","ddc":["580"],"publication":"Cell Reports","issue":"9","intvolume":"        33","language":[{"iso":"eng"}],"publisher":"Elsevier","has_accepted_license":"1","abstract":[{"text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds.","lang":"eng"}],"date_created":"2020-12-13T23:01:21Z","pmid":1},{"publication":"Physical Review B","month":"11","status":"public","issue":"18","language":[{"iso":"eng"}],"intvolume":"       102","abstract":[{"text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2.","lang":"eng"}],"date_created":"2020-12-13T23:01:21Z","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-11-01T00:00:00Z","article_number":"180508","publication_status":"published","year":"2020","article_processing_charge":"No","type":"journal_article","isi":1,"oa":1,"_id":"8944","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.04329"}],"doi":"10.1103/PhysRevB.102.180508","citation":{"ama":"Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. 2020;102(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>","ista":"Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508.","apa":"Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>","mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>.","ieee":"M. Zemlicka <i>et al.</i>, “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” <i>Physical Review B</i>, vol. 102, no. 18. American Physical Society, 2020.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020).","chicago":"Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>."},"department":[{"_id":"JoFi"}],"scopus_import":"1","volume":102,"title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","date_updated":"2025-07-10T12:01:27Z","author":[{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin"},{"first_name":"M.","last_name":"Kopčík","full_name":"Kopčík, M."},{"full_name":"Szabó, P.","first_name":"P.","last_name":"Szabó"},{"full_name":"Samuely, T.","last_name":"Samuely","first_name":"T."},{"first_name":"J.","last_name":"Kačmarčík","full_name":"Kačmarčík, J."},{"first_name":"P.","last_name":"Neilinger","full_name":"Neilinger, P."},{"full_name":"Grajcar, M.","last_name":"Grajcar","first_name":"M."},{"full_name":"Samuely, P.","first_name":"P.","last_name":"Samuely"}],"external_id":{"isi":["000591509900003"],"arxiv":["2011.04329"]},"day":"01","article_type":"original","acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"arxiv":1},{"status":"public","ddc":["570"],"month":"12","publication":"Cells","issue":"12","intvolume":"         9","language":[{"iso":"eng"}],"publisher":"MDPI","has_accepted_license":"1","abstract":[{"lang":"eng","text":"<jats:p>Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.</jats:p>"}],"pmid":1,"date_created":"2020-12-14T08:04:03Z","article_number":"2662","date_published":"2020-12-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","date_created":"2020-12-14T08:09:43Z","creator":"dernst","checksum":"5095cbdc728c9a510c5761cf60a8861c","file_name":"2020_Cells_Zhang.pdf","file_size":3504525,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"8950","date_updated":"2020-12-14T08:09:43Z"}],"publication_status":"published","year":"2020","article_processing_charge":"No","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","quality_controlled":"1","oa_version":"Published Version","_id":"8949","doi":"10.3390/cells9122662","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>, vol. 9, no. 12, 2662, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>.","ieee":"X. Zhang <i>et al.</i>, “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” <i>Cells</i>, vol. 9, no. 12. MDPI, 2020.","ama":"Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. 2020;9(12). doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>","ista":"Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662.","apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., &#38; Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>","chicago":"Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>.","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020)."},"project":[{"grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"volume":9,"department":[{"_id":"SiHi"}],"scopus_import":"1","title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","date_updated":"2025-06-12T07:02:43Z","author":[{"first_name":"Xuying","last_name":"Zhang","full_name":"Zhang, Xuying"},{"last_name":"Mennicke","first_name":"Christine V.","full_name":"Mennicke, Christine V."},{"last_name":"Xiao","first_name":"Guanxi","full_name":"Xiao, Guanxi"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","full_name":"Beattie, Robert J","first_name":"Robert J","orcid":"0000-0002-8483-8753","last_name":"Beattie"},{"first_name":"Mansoor","last_name":"Haider","full_name":"Haider, Mansoor"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"full_name":"Ghashghaei, H. Troy","last_name":"Ghashghaei","first_name":"H. Troy"}],"external_id":{"isi":["000601787300001"],"pmid":["33322301"]},"day":"11","publication_identifier":{"issn":["2073-4409"]},"article_type":"original","acknowledgement":"This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript.","file_date_updated":"2020-12-14T08:09:43Z"},{"file":[{"relation":"main_file","date_created":"2020-12-20T09:52:52Z","file_name":"readme.txt","checksum":"f57862aeee1690c7effd2b1117d40ed1","creator":"bkavcic","file_size":523,"content_type":"text/plain","access_level":"open_access","success":1,"file_id":"8952","date_updated":"2020-12-20T09:52:52Z"},{"access_level":"open_access","content_type":"application/octet-stream","file_size":379228,"file_name":"GRNs Research depository.gb","checksum":"f2c6d5232ec6d551b6993991e8689e9f","creator":"bkavcic","date_created":"2020-12-20T22:01:44Z","relation":"main_file","date_updated":"2020-12-20T22:01:44Z","file_id":"8954","success":1}],"author":[{"full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","first_name":"Anna A"}],"keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"article_processing_charge":"No","year":"2020","date_updated":"2025-06-12T06:36:16Z","date_published":"2020-12-21T00:00:00Z","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-12-20T22:01:44Z","related_material":{"record":[{"status":"public","id":"9283","relation":"used_in_publication"}]},"day":"21","oa":1,"contributor":[{"first_name":"Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Kathrin","last_name":"Tomasek"},{"last_name":"Caruso Carter","first_name":"Caroline","contributor_type":"project_member"},{"last_name":"Sonnleitner","first_name":"Elisabeth","contributor_type":"project_member"},{"first_name":"Bor","last_name":"Kavcic","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Tiago","last_name":"Paixão"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_manager","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"}],"type":"research_data","oa_version":"Published Version","ddc":["570"],"month":"12","corr_author":"1","status":"public","_id":"8951","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","department":[{"_id":"CaGu"}],"date_created":"2020-12-20T10:00:26Z","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>.","short":"A.A. Nagy-Staron, (2020).","mla":"Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>."},"doi":"10.15479/AT:ISTA:8951"},{"_id":"8955","oa_version":"Published Version","quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” <i>Frontiers in Physiology</i>, vol. 11. Frontiers, 2020.","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>, vol. 11, 558070, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>.","apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., &#38; Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>","ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>","chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>.","short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020)."},"doi":"10.3389/fphys.2020.558070","scopus_import":"1","department":[{"_id":"GaTk"}],"volume":11,"title":"Network physiology of cortico–muscular interactions","date_updated":"2025-04-14T07:43:50Z","author":[{"last_name":"Rizzo","first_name":"Rossella","full_name":"Rizzo, Rossella"},{"full_name":"Zhang, Xiyun","first_name":"Xiyun","last_name":"Zhang"},{"full_name":"Wang, Jilin W.J.L.","last_name":"Wang","first_name":"Jilin W.J.L."},{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi"},{"first_name":"Plamen Ch","last_name":"Ivanov","full_name":"Ivanov, Plamen Ch"}],"external_id":{"isi":["000596849400001"],"pmid":["33324233"]},"day":"26","article_type":"original","acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","file_date_updated":"2020-12-21T10:37:50Z","publication_identifier":{"eissn":["1664042X"]},"ddc":["570"],"publication":"Frontiers in Physiology","month":"11","status":"public","language":[{"iso":"eng"}],"intvolume":"        11","pmid":1,"date_created":"2020-12-20T23:01:18Z","abstract":[{"lang":"eng","text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies."}],"has_accepted_license":"1","publisher":"Frontiers","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-11-26T00:00:00Z","article_number":"558070","publication_status":"published","year":"2020","article_processing_charge":"No","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":13380030,"file_name":"2020_Frontiers_Rizzo.pdf","checksum":"ef9515b28c5619b7126c0f347958bcb3","creator":"dernst","relation":"main_file","date_created":"2020-12-21T10:37:50Z","date_updated":"2020-12-21T10:37:50Z","success":1,"file_id":"8961"}],"ec_funded":1,"type":"journal_article","isi":1,"oa":1},{"type":"journal_article","isi":1,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"6437","date_published":"2020-12-22T00:00:00Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"year":"2020","article_processing_charge":"No","publication_status":"published","file":[{"success":1,"file_id":"8975","date_updated":"2020-12-28T08:16:10Z","file_name":"2020_NatureComm_Faessler.pdf","checksum":"55d43ea0061cc4027ba45e966e1db8cc","creator":"dernst","relation":"main_file","date_created":"2020-12-28T08:16:10Z","content_type":"application/pdf","access_level":"open_access","file_size":3958727}],"language":[{"iso":"eng"}],"intvolume":"        11","date_created":"2020-12-23T08:25:45Z","abstract":[{"lang":"eng","text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation."}],"has_accepted_license":"1","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication":"Nature Communications","corr_author":"1","status":"public","month":"12","ddc":["570"],"external_id":{"isi":["000603078000003"]},"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","relation":"press_release"}]},"file_date_updated":"2020-12-28T08:16:10Z","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","article_type":"original","publication_identifier":{"issn":["2041-1723"]},"day":"22","date_updated":"2025-04-15T07:52:12Z","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","first_name":"Florian","orcid":"0000-0001-7149-769X","last_name":"Fäßler"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","first_name":"Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev"},{"first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"William","last_name":"Wan","full_name":"Wan, William"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02495","name":"Protein structure and function in filopodia across scales"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>."},"doi":"10.1038/s41467-020-20286-x","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"scopus_import":"1","volume":11,"_id":"8971","quality_controlled":"1","oa_version":"Published Version"},{"publication":"STAR Protocols","status":"public","ddc":["570"],"month":"12","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"issue":"3","intvolume":"         1","language":[{"iso":"eng"}],"publisher":"Elsevier","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b).","lang":"eng"}],"pmid":1,"date_created":"2020-12-30T10:17:07Z","has_accepted_license":"1","article_number":"100215","date_published":"2020-12-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2021-01-07T15:57:27Z","relation":"main_file","creator":"dernst","checksum":"f1e9a433e9cb0f41f7b6df6b76db1f6e","file_name":"2020_STARProtocols_Laukoter.pdf","file_size":4031449,"access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8996","date_updated":"2021-01-07T15:57:27Z"}],"publication_status":"published","year":"2020","article_processing_charge":"No","oa":1,"ec_funded":1,"type":"journal_article","quality_controlled":"1","oa_version":"Published Version","_id":"8978","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"chicago":"Laukoter, Susanne, Nicole Amberg, Florian Pauler, and Simon Hippenmeyer. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” <i>STAR Protocols</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">https://doi.org/10.1016/j.xpro.2020.100215</a>.","short":"S. Laukoter, N. Amberg, F. Pauler, S. Hippenmeyer, STAR Protocols 1 (2020).","ieee":"S. Laukoter, N. Amberg, F. Pauler, and S. Hippenmeyer, “Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy,” <i>STAR Protocols</i>, vol. 1, no. 3. Elsevier, 2020.","mla":"Laukoter, Susanne, et al. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” <i>STAR Protocols</i>, vol. 1, no. 3, 100215, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">10.1016/j.xpro.2020.100215</a>.","ista":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. 2020. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 1(3), 100215.","apa":"Laukoter, S., Amberg, N., Pauler, F., &#38; Hippenmeyer, S. (2020). Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">https://doi.org/10.1016/j.xpro.2020.100215</a>","ama":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. <i>STAR Protocols</i>. 2020;1(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">10.1016/j.xpro.2020.100215</a>"},"doi":"10.1016/j.xpro.2020.100215","project":[{"call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T01031"},{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002"},{"call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"volume":1,"scopus_import":"1","department":[{"_id":"SiHi"}],"title":"Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy","date_updated":"2025-04-15T08:23:06Z","author":[{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","full_name":"Laukoter, Susanne","first_name":"Susanne","orcid":"0000-0002-7903-3010","last_name":"Laukoter"},{"last_name":"Amberg","orcid":"0000-0002-3183-8207","first_name":"Nicole","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["33377108"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"18","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). N.A received support from the FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","article_type":"original","file_date_updated":"2021-01-07T15:57:27Z","publication_identifier":{"issn":["2666-1667"]}},{"abstract":[{"text":"Currently several projects aim at designing and implementing protocols for privacy preserving automated contact tracing to help fight the current pandemic. Those proposal are quite similar, and in their most basic form basically propose an app for mobile phones which broadcasts frequently changing pseudorandom identifiers via (low energy) Bluetooth, and at the same time, the app stores IDs broadcast by phones in its proximity. Only if a user is tested positive, they upload either the beacons they did broadcast (which is the case in decentralized proposals as DP-3T, east and west coast PACT or Covid watch) or received (as in Popp-PT or ROBERT) during the last two weeks or so.\r\n\r\nVaudenay [eprint 2020/399] observes that this basic scheme (he considers the DP-3T proposal) succumbs to relay and even replay attacks, and proposes more complex interactive schemes which prevent those attacks without giving up too many privacy aspects. Unfortunately interaction is problematic for this application for efficiency and security reasons. The countermeasures that have been suggested so far are either not practical or give up on key privacy aspects. We propose a simple non-interactive variant of the basic protocol that\r\n(security) Provably prevents replay and (if location data is available) relay attacks.\r\n(privacy) The data of all parties (even jointly) reveals no information on the location or time where encounters happened.\r\n(efficiency) The broadcasted message can fit into 128 bits and uses only basic crypto (commitments and secret key authentication).\r\n\r\nTowards this end we introduce the concept of “delayed authentication”, which basically is a message authentication code where verification can be done in two steps, where the first doesn’t require the key, and the second doesn’t require the message.","lang":"eng"}],"date_created":"2021-01-03T23:01:23Z","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"     12578","status":"public","publication":"Progress in Cryptology","month":"12","page":"3-15","isi":1,"type":"conference","ec_funded":1,"oa":1,"publication_status":"published","year":"2020","article_processing_charge":"No","series_title":"LNCS","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2020-12-08T00:00:00Z","department":[{"_id":"KrPi"}],"scopus_import":"1","volume":12578,"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-3-030-65277-7_1","citation":{"short":"K.Z. Pietrzak, in:, Progress in Cryptology, Springer Nature, 2020, pp. 3–15.","chicago":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” In <i>Progress in Cryptology</i>, 12578:3–15. LNCS. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">https://doi.org/10.1007/978-3-030-65277-7_1</a>.","ama":"Pietrzak KZ. Delayed authentication: Preventing replay and relay attacks in private contact tracing. In: <i>Progress in Cryptology</i>. Vol 12578. LNCS. Springer Nature; 2020:3-15. doi:<a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">10.1007/978-3-030-65277-7_1</a>","apa":"Pietrzak, K. Z. (2020). Delayed authentication: Preventing replay and relay attacks in private contact tracing. In <i>Progress in Cryptology</i> (Vol. 12578, pp. 3–15). Bangalore, India: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">https://doi.org/10.1007/978-3-030-65277-7_1</a>","ista":"Pietrzak KZ. 2020. Delayed authentication: Preventing replay and relay attacks in private contact tracing. Progress in Cryptology. INDOCRYPT: International Conference on Cryptology in IndiaLNCS vol. 12578, 3–15.","mla":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” <i>Progress in Cryptology</i>, vol. 12578, Springer Nature, 2020, pp. 3–15, doi:<a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">10.1007/978-3-030-65277-7_1</a>.","ieee":"K. Z. Pietrzak, “Delayed authentication: Preventing replay and relay attacks in private contact tracing,” in <i>Progress in Cryptology</i>, Bangalore, India, 2020, vol. 12578, pp. 3–15."},"_id":"8987","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2020/418","open_access":"1"}],"day":"08","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030652760"],"eissn":["1611-3349"]},"conference":{"location":"Bangalore, India","name":"INDOCRYPT: International Conference on Cryptology in India","start_date":"2020-12-13","end_date":"2020-12-16"},"external_id":{"isi":["000927592800001"]},"author":[{"first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"title":"Delayed authentication: Preventing replay and relay attacks in private contact tracing","date_updated":"2026-04-16T09:33:26Z"},{"file":[{"access_level":"open_access","content_type":"application/pdf","file_size":1199247,"creator":"dernst","checksum":"69039cd402a571983aa6cb4815ffa863","file_name":"2020_PNAS_Grah.pdf","date_created":"2021-01-11T08:37:31Z","relation":"main_file","date_updated":"2021-01-11T08:37:31Z","file_id":"9004","success":1}],"publication_status":"published","year":"2020","article_processing_charge":"No","date_published":"2020-12-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"31614-31622","oa":1,"type":"journal_article","isi":1,"issue":"50","status":"public","publication":"Proceedings of the National Academy of Sciences of the United States of America","ddc":["570"],"month":"12","corr_author":"1","publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future."}],"pmid":1,"date_created":"2021-01-10T23:01:17Z","has_accepted_license":"1","intvolume":"       117","language":[{"iso":"eng"}],"author":[{"full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","orcid":"0000-0003-2539-3560"},{"full_name":"Zoller, Benjamin","first_name":"Benjamin","last_name":"Zoller"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"}],"title":"Nonequilibrium models of optimal enhancer function","date_updated":"2025-05-14T10:57:50Z","day":"15","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"file_date_updated":"2021-01-11T08:37:31Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/"}]},"acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","article_type":"original","external_id":{"pmid":["33268497"],"isi":["000600608300015"]},"oa_version":"Published Version","quality_controlled":"1","_id":"9000","volume":117,"department":[{"_id":"GaTk"}],"scopus_import":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.","mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>.","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. Proceedings of the National Academy of Sciences of the United States of America. 117(50), 31614–31622.","apa":"Grah, R., Zoller, B., &#38; Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(50):31614-31622. doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>.","short":"R. Grah, B. Zoller, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 31614–31622."},"doi":"10.1073/pnas.2006731117","project":[{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}]},{"arxiv":1,"publication_identifier":{"isbn":["9781728189420"],"issn":["1097-5659"]},"related_material":{"record":[{"relation":"earlier_version","id":"7910","status":"public"}]},"acknowledgement":"This work was supported by the Institute of Science and Technology Austria (IST Austria), the European Research Council under grant agreement number 758053 (ERC StG QUNNECT) and the EU’s Horizon 2020 research and innovation programme under grant agreement number 862644 (FET Open QUARTET). S.B. acknowledges support from the Marie Skłodowska Curie\r\nfellowship number 707438 (MSC-IF SUPEREOM), DV acknowledge support from EU’s Horizon 2020 research and innovation programme under grant agreement number 732894 (FET Proactive HOT) and the Project QuaSeRT funded by the QuantERA ERANET Cofund in Quantum Technologies, and J.M.F from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and\r\ninnovation programme under grant agreement number 732894 (FET Proactive\r\nHOT).","day":"21","external_id":{"arxiv":["1908.03058"],"isi":["000612224900089"]},"conference":{"end_date":"2020-09-25","start_date":"2020-09-21","location":"Florence, Italy","name":"RadarConf: National Conference on Radar"},"author":[{"first_name":"Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"full_name":"Pirandola, Stefano","first_name":"Stefano","last_name":"Pirandola"},{"full_name":"Vitali, David","last_name":"Vitali","first_name":"David"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M"}],"date_updated":"2026-04-15T06:42:36Z","title":"Microwave quantum illumination with a digital phase-conjugated receiver","volume":2020,"scopus_import":"1","department":[{"_id":"JoFi"}],"citation":{"chicago":"Barzanjeh, Shabir, Stefano Pirandola, David Vitali, and Johannes M Fink. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” In <i>IEEE National Radar Conference - Proceedings</i>, Vol. 2020. IEEE, 2020. <a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">https://doi.org/10.1109/RadarConf2043947.2020.9266397</a>.","short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, in:, IEEE National Radar Conference - Proceedings, IEEE, 2020.","mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” <i>IEEE National Radar Conference - Proceedings</i>, vol. 2020, no. 9, 9266397, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">10.1109/RadarConf2043947.2020.9266397</a>.","ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination with a digital phase-conjugated receiver,” in <i>IEEE National Radar Conference - Proceedings</i>, Florence, Italy, 2020, vol. 2020, no. 9.","ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination with a digital phase-conjugated receiver. IEEE National Radar Conference - Proceedings. RadarConf: National Conference on Radar vol. 2020, 9266397.","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination with a digital phase-conjugated receiver. In: <i>IEEE National Radar Conference - Proceedings</i>. Vol 2020. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">10.1109/RadarConf2043947.2020.9266397</a>","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., &#38; Fink, J. M. (2020). Microwave quantum illumination with a digital phase-conjugated receiver. In <i>IEEE National Radar Conference - Proceedings</i> (Vol. 2020). Florence, Italy: IEEE. <a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">https://doi.org/10.1109/RadarConf2043947.2020.9266397</a>"},"doi":"10.1109/RadarConf2043947.2020.9266397","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862644","name":"Quantum readout techniques and technologies"},{"grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"732894","name":"Hybrid Optomechanical Technologies"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.03058"}],"oa_version":"Preprint","quality_controlled":"1","_id":"9001","oa":1,"ec_funded":1,"type":"conference","isi":1,"article_processing_charge":"No","year":"2020","publication_status":"published","article_number":"9266397","date_published":"2020-09-21T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"IEEE","abstract":[{"text":"Quantum illumination is a sensing technique that employs entangled signal-idler beams to improve the detection efficiency of low-reflectivity objects in environments with large thermal noise. The advantage over classical strategies is evident at low signal brightness, a feature which could make the protocol an ideal prototype for non-invasive scanning or low-power short-range radar. Here we experimentally investigate the concept of quantum illumination at microwave frequencies, by generating entangled fields using a Josephson parametric converter which are then amplified to illuminate a room-temperature object at a distance of 1 meter. Starting from experimental data, we simulate the case of perfect idler photon number detection, which results in a quantum advantage compared to the relative classical benchmark. Our results highlight the opportunities and challenges on the way towards a first room-temperature application of microwave quantum circuits.","lang":"eng"}],"date_created":"2021-01-10T23:01:17Z","intvolume":"      2020","language":[{"iso":"eng"}],"issue":"9","month":"09","status":"public","publication":"IEEE National Radar Conference - Proceedings"},{"volume":14,"scopus_import":"1","department":[{"_id":"ElKo"}],"citation":{"ista":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. 2020. CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. 14(4), 586–599.","ama":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. CALYPSO: Private data management for decentralized ledgers. <i>Proceedings of the VLDB Endowment</i>. 2020;14(4):586-599. doi:<a href=\"https://doi.org/10.14778/3436905.3436917\">10.14778/3436905.3436917</a>","apa":"Kokoris Kogias, E., Alp, E. C., Gasser, L., Jovanovic, P., Syta, E., &#38; Ford, B. (2020). CALYPSO: Private data management for decentralized ledgers. <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.14778/3436905.3436917\">https://doi.org/10.14778/3436905.3436917</a>","ieee":"E. Kokoris Kogias, E. C. Alp, L. Gasser, P. Jovanovic, E. Syta, and B. Ford, “CALYPSO: Private data management for decentralized ledgers,” <i>Proceedings of the VLDB Endowment</i>, vol. 14, no. 4. Association for Computing Machinery, pp. 586–599, 2020.","mla":"Kokoris Kogias, Eleftherios, et al. “CALYPSO: Private Data Management for Decentralized Ledgers.” <i>Proceedings of the VLDB Endowment</i>, vol. 14, no. 4, Association for Computing Machinery, 2020, pp. 586–99, doi:<a href=\"https://doi.org/10.14778/3436905.3436917\">10.14778/3436905.3436917</a>.","short":"E. Kokoris Kogias, E.C. Alp, L. Gasser, P. Jovanovic, E. Syta, B. Ford, Proceedings of the VLDB Endowment 14 (2020) 586–599.","chicago":"Kokoris Kogias, Eleftherios, Enis Ceyhun Alp, Linus Gasser, Philipp Jovanovic, Ewa Syta, and Bryan Ford. “CALYPSO: Private Data Management for Decentralized Ledgers.” <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.14778/3436905.3436917\">https://doi.org/10.14778/3436905.3436917</a>."},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.14778/3436905.3436917","quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.14778/3436905.3436917"}],"_id":"9011","day":"01","publication_identifier":{"eissn":["2150-8097"]},"acknowledgement":"We thank Nicolas Gailly, Vincent Graf, Jean-Pierre Hubaux, Wouter Lueks, Massimo Marelli, Carmela Troncoso, Juan-Ramón Troncoso Pastoriza, Frédéric Pont, and Sandra Siby for their valuable feedback. This project was supported in part by the ETH domain under PHRT grant #2017−201, and by the AXA Research Fund, Byzgen, DFINITY, and the Swiss Data Science Center (SDSC).","article_type":"original","external_id":{"isi":["000658495400012"]},"author":[{"first_name":"Eleftherios","last_name":"Kokoris Kogias","orcid":"0000-0002-8827-3382","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"last_name":"Alp","first_name":"Enis Ceyhun","full_name":"Alp, Enis Ceyhun"},{"last_name":"Gasser","first_name":"Linus","full_name":"Gasser, Linus"},{"full_name":"Jovanovic, Philipp","last_name":"Jovanovic","first_name":"Philipp"},{"first_name":"Ewa","last_name":"Syta","full_name":"Syta, Ewa"},{"last_name":"Ford","first_name":"Bryan","full_name":"Ford, Bryan"}],"title":"CALYPSO: Private data management for decentralized ledgers","date_updated":"2026-06-18T19:40:17Z","publisher":"Association for Computing Machinery","date_created":"2021-01-17T23:01:13Z","abstract":[{"lang":"eng","text":"Distributed ledgers provide high availability and integrity, making them a key enabler for practical and secure computation of distributed workloads among mutually distrustful parties. Many practical applications also require strong confidentiality, however. This work enhances permissioned and permissionless blockchains with the ability to manage confidential data without forfeiting availability or decentralization. The proposed Calypso architecture addresses two orthogonal challenges confronting modern distributed ledgers: (a) enabling the auditable management of secrets and (b) protecting distributed computations against arbitrage attacks when their results depend on the ordering and secrecy of inputs.\r\n\r\nCalypso introduces on-chain secrets, a novel abstraction that enforces atomic deposition of an auditable trace whenever users access confidential data. Calypso provides user-controlled consent management that ensures revocation atomicity and accountable anonymity. To enable permissionless deployment, we introduce an incentive scheme and provide users with the option to select their preferred trustees. We evaluated our Calypso prototype with a confidential document-sharing application and a decentralized lottery. Our benchmarks show that transaction-processing latency increases linearly in terms of security (number of trustees) and is in the range of 0.2 to 8 seconds for 16 to 128 trustees."}],"intvolume":"        14","language":[{"iso":"eng"}],"issue":"4","corr_author":"1","month":"12","ddc":["000"],"status":"public","publication":"Proceedings of the VLDB Endowment","page":"586-599","oa":1,"type":"journal_article","isi":1,"publication_status":"published","year":"2020","article_processing_charge":"No","date_published":"2020-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"acknowledgement":"This work was supported by the European Union's Horizon 2020 Research and Innovation\r\nProgramme under Marie Sklodowska-Curie grant agreement 665385 and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy, EXC-2047/1--390685813.","article_type":"original","file_date_updated":"2021-01-25T07:48:39Z","publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"day":"15","external_id":{"isi":["000600695200027"]},"author":[{"full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","orcid":"0000-0002-0479-558X"},{"first_name":"Tim","last_name":"Laux","full_name":"Laux, Tim"},{"last_name":"Simon","first_name":"Theresa M.","full_name":"Simon, Theresa M."}],"date_updated":"2025-07-10T12:01:32Z","title":"Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies","volume":52,"scopus_import":"1","department":[{"_id":"JuFi"}],"doi":"10.1137/20M1322182","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Fischer, J. L., Laux, T., &#38; Simon, T. M. (2020). Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1322182\">https://doi.org/10.1137/20M1322182</a>","ama":"Fischer JL, Laux T, Simon TM. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. <i>SIAM Journal on Mathematical Analysis</i>. 2020;52(6):6222-6233. doi:<a href=\"https://doi.org/10.1137/20M1322182\">10.1137/20M1322182</a>","ista":"Fischer JL, Laux T, Simon TM. 2020. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 52(6), 6222–6233.","mla":"Fischer, Julian L., et al. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 6, Society for Industrial and Applied Mathematics, 2020, pp. 6222–33, doi:<a href=\"https://doi.org/10.1137/20M1322182\">10.1137/20M1322182</a>.","ieee":"J. L. Fischer, T. Laux, and T. M. Simon, “Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 6. Society for Industrial and Applied Mathematics, pp. 6222–6233, 2020.","short":"J.L. Fischer, T. Laux, T.M. Simon, SIAM Journal on Mathematical Analysis 52 (2020) 6222–6233.","chicago":"Fischer, Julian L, Tim Laux, and Theresa M. Simon. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2020. <a href=\"https://doi.org/10.1137/20M1322182\">https://doi.org/10.1137/20M1322182</a>."},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","quality_controlled":"1","_id":"9039","page":"6222-6233","oa":1,"isi":1,"type":"journal_article","ec_funded":1,"file":[{"checksum":"21aa1cf4c30a86a00cae15a984819b5d","creator":"dernst","file_name":"2020_SIAM_Fischer.pdf","relation":"main_file","date_created":"2021-01-25T07:48:39Z","content_type":"application/pdf","access_level":"open_access","file_size":310655,"success":1,"file_id":"9041","date_updated":"2021-01-25T07:48:39Z"}],"article_processing_charge":"No","year":"2020","publication_status":"published","date_published":"2020-12-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics","date_created":"2021-01-24T23:01:09Z","abstract":[{"lang":"eng","text":"We give a short and self-contained proof for rates of convergence of the Allen--Cahn equation towards mean curvature flow, assuming that a classical (smooth) solution to the latter exists and starting from well-prepared initial data. Our approach is based on a relative entropy technique. In particular, it does not require a stability analysis for the linearized Allen--Cahn operator. As our analysis also does not rely on the comparison principle, we expect it to be applicable to more complex equations and systems."}],"has_accepted_license":"1","intvolume":"        52","language":[{"iso":"eng"}],"issue":"6","ddc":["510"],"publication":"SIAM Journal on Mathematical Analysis","corr_author":"1","status":"public","month":"12"},{"page":"138-147","oa":1,"type":"conference","file":[{"success":1,"file_id":"9109","date_updated":"2021-02-09T09:39:02Z","creator":"dernst","checksum":"d616d549a0ade78606b16f8a9540820f","file_name":"2020_FMCAD_Alamdari.pdf","relation":"main_file","date_created":"2021-02-09T09:39:02Z","content_type":"application/pdf","access_level":"open_access","file_size":990999}],"article_processing_charge":"No","year":"2020","publication_status":"published","date_published":"2020-09-21T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"TU Wien Academic Press","abstract":[{"lang":"eng","text":"Machine learning and formal methods have complimentary benefits and drawbacks. In this work, we address the controller-design problem with a combination of techniques from both fields. The use of black-box neural networks in deep reinforcement learning (deep RL) poses a challenge for such a combination. Instead of reasoning formally about the output of deep RL, which we call the wizard, we extract from it a decision-tree based model, which we refer to as the magic book. Using the extracted model as an intermediary, we are able to handle problems that are infeasible for either deep RL or formal methods by themselves. First, we suggest, for the first time, a synthesis procedure that is based on a magic book. We synthesize a stand-alone correct-by-design controller that enjoys the favorable performance of RL. Second, we incorporate a magic book in a bounded model checking (BMC) procedure. BMC allows us to find numerous traces of the plant under the control of the wizard, which a user can use to increase the trustworthiness of the wizard and direct further training."}],"date_created":"2021-01-24T23:01:10Z","has_accepted_license":"1","language":[{"iso":"eng"}],"ddc":["000"],"publication":"Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design","month":"09","status":"public","publication_identifier":{"eissn":["2708-7824"],"isbn":["9783854480426"]},"file_date_updated":"2021-02-09T09:39:02Z","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","day":"21","conference":{"end_date":"2020-09-24","start_date":"2020-09-21","location":"Online Conference","name":"FMCAD: Formal Methods in Computer-Aided Design"},"author":[{"last_name":"Alamdari","first_name":"Par Alizadeh","full_name":"Alamdari, Par Alizadeh"},{"orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724"},{"last_name":"Lukina","first_name":"Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","full_name":"Lukina, Anna"}],"date_updated":"2025-07-10T12:01:32Z","title":"Formal methods with a touch of magic","department":[{"_id":"ToHe"}],"scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Alamdari, P. A., Avni, G., Henzinger, T. A., &#38; Lukina, A. (2020). Formal methods with a touch of magic. In <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i> (pp. 138–147). Online Conference: TU Wien Academic Press. <a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21</a>","ista":"Alamdari PA, Avni G, Henzinger TA, Lukina A. 2020. Formal methods with a touch of magic. Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 138–147.","ama":"Alamdari PA, Avni G, Henzinger TA, Lukina A. Formal methods with a touch of magic. In: <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>. TU Wien Academic Press; 2020:138-147. doi:<a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">10.34727/2020/isbn.978-3-85448-042-6_21</a>","mla":"Alamdari, Par Alizadeh, et al. “Formal Methods with a Touch of Magic.” <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, TU Wien Academic Press, 2020, pp. 138–47, doi:<a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">10.34727/2020/isbn.978-3-85448-042-6_21</a>.","ieee":"P. A. Alamdari, G. Avni, T. A. Henzinger, and A. Lukina, “Formal methods with a touch of magic,” in <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, Online Conference, 2020, pp. 138–147.","short":"P.A. Alamdari, G. Avni, T.A. Henzinger, A. Lukina, in:, Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design, TU Wien Academic Press, 2020, pp. 138–147.","chicago":"Alamdari, Par Alizadeh, Guy Avni, Thomas A Henzinger, and Anna Lukina. “Formal Methods with a Touch of Magic.” In <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, 138–47. TU Wien Academic Press, 2020. <a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21</a>."},"doi":"10.34727/2020/isbn.978-3-85448-042-6_21","project":[{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","quality_controlled":"1","_id":"9040"},{"oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/d0ra05394e"}],"_id":"9067","extern":"1","citation":{"mla":"Nauman, Muhammad, et al. “Size-Dependent Magnetic and Magnetothermal Properties of Gadolinium Silicide Nanoparticles.” <i>RSC Advances</i>, vol. 10, no. 47, Royal Society of Chemistry, 2020, pp. 28383–89, doi:<a href=\"https://doi.org/10.1039/d0ra05394e\">10.1039/d0ra05394e</a>.","ieee":"M. Nauman, M. H. Alnasir, M. A. Hamayun, Y. Wang, M. Shatruk, and S. Manzoor, “Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles,” <i>RSC Advances</i>, vol. 10, no. 47. Royal Society of Chemistry, pp. 28383–28389, 2020.","apa":"Nauman, M., Alnasir, M. H., Hamayun, M. A., Wang, Y., Shatruk, M., &#38; Manzoor, S. (2020). Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles. <i>RSC Advances</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0ra05394e\">https://doi.org/10.1039/d0ra05394e</a>","ama":"Nauman M, Alnasir MH, Hamayun MA, Wang Y, Shatruk M, Manzoor S. Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles. <i>RSC Advances</i>. 2020;10(47):28383-28389. doi:<a href=\"https://doi.org/10.1039/d0ra05394e\">10.1039/d0ra05394e</a>","ista":"Nauman M, Alnasir MH, Hamayun MA, Wang Y, Shatruk M, Manzoor S. 2020. Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles. RSC Advances. 10(47), 28383–28389.","chicago":"Nauman, Muhammad, Muhammad Hisham Alnasir, Muhammad Asif Hamayun, YiXu Wang, Michael Shatruk, and Sadia Manzoor. “Size-Dependent Magnetic and Magnetothermal Properties of Gadolinium Silicide Nanoparticles.” <i>RSC Advances</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/d0ra05394e\">https://doi.org/10.1039/d0ra05394e</a>.","short":"M. Nauman, M.H. Alnasir, M.A. Hamayun, Y. Wang, M. Shatruk, S. Manzoor, RSC Advances 10 (2020) 28383–28389."},"doi":"10.1039/d0ra05394e","volume":10,"title":"Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles","date_updated":"2024-10-15T13:44:01Z","author":[{"id":"32c21954-2022-11eb-9d5f-af9f93c24e71","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846","last_name":"Nauman","first_name":"Muhammad"},{"first_name":"Muhammad Hisham","last_name":"Alnasir","full_name":"Alnasir, Muhammad Hisham"},{"full_name":"Hamayun, Muhammad Asif","last_name":"Hamayun","first_name":"Muhammad Asif"},{"last_name":"Wang","first_name":"YiXu","full_name":"Wang, YiXu"},{"last_name":"Shatruk","first_name":"Michael","full_name":"Shatruk, Michael"},{"first_name":"Sadia","last_name":"Manzoor","full_name":"Manzoor, Sadia"}],"OA_place":"publisher","DOAJ_listed":"1","day":"29","article_type":"original","publication_identifier":{"issn":["2046-2069"]},"month":"07","publication":"RSC Advances","status":"public","issue":"47","intvolume":"        10","language":[{"iso":"eng"}],"OA_type":"gold","publisher":"Royal Society of Chemistry","abstract":[{"text":"Gadolinium silicide (Gd5Si4) nanoparticles are an interesting class of materials due to their high magnetization, low Curie temperature, low toxicity in biological environments and their multifunctional properties. We report the magnetic and magnetothermal properties of gadolinium silicide (Gd5Si4) nanoparticles prepared by surfactant-assisted ball milling of arc melted bulk ingots of the compound. Using different milling times and speeds, a wide range of crystallite sizes (13–43 nm) could be produced and a reduction in Curie temperature (TC) from 340 K to 317 K was achieved, making these nanoparticles suitable for self-controlled magnetic hyperthermia applications. The magnetothermal effect was measured in applied AC magnetic fields of amplitude 164–239 Oe and frequencies 163–519 kHz. All particles showed magnetic heating with a strong dependence of the specific absorption rate (SAR) on the average crystallite size. The highest SAR of 3.7 W g−1 was measured for 43 nm sized nanoparticles of Gd5Si4. The high SAR and low TC, (within the therapeutic range for magnetothermal therapy) makes the Gd5Si4 behave like self-regulating heat switches that would be suitable for self-controlled magnetic hyperthermia applications after biocompatibility and cytotoxicity tests.","lang":"eng"}],"date_created":"2021-02-02T15:51:23Z","date_published":"2020-07-29T00:00:00Z","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","publication_status":"published","article_processing_charge":"No","year":"2020","keyword":["General Chemistry","General Chemical Engineering"],"oa":1,"type":"journal_article","page":"28383-28389"},{"date_updated":"2026-04-16T09:34:59Z","title":"Lagrangian reachtubes: The next generation","author":[{"full_name":"Gruenbacher, Sophie","last_name":"Gruenbacher","first_name":"Sophie"},{"full_name":"Cyranka, Jacek","first_name":"Jacek","last_name":"Cyranka"},{"last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"full_name":"Islam, Md Ariful","last_name":"Islam","first_name":"Md Ariful"},{"first_name":"Scott A.","last_name":"Smolka","full_name":"Smolka, Scott A."},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"external_id":{"arxiv":["2012.07458"]},"conference":{"end_date":"2020-12-18","start_date":"2020-12-14","name":"CDC: Conference on Decision and Control","location":"Jeju Islang, Korea (South)"},"arxiv":1,"acknowledgement":"The authors would like to thank Ramin Hasani and Guillaume Berger for intellectual discussions about the research which lead to the generation of new ideas. ML was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Smolka’s research was supported by NSF grants CPS-1446832 and CCF-1918225. Gruenbacher is funded by FWF project W1255-N23. JC was partially supported by NAWA Polish Returns grant\r\nPPN/PPO/2018/1/00029.\r\n","publication_identifier":{"issn":["0743-1546"],"isbn":["9781728174471"]},"day":"14","main_file_link":[{"url":"https://arxiv.org/abs/2012.07458","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","_id":"9103","citation":{"ista":"Gruenbacher S, Cyranka J, Lechner M, Islam MA, Smolka SA, Grosu R. 2020. Lagrangian reachtubes: The next generation. Proceedings of the 59th IEEE Conference on Decision and Control. CDC: Conference on Decision and Control vol. 2020, 1556–1563.","ama":"Gruenbacher S, Cyranka J, Lechner M, Islam MA, Smolka SA, Grosu R. Lagrangian reachtubes: The next generation. In: <i>Proceedings of the 59th IEEE Conference on Decision and Control</i>. Vol 2020. IEEE; 2020:1556-1563. doi:<a href=\"https://doi.org/10.1109/CDC42340.2020.9304042\">10.1109/CDC42340.2020.9304042</a>","apa":"Gruenbacher, S., Cyranka, J., Lechner, M., Islam, M. A., Smolka, S. A., &#38; Grosu, R. (2020). Lagrangian reachtubes: The next generation. In <i>Proceedings of the 59th IEEE Conference on Decision and Control</i> (Vol. 2020, pp. 1556–1563). Jeju Islang, Korea (South): IEEE. <a href=\"https://doi.org/10.1109/CDC42340.2020.9304042\">https://doi.org/10.1109/CDC42340.2020.9304042</a>","mla":"Gruenbacher, Sophie, et al. “Lagrangian Reachtubes: The next Generation.” <i>Proceedings of the 59th IEEE Conference on Decision and Control</i>, vol. 2020, IEEE, 2020, pp. 1556–63, doi:<a href=\"https://doi.org/10.1109/CDC42340.2020.9304042\">10.1109/CDC42340.2020.9304042</a>.","ieee":"S. Gruenbacher, J. Cyranka, M. Lechner, M. A. Islam, S. A. Smolka, and R. Grosu, “Lagrangian reachtubes: The next generation,” in <i>Proceedings of the 59th IEEE Conference on Decision and Control</i>, Jeju Islang, Korea (South), 2020, vol. 2020, pp. 1556–1563.","short":"S. Gruenbacher, J. Cyranka, M. Lechner, M.A. Islam, S.A. Smolka, R. Grosu, in:, Proceedings of the 59th IEEE Conference on Decision and Control, IEEE, 2020, pp. 1556–1563.","chicago":"Gruenbacher, Sophie, Jacek Cyranka, Mathias Lechner, Md Ariful Islam, Scott A. Smolka, and Radu Grosu. “Lagrangian Reachtubes: The next Generation.” In <i>Proceedings of the 59th IEEE Conference on Decision and Control</i>, 2020:1556–63. IEEE, 2020. <a href=\"https://doi.org/10.1109/CDC42340.2020.9304042\">https://doi.org/10.1109/CDC42340.2020.9304042</a>."},"doi":"10.1109/CDC42340.2020.9304042","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"}],"volume":2020,"department":[{"_id":"ToHe"}],"scopus_import":"1","date_published":"2020-12-14T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","year":"2020","publication_status":"published","oa":1,"type":"conference","page":"1556-1563","status":"public","publication":"Proceedings of the 59th IEEE Conference on Decision and Control","month":"12","intvolume":"      2020","language":[{"iso":"eng"}],"publisher":"IEEE","date_created":"2021-02-07T23:01:14Z","abstract":[{"lang":"eng","text":"We introduce LRT-NG, a set of techniques and an associated toolset that computes a reachtube (an over-approximation of the set of reachable states over a given time horizon) of a nonlinear dynamical system. LRT-NG significantly advances the state-of-the-art Langrangian Reachability and its associated tool LRT. From a theoretical perspective, LRT-NG is superior to LRT in three ways. First, it uses for the first time an analytically computed metric for the propagated ball which is proven to minimize the ball’s volume. We emphasize that the metric computation is the centerpiece of all bloating-based techniques. Secondly, it computes the next reachset as the intersection of two balls: one based on the Cartesian metric and the other on the new metric. While the two metrics were previously considered opposing approaches, their joint use considerably tightens the reachtubes. Thirdly, it avoids the \"wrapping effect\" associated with the validated integration of the center of the reachset, by optimally absorbing the interval approximation in the radius of the next ball. From a tool-development perspective, LRT-NG is superior to LRT in two ways. First, it is a standalone tool that no longer relies on CAPD. This required the implementation of the Lohner method and a Runge-Kutta time-propagation method. Secondly, it has an improved interface, allowing the input model and initial conditions to be provided as external input files. Our experiments on a comprehensive set of benchmarks, including two Neural ODEs, demonstrates LRT-NG’s superior performance compared to LRT, CAPD, and Flow*."}]},{"isi":1,"ec_funded":1,"type":"journal_article","oa":1,"page":"323-348","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-11-01T00:00:00Z","publication_status":"published","year":"2020","article_processing_charge":"No","language":[{"iso":"eng"}],"intvolume":"       142","abstract":[{"text":"We consider the free additive convolution of two probability measures μ and ν on the real line and show that μ ⊞ v is supported on a single interval if μ and ν each has single interval support. Moreover, the density of μ ⊞ ν is proven to vanish as a square root near the edges of its support if both μ and ν have power law behavior with exponents between −1 and 1 near their edges. In particular, these results show the ubiquity of the conditions in our recent work on optimal local law at the spectral edges for addition of random matrices [5].","lang":"eng"}],"date_created":"2021-02-07T23:01:15Z","publisher":"Springer Nature","month":"11","status":"public","publication":"Journal d'Analyse Mathematique","external_id":{"isi":["000611879400008"],"arxiv":["1804.11199"]},"day":"01","publication_identifier":{"issn":["0021-7670"],"eissn":["1565-8538"]},"article_type":"original","acknowledgement":"Supported in part by Hong Kong RGC Grant ECS 26301517.\r\nSupported in part by ERC Advanced Grant RANMAT No. 338804.\r\nSupported in part by the Knut and Alice Wallenberg Foundation and the Swedish Research Council Grant VR-2017-05195.","arxiv":1,"title":"On the support of the free additive convolution","date_updated":"2025-07-10T12:01:37Z","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","first_name":"Zhigang","orcid":"0000-0003-3036-1475","last_name":"Bao"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schnelli","orcid":"0000-0003-0954-3231","first_name":"Kevin","full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"mla":"Bao, Zhigang, et al. “On the Support of the Free Additive Convolution.” <i>Journal d’Analyse Mathematique</i>, vol. 142, Springer Nature, 2020, pp. 323–48, doi:<a href=\"https://doi.org/10.1007/s11854-020-0135-2\">10.1007/s11854-020-0135-2</a>.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “On the support of the free additive convolution,” <i>Journal d’Analyse Mathematique</i>, vol. 142. Springer Nature, pp. 323–348, 2020.","ista":"Bao Z, Erdös L, Schnelli K. 2020. On the support of the free additive convolution. Journal d’Analyse Mathematique. 142, 323–348.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2020). On the support of the free additive convolution. <i>Journal d’Analyse Mathematique</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11854-020-0135-2\">https://doi.org/10.1007/s11854-020-0135-2</a>","ama":"Bao Z, Erdös L, Schnelli K. On the support of the free additive convolution. <i>Journal d’Analyse Mathematique</i>. 2020;142:323-348. doi:<a href=\"https://doi.org/10.1007/s11854-020-0135-2\">10.1007/s11854-020-0135-2</a>","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “On the Support of the Free Additive Convolution.” <i>Journal d’Analyse Mathematique</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11854-020-0135-2\">https://doi.org/10.1007/s11854-020-0135-2</a>.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal d’Analyse Mathematique 142 (2020) 323–348."},"doi":"10.1007/s11854-020-0135-2","scopus_import":"1","department":[{"_id":"LaEr"}],"volume":142,"_id":"9104","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11199"}]},{"extern":"1","_id":"9124","main_file_link":[{"url":"https://doi.org/10.5194/essd-2020-269","open_access":"1"}],"status":"public","oa_version":"Preprint","month":"09","publication":"Earth System Science Data","language":[{"iso":"eng"}],"citation":{"ama":"Albright AL, Fildier B, Touzé-Peiffer L, Pincus R, Vial J, Muller CJ. Atmospheric radiative profiles during EUREC4A. <i>Earth System Science Data</i>. doi:<a href=\"https://doi.org/10.5194/essd-2020-269\">10.5194/essd-2020-269</a>","ista":"Albright AL, Fildier B, Touzé-Peiffer L, Pincus R, Vial J, Muller CJ. Atmospheric radiative profiles during EUREC4A. Earth System Science Data, <a href=\"https://doi.org/10.5194/essd-2020-269\">10.5194/essd-2020-269</a>.","apa":"Albright, A. L., Fildier, B., Touzé-Peiffer, L., Pincus, R., Vial, J., &#38; Muller, C. J. (n.d.). Atmospheric radiative profiles during EUREC4A. <i>Earth System Science Data</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/essd-2020-269\">https://doi.org/10.5194/essd-2020-269</a>","ieee":"A. L. Albright, B. Fildier, L. Touzé-Peiffer, R. Pincus, J. Vial, and C. J. Muller, “Atmospheric radiative profiles during EUREC4A,” <i>Earth System Science Data</i>. Copernicus Publications.","mla":"Albright, Anna Lea, et al. “Atmospheric Radiative Profiles during EUREC4A.” <i>Earth System Science Data</i>, Copernicus Publications, doi:<a href=\"https://doi.org/10.5194/essd-2020-269\">10.5194/essd-2020-269</a>.","short":"A.L. Albright, B. Fildier, L. Touzé-Peiffer, R. Pincus, J. Vial, C.J. Muller, Earth System Science Data (n.d.).","chicago":"Albright, Anna Lea, Benjamin Fildier, Ludovic Touzé-Peiffer, Robert Pincus, Jessica Vial, and Caroline J Muller. “Atmospheric Radiative Profiles during EUREC4A.” <i>Earth System Science Data</i>. Copernicus Publications, n.d. <a href=\"https://doi.org/10.5194/essd-2020-269\">https://doi.org/10.5194/essd-2020-269</a>."},"doi":"10.5194/essd-2020-269","date_created":"2021-02-15T14:05:54Z","abstract":[{"lang":"eng","text":"The couplings among clouds, convection, and circulation in trade-wind regimes remain a fundamental puzzle that limits our ability to constrain future climate change. Radiative heating plays an important role in these couplings. Here we calculate the clear-sky radiative profiles from 2001 in-situ soundings (978 dropsondes and 1023 radiosondes) collected during the EUREC4A field campaign, which took place south and east of Barbados in January–February 2020. We describe the method used to calculate these radiative profiles and present preliminary results sampling variability at multiple scales, from the variability across all soundings to groupings by diurnal cycle and mesoscale organization state, as well as individual soundings associated with elevated moisture layers. This clear-sky radiative profiles data set can provide important missing detail to what can be learned from calculations based on passive remote sensing and help in investigating the role of radiation in dynamic and thermodynamic variability in trade-wind regimes. All data are archived and freely available for public access on AERIS (Albright et al. (2020), https://doi.org/10.25326/78)."}],"publisher":"Copernicus Publications","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2020-09-24T00:00:00Z","date_updated":"2022-01-24T12:27:08Z","title":"Atmospheric radiative profiles during EUREC4A","year":"2020","article_processing_charge":"No","publication_status":"submitted","author":[{"full_name":"Albright, Anna Lea","first_name":"Anna Lea","last_name":"Albright"},{"full_name":"Fildier, Benjamin","first_name":"Benjamin","last_name":"Fildier"},{"last_name":"Touzé-Peiffer","first_name":"Ludovic","full_name":"Touzé-Peiffer, Ludovic"},{"first_name":"Robert","last_name":"Pincus","full_name":"Pincus, Robert"},{"first_name":"Jessica","last_name":"Vial","full_name":"Vial, Jessica"},{"orcid":"0000-0001-5836-5350","last_name":"Muller","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J"}],"type":"preprint","oa":1,"day":"24"},{"intvolume":"        12","OA_type":"gold","language":[{"iso":"eng"}],"publisher":"American Geophysical Union","date_created":"2021-02-15T14:06:23Z","abstract":[{"text":"This study investigates the feedbacks between an interactive sea surface temperature (SST) and the self‐aggregation of deep convective clouds, using a cloud‐resolving model in nonrotating radiative‐convective equilibrium. The ocean is modeled as one layer slab with a temporally fixed mean but spatially varying temperature. We find that the interactive SST decelerates the aggregation and that the deceleration is larger with a shallower slab, consistent with earlier studies. The surface temperature anomaly in dry regions is positive at first, thus opposing the diverging shallow circulation known to favor self‐aggregation, consistent with the slower aggregation. But surprisingly, the driest columns then have a negative SST anomaly, thus strengthening the diverging shallow circulation and favoring aggregation. This diverging circulation out of dry regions is found to be well correlated with the aggregation speed. It can be linked to a positive surface pressure anomaly (PSFC), itself the consequence of SST anomalies and boundary layer radiative cooling. The latter cools and dries the boundary layer, thus increasing PSFC anomalies through virtual effects and hydrostasy. Sensitivity experiments confirm the key role played by boundary layer radiative cooling in determining PSFC anomalies in dry regions, and thus the shallow diverging circulation and the aggregation speed.","lang":"eng"}],"status":"public","publication":"Journal of Advances in Modeling Earth Systems","month":"11","issue":"11","oa":1,"type":"journal_article","date_published":"2020-11-01T00:00:00Z","article_number":"e2020MS002164","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","publication_status":"published","keyword":["Global and Planetary Change","General Earth and Planetary Sciences","Environmental Chemistry"],"year":"2020","article_processing_charge":"No","doi":"10.1029/2020ms002164","citation":{"ieee":"S. Shamekh, C. J. Muller, J. ‐P. Duvel, and F. D’Andrea, “Self‐aggregation of convective clouds with interactive sea surface temperature,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 12, no. 11. American Geophysical Union, 2020.","mla":"Shamekh, S., et al. “Self‐aggregation of Convective Clouds with Interactive Sea Surface Temperature.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 12, no. 11, e2020MS002164, American Geophysical Union, 2020, doi:<a href=\"https://doi.org/10.1029/2020ms002164\">10.1029/2020ms002164</a>.","ama":"Shamekh S, Muller CJ, Duvel J ‐P., D’Andrea F. Self‐aggregation of convective clouds with interactive sea surface temperature. <i>Journal of Advances in Modeling Earth Systems</i>. 2020;12(11). doi:<a href=\"https://doi.org/10.1029/2020ms002164\">10.1029/2020ms002164</a>","ista":"Shamekh S, Muller CJ, Duvel J ‐P., D’Andrea F. 2020. Self‐aggregation of convective clouds with interactive sea surface temperature. Journal of Advances in Modeling Earth Systems. 12(11), e2020MS002164.","apa":"Shamekh, S., Muller, C. J., Duvel, J. ‐P., &#38; D’Andrea, F. (2020). Self‐aggregation of convective clouds with interactive sea surface temperature. <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2020ms002164\">https://doi.org/10.1029/2020ms002164</a>","chicago":"Shamekh, S., Caroline J Muller, J.‐P. Duvel, and F. D’Andrea. “Self‐aggregation of Convective Clouds with Interactive Sea Surface Temperature.” <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union, 2020. <a href=\"https://doi.org/10.1029/2020ms002164\">https://doi.org/10.1029/2020ms002164</a>.","short":"S. Shamekh, C.J. Muller, J. ‐P. Duvel, F. D’Andrea, Journal of Advances in Modeling Earth Systems 12 (2020)."},"volume":12,"oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1029/2020MS002164","open_access":"1"}],"_id":"9125","extern":"1","OA_place":"publisher","DOAJ_listed":"1","day":"01","publication_identifier":{"issn":["1942-2466","1942-2466"]},"article_type":"original","title":"Self‐aggregation of convective clouds with interactive sea surface temperature","date_updated":"2024-10-15T13:46:02Z","author":[{"full_name":"Shamekh, S.","first_name":"S.","last_name":"Shamekh"},{"last_name":"Muller","orcid":"0000-0001-5836-5350","first_name":"Caroline J","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"},{"last_name":"Duvel","first_name":"J.‐P.","full_name":"Duvel, J.‐P."},{"full_name":"D'Andrea, F.","last_name":"D'Andrea","first_name":"F."}]},{"DOAJ_listed":"1","article_type":"original","publication_identifier":{"issn":["1942-2466","1942-2466"]},"day":"01","OA_place":"publisher","author":[{"last_name":"Risi","first_name":"Camille","full_name":"Risi, Camille"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller","first_name":"Caroline J"},{"first_name":"Peter","last_name":"Blossey","full_name":"Blossey, Peter"}],"date_updated":"2024-10-15T13:47:23Z","title":"What controls the water vapor isotopic composition near the surface of tropical oceans? Results from an analytical model constrained by large‐eddy simulations","volume":12,"citation":{"chicago":"Risi, Camille, Caroline J Muller, and Peter Blossey. “What Controls the Water Vapor Isotopic Composition near the Surface of Tropical Oceans? Results from an Analytical Model Constrained by Large‐eddy Simulations.” <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union, 2020. <a href=\"https://doi.org/10.1029/2020ms002106\">https://doi.org/10.1029/2020ms002106</a>.","short":"C. Risi, C.J. Muller, P. Blossey, Journal of Advances in Modeling Earth Systems 12 (2020).","ieee":"C. Risi, C. J. Muller, and P. Blossey, “What controls the water vapor isotopic composition near the surface of tropical oceans? Results from an analytical model constrained by large‐eddy simulations,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 12, no. 8. American Geophysical Union, 2020.","mla":"Risi, Camille, et al. “What Controls the Water Vapor Isotopic Composition near the Surface of Tropical Oceans? Results from an Analytical Model Constrained by Large‐eddy Simulations.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 12, no. 8, e2020MS002106, American Geophysical Union, 2020, doi:<a href=\"https://doi.org/10.1029/2020ms002106\">10.1029/2020ms002106</a>.","ama":"Risi C, Muller CJ, Blossey P. What controls the water vapor isotopic composition near the surface of tropical oceans? Results from an analytical model constrained by large‐eddy simulations. <i>Journal of Advances in Modeling Earth Systems</i>. 2020;12(8). doi:<a href=\"https://doi.org/10.1029/2020ms002106\">10.1029/2020ms002106</a>","ista":"Risi C, Muller CJ, Blossey P. 2020. What controls the water vapor isotopic composition near the surface of tropical oceans? Results from an analytical model constrained by large‐eddy simulations. Journal of Advances in Modeling Earth Systems. 12(8), e2020MS002106.","apa":"Risi, C., Muller, C. J., &#38; Blossey, P. (2020). What controls the water vapor isotopic composition near the surface of tropical oceans? Results from an analytical model constrained by large‐eddy simulations. <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2020ms002106\">https://doi.org/10.1029/2020ms002106</a>"},"doi":"10.1029/2020ms002106","main_file_link":[{"url":"https://doi.org/10.1029/2020MS002106","open_access":"1"}],"oa_version":"Published Version","quality_controlled":"1","_id":"9126","extern":"1","oa":1,"type":"journal_article","article_processing_charge":"No","year":"2020","keyword":["Global and Planetary Change","General Earth and Planetary Sciences","Environmental Chemistry"],"publication_status":"published","date_published":"2020-08-01T00:00:00Z","article_number":"e2020MS002106","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","publisher":"American Geophysical Union","date_created":"2021-02-15T14:06:38Z","abstract":[{"text":"The goal of this study is to understand the mechanisms controlling the isotopic composition of the water vapor near the surface of tropical oceans, at the scale of about a hundred kilometers and a month. In the tropics, it has long been observed that the isotopic compositions of rain and vapor near the surface are more depleted when the precipitation rate is high. This is called the “amount effect.” Previous studies, based on observations or models with parameterized convection, have highlighted the roles of deep convective and mesoscale downdrafts and rain evaporation. But the relative importance of these processes has never been quantified. We hypothesize that it can be quantified using an analytical model constrained by large‐eddy simulations. Results from large‐eddy simulations confirm that the classical amount effect can be simulated only if precipitation rate changes result from changes in the large‐scale circulation. We find that the main process depleting the water vapor compared to the equilibrium with the ocean is the fact that updrafts stem from areas where the water vapor is more enriched. The main process responsible for the amount effect is the fact that when the large‐scale ascent increases, isotopic vertical gradients are steeper, so that updrafts and downdrafts deplete the subcloud layer more efficiently.","lang":"eng"}],"intvolume":"        12","language":[{"iso":"eng"}],"OA_type":"gold","issue":"8","status":"public","month":"08","publication":"Journal of Advances in Modeling Earth Systems"},{"date_updated":"2022-01-24T12:28:49Z","title":"How warmer and drier will the Mediterranean region be at the end of the twenty-first century?","author":[{"last_name":"Drobinski","first_name":"Philippe","full_name":"Drobinski, Philippe"},{"first_name":"Nicolas","last_name":"Da Silva","full_name":"Da Silva, Nicolas"},{"full_name":"Bastin, Sophie","first_name":"Sophie","last_name":"Bastin"},{"full_name":"Mailler, Sylvain","last_name":"Mailler","first_name":"Sylvain"},{"last_name":"Muller","orcid":"0000-0001-5836-5350","first_name":"Caroline J","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"},{"first_name":"Bodo","last_name":"Ahrens","full_name":"Ahrens, Bodo"},{"full_name":"Christensen, Ole B.","first_name":"Ole B.","last_name":"Christensen"},{"full_name":"Lionello, Piero","last_name":"Lionello","first_name":"Piero"}],"article_type":"original","publication_identifier":{"issn":["1436-3798","1436-378X"]},"day":"11","main_file_link":[{"open_access":"1","url":"https://hal-insu.archives-ouvertes.fr/insu-02881534"}],"quality_controlled":"1","oa_version":"Submitted Version","extern":"1","_id":"9127","citation":{"ista":"Drobinski P, Da Silva N, Bastin S, Mailler S, Muller CJ, Ahrens B, Christensen OB, Lionello P. 2020. How warmer and drier will the Mediterranean region be at the end of the twenty-first century? Regional Environmental Change. 20(9), 78.","ama":"Drobinski P, Da Silva N, Bastin S, et al. How warmer and drier will the Mediterranean region be at the end of the twenty-first century? <i>Regional Environmental Change</i>. 2020;20(9). doi:<a href=\"https://doi.org/10.1007/s10113-020-01659-w\">10.1007/s10113-020-01659-w</a>","apa":"Drobinski, P., Da Silva, N., Bastin, S., Mailler, S., Muller, C. J., Ahrens, B., … Lionello, P. (2020). How warmer and drier will the Mediterranean region be at the end of the twenty-first century? <i>Regional Environmental Change</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10113-020-01659-w\">https://doi.org/10.1007/s10113-020-01659-w</a>","mla":"Drobinski, Philippe, et al. “How Warmer and Drier Will the Mediterranean Region Be at the End of the Twenty-First Century?” <i>Regional Environmental Change</i>, vol. 20, no. 9, 78, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1007/s10113-020-01659-w\">10.1007/s10113-020-01659-w</a>.","ieee":"P. Drobinski <i>et al.</i>, “How warmer and drier will the Mediterranean region be at the end of the twenty-first century?,” <i>Regional Environmental Change</i>, vol. 20, no. 9. Springer Nature, 2020.","short":"P. Drobinski, N. Da Silva, S. Bastin, S. Mailler, C.J. Muller, B. Ahrens, O.B. Christensen, P. Lionello, Regional Environmental Change 20 (2020).","chicago":"Drobinski, Philippe, Nicolas Da Silva, Sophie Bastin, Sylvain Mailler, Caroline J Muller, Bodo Ahrens, Ole B. Christensen, and Piero Lionello. “How Warmer and Drier Will the Mediterranean Region Be at the End of the Twenty-First Century?” <i>Regional Environmental Change</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10113-020-01659-w\">https://doi.org/10.1007/s10113-020-01659-w</a>."},"doi":"10.1007/s10113-020-01659-w","volume":20,"date_published":"2020-09-11T00:00:00Z","article_number":"78","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["Global and Planetary Change"],"year":"2020","article_processing_charge":"No","publication_status":"published","oa":1,"type":"journal_article","publication":"Regional Environmental Change","month":"09","status":"public","issue":"9","intvolume":"        20","language":[{"iso":"eng"}],"publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Nearly all regions in the world are projected to become dryer in a warming climate. Here, we investigate the Mediterranean region, often referred to as a climate change “hot spot”. From regional climate simulations, it is shown that although enhanced warming and drying over land is projected, the spatial pattern displays high variability. Indeed, drying is largely caused by enhanced warming over land. However, in Northern Europe, soil moisture alleviates warming induced drying by up to 50% due to humidity uptake from land. In already arid regions, the Mediterranean Sea is generally the only humidity source, and drying is only due to land warming. However, over Sahara and the Iberian Peninsula, enhanced warming over land is insufficient to explain the extreme drying. These regions are also isolated from humidity advection by heat lows, which are cyclonic circulation anomalies associated with surface heating over land. The cyclonic circulation scales with the temperature gradient between land and ocean which increases with climate change, reinforcing the cyclonic circulation over Sahara and the Iberian Peninsula, both diverting the zonal advection of humidity to the south of the Iberian Peninsula. The dynamics are therefore key in the warming and drying of the Mediterranean region, with extreme aridification over the Sahara and Iberian Peninsula. In these regions, the risk for human health due to the thermal load which accounts for air temperature and humidity is therefore projected to increase significantly with climate change at a level of extreme danger."}],"date_created":"2021-02-15T14:06:58Z"}]