[{"intvolume":"       117","date_published":"2020-07-21T00:00:00Z","day":"21","doi":"10.1073/pnas.1921205117","oa":1,"file":[{"creator":"dernst","file_size":1111604,"date_created":"2020-08-10T06:50:28Z","file_name":"2020_PNAS_Corominas.pdf","success":1,"access_level":"open_access","date_updated":"2020-08-10T06:50:28Z","file_id":"8223","content_type":"application/pdf","relation":"main_file"}],"ec_funded":1,"article_type":"original","year":"2020","publication_identifier":{"eissn":["1091-6490"]},"acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"ddc":["570"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020"}],"oa_version":"Published Version","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"page":"16969-16975","date_updated":"2026-04-03T09:29:04Z","author":[{"first_name":"Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele","first_name":"Colinda L.G.J."},{"orcid":"0000-0001-6060-4795","last_name":"Kishi","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi"},{"first_name":"Saskia I.J.","last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I.J."},{"first_name":"Benjamin D.","full_name":"Simons, Benjamin D.","last_name":"Simons"},{"full_name":"Van Rheenen, Jacco","last_name":"Van Rheenen","first_name":"Jacco"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B"}],"title":"Stem cell lineage survival as a noisy competition for niche access","file_date_updated":"2020-08-10T06:50:28Z","has_accepted_license":"1","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","pmid":1,"abstract":[{"lang":"eng","text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings."}],"type":"journal_article","citation":{"short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., &#38; Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. <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.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>","ieee":"B. Corominas-Murtra <i>et al.</i>, “Stem cell lineage survival as a noisy competition for niche access,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(29):16969-16975. doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <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.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>.","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975."},"department":[{"_id":"EdHa"}],"volume":117,"corr_author":"1","publisher":"National Academy of Sciences","date_created":"2020-08-09T22:00:52Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000553292900014"],"pmid":["32611816"]},"_id":"8220","issue":"29","scopus_import":"1","month":"07"},{"isi":1,"publication":"Nature Communications","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["570"],"file":[{"access_level":"open_access","file_name":"2020_NatureComm_Flynn.pdf","date_created":"2020-05-11T10:36:33Z","file_size":4609120,"creator":"dernst","relation":"main_file","checksum":"dce367abf2c1a1d15f58fe6f7de82893","content_type":"application/pdf","file_id":"7817","date_updated":"2020-07-14T12:48:03Z"}],"oa":1,"day":"29","doi":"10.1038/s41467-020-15872-y","date_published":"2020-04-29T00:00:00Z","intvolume":"        11","article_number":"2099","year":"2020","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","title":"MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity","author":[{"full_name":"Flynn, Sean M.","last_name":"Flynn","first_name":"Sean M."},{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"},{"first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat","last_name":"Artan","orcid":"0000-0001-8945-6992"},{"first_name":"Stephen","last_name":"Barratt","full_name":"Barratt, Stephen"},{"first_name":"Alastair","last_name":"Crisp","full_name":"Crisp, Alastair"},{"full_name":"Nelson, Geoffrey M.","last_name":"Nelson","first_name":"Geoffrey M."},{"full_name":"Peak-Chew, Sew Yeu","last_name":"Peak-Chew","first_name":"Sew Yeu"},{"last_name":"Begum","full_name":"Begum, Farida","first_name":"Farida"},{"first_name":"Mark","full_name":"Skehel, Mark","last_name":"Skehel"},{"first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","full_name":"De Bono, Mario"}],"date_updated":"2026-04-03T09:27:08Z","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2020-07-14T12:48:03Z","oa_version":"Published Version","volume":11,"department":[{"_id":"MaDe"}],"corr_author":"1","publisher":"Springer Nature","citation":{"short":"S.M. Flynn, C. Chen, M. Artan, S. Barratt, A. Crisp, G.M. Nelson, S.Y. Peak-Chew, F. Begum, M. Skehel, M. de Bono, Nature Communications 11 (2020).","apa":"Flynn, S. M., Chen, C., Artan, M., Barratt, S., Crisp, A., Nelson, G. M., … de Bono, M. (2020). MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-15872-y\">https://doi.org/10.1038/s41467-020-15872-y</a>","ama":"Flynn SM, Chen C, Artan M, et al. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-15872-y\">10.1038/s41467-020-15872-y</a>","ieee":"S. M. Flynn <i>et al.</i>, “MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Flynn SM, Chen C, Artan M, Barratt S, Crisp A, Nelson GM, Peak-Chew SY, Begum F, Skehel M, de Bono M. 2020. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 11, 2099.","chicago":"Flynn, Sean M., Changchun Chen, Murat Artan, Stephen Barratt, Alastair Crisp, Geoffrey M. Nelson, Sew Yeu Peak-Chew, Farida Begum, Mark Skehel, and Mario de Bono. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-15872-y\">https://doi.org/10.1038/s41467-020-15872-y</a>.","mla":"Flynn, Sean M., et al. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” <i>Nature Communications</i>, vol. 11, 2099, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-15872-y\">10.1038/s41467-020-15872-y</a>."},"pmid":1,"abstract":[{"text":"Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate IL-17 signaling in neurons, and the extent it can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans neurons. We identify the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling from many immune receptors in mammals, but was not previously implicated in IL-17 signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1 is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1 signaling regulates multiple phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural circuit function downstream of IL-17 to remodel physiology and behavior.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","_id":"7804","month":"04","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2020-05-10T22:00:47Z","external_id":{"pmid":["32350248"],"isi":["000531855500029"]}},{"volume":10,"OA_type":"green","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","main_file_link":[{"open_access":"1","url":"https://repository.uantwerpen.be/docman/irua/190103/173803.pdf"}],"citation":{"ista":"Irtem E, Arenas Esteban D, Duarte M, Choukroun D, Lee S, Ibáñez M, Bals S, Breugelmans T. 2020. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 10(22), 13468–13478.","chicago":"Irtem, Erdem, Daniel Arenas Esteban, Miguel Duarte, Daniel Choukroun, Seungho Lee, Maria Ibáñez, Sara Bals, and Tom Breugelmans. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” <i>ACS Catalysis</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acscatal.0c03210\">https://doi.org/10.1021/acscatal.0c03210</a>.","mla":"Irtem, Erdem, et al. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” <i>ACS Catalysis</i>, vol. 10, no. 22, American Chemical Society, 2020, pp. 13468–78, doi:<a href=\"https://doi.org/10.1021/acscatal.0c03210\">10.1021/acscatal.0c03210</a>.","ama":"Irtem E, Arenas Esteban D, Duarte M, et al. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. <i>ACS Catalysis</i>. 2020;10(22):13468-13478. doi:<a href=\"https://doi.org/10.1021/acscatal.0c03210\">10.1021/acscatal.0c03210</a>","apa":"Irtem, E., Arenas Esteban, D., Duarte, M., Choukroun, D., Lee, S., Ibáñez, M., … Breugelmans, T. (2020). Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. <i>ACS Catalysis</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acscatal.0c03210\">https://doi.org/10.1021/acscatal.0c03210</a>","ieee":"E. Irtem <i>et al.</i>, “Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction,” <i>ACS Catalysis</i>, vol. 10, no. 22. American Chemical Society, pp. 13468–13478, 2020.","short":"E. Irtem, D. Arenas Esteban, M. Duarte, D. Choukroun, S. Lee, M. Ibáñez, S. Bals, T. Breugelmans, ACS Catalysis 10 (2020) 13468–13478."},"abstract":[{"lang":"eng","text":"Bimetallic nanoparticles with tailored size and specific composition have shown promise as stable and selective catalysts for electrochemical reduction of CO2 (CO2R) in batch systems. Yet, limited effort was devoted to understand the effect of ligand coverage and postsynthesis treatments on CO2 reduction, especially under industrially applicable conditions, such as at high currents (>100 mA/cm2) using gas diffusion electrodes (GDE) and flow reactors. In this work, Cu–Ag core–shell nanoparticles (11 ± 2 nm) were prepared with three different surface modes: (i) capped with oleylamine, (ii) capped with monoisopropylamine, and (iii) surfactant-free with a reducing borohydride agent; Cu–Ag (OAm), Cu–Ag (MIPA), and Cu–Ag (NaBH4), respectively. The ligand exchange and removal was evidenced by infrared spectroscopy (ATR-FTIR) analysis, whereas high-resolution scanning transmission electron microscopy (HAADF-STEM) showed their effect on the interparticle distance and nanoparticle rearrangement. Later on, we developed a process-on-substrate method to track these effects on CO2R. Cu–Ag (OAm) gave a lower on-set potential for hydrocarbon production, whereas Cu–Ag (MIPA) and Cu–Ag (NaBH4) promoted syngas production. The electrochemical impedance and surface area analysis on the well-controlled electrodes showed gradual increases in the electrical conductivity and active surface area after each surface treatment. We found that the increasing amount of the triple phase boundaries (the meeting point for the electron–electrolyte–CO2 reactant) affect the required electrode potential and eventually the C+2e̅/C2e̅ product ratio. This study highlights the importance of the electron transfer to those active sites affected by the capping agents—particularly on larger substrates that are crucial for their industrial application."}],"type":"journal_article","quality_controlled":"1","_id":"8926","month":"11","issue":"22","scopus_import":"1","publication_status":"published","date_created":"2020-12-06T23:01:15Z","external_id":{"isi":["000592978900031"]},"isi":1,"publication":"ACS Catalysis","project":[{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"repository","oa":1,"doi":"10.1021/acscatal.0c03210","day":"20","date_published":"2020-11-20T00:00:00Z","intvolume":"        10","acknowledgement":"The authors also acknowledge financial support from the University Research Fund (BOF-GOA-PS ID No. 33928). S.L. has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2020","article_type":"original","publication_identifier":{"eissn":["2155-5435"]},"ec_funded":1,"author":[{"first_name":"Erdem","full_name":"Irtem, Erdem","last_name":"Irtem"},{"full_name":"Arenas Esteban, Daniel","last_name":"Arenas Esteban","first_name":"Daniel"},{"full_name":"Duarte, Miguel","last_name":"Duarte","first_name":"Miguel"},{"first_name":"Daniel","last_name":"Choukroun","full_name":"Choukroun, Daniel"},{"full_name":"Lee, Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","first_name":"Seungho"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","first_name":"Maria"},{"full_name":"Bals, Sara","last_name":"Bals","first_name":"Sara"},{"full_name":"Breugelmans, Tom","last_name":"Breugelmans","first_name":"Tom"}],"title":"Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction","page":"13468-13478","date_updated":"2026-04-03T09:31:02Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Submitted Version"},{"month":"02","scopus_import":"1","_id":"7511","external_id":{"pmid":["32054835"],"isi":["000514928000017"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2020-02-23T23:00:35Z","publisher":"Springer Nature","volume":11,"department":[{"_id":"FlSc"}],"citation":{"short":"B. Turoňová, W.J.H. Hagen, M. Obr, S. Mosalaganti, J.W. Beugelink, C.E. Zimmerli, H.G. Kräusslich, M. Beck, Nature Communications 11 (2020).","apa":"Turoňová, B., Hagen, W. J. H., Obr, M., Mosalaganti, S., Beugelink, J. W., Zimmerli, C. E., … Beck, M. (2020). Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>","ama":"Turoňová B, Hagen WJH, Obr M, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>","ieee":"B. Turoňová <i>et al.</i>, “Benchmarking tomographic acquisition schemes for high-resolution structural biology,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Turoňová, Beata, Wim J.H. Hagen, Martin Obr, Shyamal Mosalaganti, J. Wouter Beugelink, Christian E. Zimmerli, Hans Georg Kräusslich, and Martin Beck. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-14535-2\">https://doi.org/10.1038/s41467-020-14535-2</a>.","ista":"Turoňová B, Hagen WJH, Obr M, Mosalaganti S, Beugelink JW, Zimmerli CE, Kräusslich HG, Beck M. 2020. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nature Communications. 11, 876.","mla":"Turoňová, Beata, et al. “Benchmarking Tomographic Acquisition Schemes for High-Resolution Structural Biology.” <i>Nature Communications</i>, vol. 11, 876, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-14535-2\">10.1038/s41467-020-14535-2</a>."},"pmid":1,"type":"journal_article","abstract":[{"text":"Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.","lang":"eng"}],"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:59Z","author":[{"first_name":"Beata","full_name":"Turoňová, Beata","last_name":"Turoňová"},{"last_name":"Hagen","full_name":"Hagen, Wim J.H.","first_name":"Wim J.H."},{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","full_name":"Obr, Martin","orcid":"0000-0003-1756-6564"},{"first_name":"Shyamal","full_name":"Mosalaganti, Shyamal","last_name":"Mosalaganti"},{"last_name":"Beugelink","full_name":"Beugelink, J. Wouter","first_name":"J. Wouter"},{"first_name":"Christian E.","full_name":"Zimmerli, Christian E.","last_name":"Zimmerli"},{"last_name":"Kräusslich","full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg"},{"last_name":"Beck","full_name":"Beck, Martin","first_name":"Martin"}],"title":"Benchmarking tomographic acquisition schemes for high-resolution structural biology","date_updated":"2026-04-03T09:27:26Z","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["570"],"isi":1,"publication":"Nature Communications","article_number":"876","year":"2020","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","file":[{"relation":"main_file","checksum":"2c8d10475e1b0d397500760e28bdf561","content_type":"application/pdf","file_id":"7517","date_updated":"2020-07-14T12:47:59Z","access_level":"open_access","file_size":2027529,"creator":"dernst","date_created":"2020-02-24T14:00:54Z","file_name":"2020_NatureComm_Turonova.pdf"}],"oa":1,"doi":"10.1038/s41467-020-14535-2","day":"13","date_published":"2020-02-13T00:00:00Z","intvolume":"        11"},{"quality_controlled":"1","citation":{"ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” <i>Forum of Mathematics, Sigma</i>, vol. 8. Cambridge University Press, 2020.","apa":"Deuchert, A., Mayer, S., &#38; Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2020.17\">https://doi.org/10.1017/fms.2020.17</a>","ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>Forum of Mathematics, Sigma</i>. 2020;8. doi:<a href=\"https://doi.org/10.1017/fms.2020.17\">10.1017/fms.2020.17</a>","ista":"Deuchert A, Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 8, e20.","chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. 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The result is valid in the dilute limit 𝜌 and if 𝛽𝜌 ."}],"type":"journal_article","department":[{"_id":"RoSe"}],"volume":8,"publisher":"Cambridge University Press","corr_author":"1","date_created":"2020-05-03T22:00:48Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"isi":["000527342000001"],"arxiv":["1910.03372"]},"_id":"7790","scopus_import":"1","month":"03","date_published":"2020-03-14T00:00:00Z","intvolume":"         8","oa":1,"file":[{"file_size":692530,"creator":"dernst","date_created":"2020-05-04T12:02:41Z","file_name":"2020_ForumMath_Deuchert.pdf","access_level":"open_access","file_id":"7797","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","checksum":"8a64da99d107686997876d7cad8cfe1e","content_type":"application/pdf"}],"doi":"10.1017/fms.2020.17","day":"14","year":"2020","article_type":"original","publication_identifier":{"eissn":["2050-5094"]},"ec_funded":1,"article_number":"e20","isi":1,"publication":"Forum of Mathematics, Sigma","arxiv":1,"ddc":["510"],"project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","date_updated":"2026-04-03T09:30:21Z","related_material":{"record":[{"id":"7524","relation":"earlier_version","status":"public"}]},"title":"The free energy of the two-dimensional dilute Bose gas. 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Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"type":"conference","citation":{"short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In <i>Proceedings of the International Conference on Embedded Software</i>, 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: Embedded Software.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” <i>Proceedings of the International Conference on Embedded Software</i>, 2020.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. 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Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the United States Air Force. ","publication_identifier":{"issn":["0278-0070"],"eissn":["1937-4151"]},"year":"2020","article_type":"original","arxiv":1,"publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","isi":1,"project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","oa_version":"Preprint","title":"Reachability analysis of linear hybrid systems via block decomposition","author":[{"first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365"},{"full_name":"Forets, Marcelo","last_name":"Forets","first_name":"Marcelo"},{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"full_name":"Potomkin, Kostiantyn","last_name":"Potomkin","first_name":"Kostiantyn"},{"orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"page":"4018-4029","date_updated":"2026-04-03T09:32:00Z","related_material":{"record":[{"relation":"earlier_version","id":"8287","status":"public"}]},"language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this article, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks."}],"type":"journal_article","citation":{"short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 4018–4029.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11. IEEE, pp. 4018–4029, 2020.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., &#38; Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE. <a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">https://doi.org/10.1109/TCAD.2020.3012859</a>","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. 2020;39(11):4018-4029. doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">10.1109/TCAD.2020.3012859</a>","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11, IEEE, 2020, pp. 4018–29, doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">10.1109/TCAD.2020.3012859</a>.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 4018–4029.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">https://doi.org/10.1109/TCAD.2020.3012859</a>."},"quality_controlled":"1","volume":39,"department":[{"_id":"ToHe"}],"OA_type":"hybrid","publisher":"IEEE","main_file_link":[{"url":"https://arxiv.org/abs/1905.02458","open_access":"1"}],"publication_status":"published","date_created":"2020-11-22T23:01:25Z","external_id":{"arxiv":["1905.02458"],"isi":["000587712700072"]},"_id":"8790","month":"11","issue":"11","scopus_import":"1"},{"publisher":"The Royal Society","volume":375,"OA_type":"closed access","department":[{"_id":"NiBa"}],"citation":{"short":"H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0544\">10.1098/rstb.2019.0544</a>.","chicago":"Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0544\">https://doi.org/10.1098/rstb.2019.0544</a>.","ista":"Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544.","ieee":"H. Shang <i>et al.</i>, “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806. The Royal Society, 2020.","ama":"Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. <i>Philosophical Transactions of the Royal Society Series B: Biological Sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0544\">10.1098/rstb.2019.0544</a>","apa":"Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., &#38; Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0544\">https://doi.org/10.1098/rstb.2019.0544</a>"},"type":"journal_article","pmid":1,"abstract":[{"text":"Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.","lang":"eng"}],"quality_controlled":"1","month":"07","issue":"1806","scopus_import":"1","_id":"8169","external_id":{"pmid":["32654641"],"isi":["000552662100013"]},"publication_status":"published","date_created":"2020-07-26T22:01:02Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","article_number":"20190544","acknowledgement":"This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions.","publication_identifier":{"eissn":["1471-2970"]},"article_type":"original","year":"2020","day":"12","doi":"10.1098/rstb.2019.0544","date_published":"2020-07-12T00:00:00Z","intvolume":"       375","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group","author":[{"first_name":"Huiying","last_name":"Shang","full_name":"Shang, Huiying"},{"full_name":"Hess, Jaqueline","last_name":"Hess","first_name":"Jaqueline"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541"},{"first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","last_name":"Field"},{"first_name":"Pär K.","full_name":"Ingvarsson, Pär K.","last_name":"Ingvarsson"},{"last_name":"Liu","full_name":"Liu, Jianquan","first_name":"Jianquan"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"}],"date_updated":"2026-04-03T09:31:37Z","oa_version":"None"},{"acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411, the Australian Research Council Discovery Grants DP160101236 and DP150100618, and the European Research Council Consolidator Grant 863818 (FoRM-SMArt).\r\nAuthors would like to thank Patrick McKinlay for his work on the preliminary results for this paper.","year":"2020","publication_identifier":{"eissn":["2227-7390"]},"article_type":"original","ec_funded":1,"article_number":"1945","date_published":"2020-11-04T00:00:00Z","intvolume":"         8","oa":1,"file":[{"date_created":"2020-11-23T13:06:30Z","success":1,"file_name":"2020_Mathematics_Kleshnina.pdf","file_size":565191,"creator":"dernst","access_level":"open_access","file_id":"8797","date_updated":"2020-11-23T13:06:30Z","relation":"main_file","checksum":"61cfcc3b35760656ce7a9385a4ace5d2","content_type":"application/pdf"}],"doi":"10.3390/math8111945","day":"04","ddc":["000"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"isi":1,"publication":"Mathematics","oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-11-23T13:06:30Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2026-04-07T08:37:03Z","title":"Prioritised learning in snowdrift-type games","author":[{"full_name":"Kleshnina, Maria","last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5518-8317","first_name":"Maria"},{"first_name":"Sabrina","last_name":"Streipert","full_name":"Streipert, Sabrina"},{"full_name":"Filar, Jerzy","last_name":"Filar","first_name":"Jerzy"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","citation":{"short":"M. Kleshnina, S. Streipert, J. Filar, K. Chatterjee, Mathematics 8 (2020).","apa":"Kleshnina, M., Streipert, S., Filar, J., &#38; Chatterjee, K. (2020). Prioritised learning in snowdrift-type games. <i>Mathematics</i>. MDPI. <a href=\"https://doi.org/10.3390/math8111945\">https://doi.org/10.3390/math8111945</a>","ama":"Kleshnina M, Streipert S, Filar J, Chatterjee K. Prioritised learning in snowdrift-type games. <i>Mathematics</i>. 2020;8(11). doi:<a href=\"https://doi.org/10.3390/math8111945\">10.3390/math8111945</a>","ieee":"M. Kleshnina, S. Streipert, J. Filar, and K. Chatterjee, “Prioritised learning in snowdrift-type games,” <i>Mathematics</i>, vol. 8, no. 11. MDPI, 2020.","mla":"Kleshnina, Maria, et al. “Prioritised Learning in Snowdrift-Type Games.” <i>Mathematics</i>, vol. 8, no. 11, 1945, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/math8111945\">10.3390/math8111945</a>.","ista":"Kleshnina M, Streipert S, Filar J, Chatterjee K. 2020. Prioritised learning in snowdrift-type games. Mathematics. 8(11), 1945.","chicago":"Kleshnina, Maria, Sabrina Streipert, Jerzy Filar, and Krishnendu Chatterjee. “Prioritised Learning in Snowdrift-Type Games.” <i>Mathematics</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/math8111945\">https://doi.org/10.3390/math8111945</a>."},"abstract":[{"text":"Cooperation is a ubiquitous and beneficial behavioural trait despite being prone to exploitation by free-riders. Hence, cooperative populations are prone to invasions by selfish individuals. However, a population consisting of only free-riders typically does not survive. Thus, cooperators and free-riders often coexist in some proportion. An evolutionary version of a Snowdrift Game proved its efficiency in analysing this phenomenon. However, what if the system has already reached its stable state but was perturbed due to a change in environmental conditions? Then, individuals may have to re-learn their effective strategies. To address this, we consider behavioural mistakes in strategic choice execution, which we refer to as incompetence. Parametrising the propensity to make such mistakes allows for a mathematical description of learning. We compare strategies based on their relative strategic advantage relying on both fitness and learning factors. When strategies are learned at distinct rates, allowing learning according to a prescribed order is optimal. Interestingly, the strategy with the lowest strategic advantage should be learnt first if we are to optimise fitness over the learning path. Then, the differences between strategies are balanced out in order to minimise the effect of behavioural uncertainty.","lang":"eng"}],"type":"journal_article","corr_author":"1","publisher":"MDPI","department":[{"_id":"KrCh"}],"volume":8,"external_id":{"isi":["000593962100001"]},"date_created":"2020-11-22T23:01:24Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","scopus_import":"1","issue":"11","month":"11","_id":"8789"},{"article_number":"61106","acknowledgement":"We thank Michele Nardin and Federico Stella for comments on an earlier version of the manuscript. K Deisseroth for providing the pAAV-CaMKIIα::eNpHR3.0-YFP plasmid through Addgene. E Boyden for providing AAV2/1.CaMKII::ArchT.GFP.WPRE.SV40 plasmid through Penn Vector Core. This work was supported by the Austrian Science Fund (I02072 and I03713) and a Swiss National Science Foundation grant to PS. The authors declare no conflicts of interest.","article_type":"original","year":"2020","publication_identifier":{"eissn":["2050-084X"]},"oa":1,"file":[{"access_level":"open_access","file_size":447669,"creator":"dernst","success":1,"date_created":"2020-11-09T09:17:40Z","file_name":"2020_eLife_Gridchyn.pdf","relation":"main_file","content_type":"application/pdf","checksum":"6a7b0543c440f4c000a1864e69377d95","file_id":"8749","date_updated":"2020-11-09T09:17:40Z"}],"day":"05","doi":"10.7554/eLife.61106","date_published":"2020-10-05T00:00:00Z","intvolume":"         9","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","project":[{"call_identifier":"FWF","grant_number":"I2072-B27","_id":"257D4372-B435-11E9-9278-68D0E5697425","name":"Interneuron plasticity during spatial learning"},{"grant_number":"I 3713-B27","_id":"2654F984-B435-11E9-9278-68D0E5697425","name":"Interneuro plasticity during spatial learning","call_identifier":"FWF"}],"ddc":["570"],"isi":1,"publication":"eLife","oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-11-09T09:17:40Z","author":[{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn","full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","first_name":"Igor"},{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp","last_name":"Schönenberger","first_name":"Philipp"},{"last_name":"O'Neill","full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"title":"Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior","related_material":{"record":[{"status":"public","relation":"research_data","id":"8563"}]},"date_updated":"2026-04-07T08:37:11Z","citation":{"short":"I. Gridchyn, P. Schönenberger, J. O’Neill, J.L. Csicsvari, ELife 9 (2020).","ama":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.61106\">10.7554/eLife.61106</a>","ieee":"I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","apa":"Gridchyn, I., Schönenberger, P., O’Neill, J., &#38; Csicsvari, J. L. (2020). Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.61106\">https://doi.org/10.7554/eLife.61106</a>","mla":"Gridchyn, Igor, et al. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” <i>ELife</i>, vol. 9, 61106, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.61106\">10.7554/eLife.61106</a>.","chicago":"Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.61106\">https://doi.org/10.7554/eLife.61106</a>.","ista":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. eLife. 9, 61106."},"type":"journal_article","pmid":1,"abstract":[{"text":"In vitro work revealed that excitatory synaptic inputs to hippocampal inhibitory interneurons could undergo Hebbian, associative, or non-associative plasticity. Both behavioral and learning-dependent reorganization of these connections has also been demonstrated by measuring spike transmission probabilities in pyramidal cell-interneuron spike cross-correlations that indicate monosynaptic connections. Here we investigated the activity-dependent modification of these connections during exploratory behavior in rats by optogenetically inhibiting pyramidal cell and interneuron subpopulations. Light application and associated firing alteration of pyramidal and interneuron populations led to lasting changes in pyramidal-interneuron connection weights as indicated by spike transmission changes. Spike transmission alterations were predicted by the light-mediated changes in the number of pre- and postsynaptic spike pairing events and by firing rate changes of interneurons but not pyramidal cells. This work demonstrates the presence of activity-dependent associative and non-associative reorganization of pyramidal-interneuron connections triggered by the optogenetic modification of the firing rate and spike synchrony of cells.","lang":"eng"}],"quality_controlled":"1","publisher":"eLife Sciences Publications","corr_author":"1","volume":9,"department":[{"_id":"JoCs"}],"external_id":{"pmid":["33016875"],"isi":["000584369000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2020-11-08T23:01:25Z","month":"10","scopus_import":"1","_id":"8740"},{"_id":"8563","contributor":[{"first_name":"Jozsef L","contributor_type":"project_leader","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"}],"related_material":{"record":[{"status":"public","id":"8740","relation":"used_in_publication"}]},"date_updated":"2026-04-07T08:37:11Z","title":"Optogenetic alteration of hippocampal network activity","author":[{"first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"},{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","full_name":"Gridchyn, Igor","last_name":"Gridchyn","orcid":"0000-0002-1807-1929","first_name":"Igor"},{"last_name":"Schönenberger","full_name":"Schönenberger, Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"}],"file_date_updated":"2020-10-19T10:12:29Z","has_accepted_license":"1","article_processing_charge":"No","month":"10","status":"public","date_created":"2020-09-23T14:39:54Z","oa_version":"Published Version","tmp":{"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)","image":"/images/cc_by_nc_nd.png"},"department":[{"_id":"JoCs"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","publisher":"Institute of Science and Technology Austria","date_published":"2020-10-19T00:00:00Z","abstract":[{"text":"Supplementary data  provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife.","lang":"eng"}],"type":"research_data","day":"19","doi":"10.15479/AT:ISTA:8563","citation":{"short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>.","chicago":"Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">https://doi.org/10.15479/AT:ISTA:8563</a>.","mla":"Csicsvari, Jozsef L., et al. <i>Optogenetic Alteration of Hippocampal Network Activity</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>.","apa":"Csicsvari, J. L., Gridchyn, I., &#38; Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">https://doi.org/10.15479/AT:ISTA:8563</a>","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020."},"file":[{"access_level":"open_access","file_size":145243906,"creator":"jozsef","date_created":"2020-09-23T14:36:17Z","success":1,"file_name":"upload.tgz","relation":"main_file","content_type":"application/x-compressed","checksum":"a16098a6d172f9c42ab5af5f6991668c","file_id":"8564","date_updated":"2020-09-23T14:36:17Z"},{"date_created":"2020-10-19T10:12:29Z","file_name":"redme.docx","success":1,"file_size":11648,"creator":"jozsef","access_level":"open_access","file_id":"8675","date_updated":"2020-10-19T10:12:29Z","relation":"main_file","checksum":"0bfc54b7e14c0694cd081617318ba606","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"oa":1,"year":"2020"},{"department":[{"_id":"BjHo"}],"volume":30,"main_file_link":[{"url":"https://doi.org/10.1063/1.5122969","open_access":"1"}],"publisher":"AIP Publishing","corr_author":"1","quality_controlled":"1","citation":{"short":"G. Yalniz, N.B. Budanur, Chaos 30 (2020).","ieee":"G. Yalniz and N. B. Budanur, “Inferring symbolic dynamics of chaotic flows from persistence,” <i>Chaos</i>, vol. 30, no. 3. AIP Publishing, 2020.","apa":"Yalniz, G., &#38; Budanur, N. B. (2020). Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>","ama":"Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. 2020;30(3). doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>","mla":"Yalniz, Gökhan, and Nazmi B. Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>, vol. 30, no. 3, 033109, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>.","ista":"Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 30(3), 033109.","chicago":"Yalniz, Gökhan, and Nazmi B Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>."},"abstract":[{"text":"We introduce “state space persistence analysis” for deducing the symbolic dynamics of time series data obtained from high-dimensional chaotic attractors. To this end, we adapt a topological data analysis technique known as persistent homology for the characterization of state space projections of chaotic trajectories and periodic orbits. By comparing the shapes along a chaotic trajectory to those of the periodic orbits, state space persistence analysis quantifies the shape similarity of chaotic trajectory segments and periodic orbits. We demonstrate the method by applying it to the three-dimensional Rössler system and a 30-dimensional discretization of the Kuramoto–Sivashinsky partial differential equation in (1+1) dimensions.\r\nOne way of studying chaotic attractors systematically is through their symbolic dynamics, in which one partitions the state space into qualitatively different regions and assigns a symbol to each such region.1–3 This yields a “coarse-grained” state space of the system, which can then be reduced to a Markov chain encoding all possible transitions between the states of the system. While it is possible to obtain the symbolic dynamics of low-dimensional chaotic systems with standard tools such as Poincaré maps, when applied to high-dimensional systems such as turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5 In this paper, we develop “state space persistence analysis” and demonstrate that it can be utilized to infer the symbolic dynamics in very high-dimensional settings.","lang":"eng"}],"type":"journal_article","_id":"7563","issue":"3","scopus_import":"1","month":"03","date_created":"2020-03-04T08:06:25Z","publication_status":"published","external_id":{"arxiv":["1910.04584"],"isi":["000519254800002"]},"isi":1,"arxiv":1,"publication":"Chaos","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-03-03T00:00:00Z","intvolume":"        30","oa":1,"day":"03","doi":"10.1063/1.5122969","year":"2020","publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"article_type":"original","article_number":"033109","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19684"}]},"date_updated":"2026-04-07T11:47:05Z","title":"Inferring symbolic dynamics of chaotic flows from persistence","author":[{"full_name":"Yalniz, Gökhan","last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312","first_name":"Gökhan"},{"first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","last_name":"Budanur"}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","call_identifier":"FWF"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020"}],"isi":1,"arxiv":1,"publication":"Physical Review B","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"article_type":"original","year":"2020","ec_funded":1,"article_number":"184104 ","date_published":"2020-05-01T00:00:00Z","intvolume":"       101","oa":1,"doi":"10.1103/PhysRevB.101.184104","day":"01","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2026-04-07T11:52:53Z","related_material":{"record":[{"relation":"dissertation_contains","id":"19048","status":"public"}]},"title":"Synthetic spin-orbit coupling mediated by a bosonic environment","author":[{"last_name":"Maslov","full_name":"Maslov, Mikhail","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4074-2570","first_name":"Mikhail"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail"},{"last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","first_name":"Enderalp"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.03092"}],"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"volume":101,"quality_controlled":"1","citation":{"ama":"Maslov M, Lemeshko M, Yakaboylu E. Synthetic spin-orbit coupling mediated by a bosonic environment. <i>Physical Review B</i>. 2020;101(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">10.1103/PhysRevB.101.184104</a>","apa":"Maslov, M., Lemeshko, M., &#38; Yakaboylu, E. (2020). Synthetic spin-orbit coupling mediated by a bosonic environment. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">https://doi.org/10.1103/PhysRevB.101.184104</a>","ieee":"M. Maslov, M. Lemeshko, and E. Yakaboylu, “Synthetic spin-orbit coupling mediated by a bosonic environment,” <i>Physical Review B</i>, vol. 101, no. 18. American Physical Society, 2020.","mla":"Maslov, Mikhail, et al. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” <i>Physical Review B</i>, vol. 101, no. 18, 184104, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">10.1103/PhysRevB.101.184104</a>.","chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Enderalp Yakaboylu. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">https://doi.org/10.1103/PhysRevB.101.184104</a>.","ista":"Maslov M, Lemeshko M, Yakaboylu E. 2020. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 101(18), 184104.","short":"M. Maslov, M. Lemeshko, E. Yakaboylu, Physical Review B 101 (2020)."},"type":"journal_article","abstract":[{"text":"We study a mobile quantum impurity, possessing internal rotational degrees of freedom, confined to a ring in the presence of a many-particle bosonic bath. By considering the recently introduced rotating polaron problem, we define the Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied by means of a variational ansatz in the truncated Fock space. The corresponding spectrum indicates that there emerges a coupling between the internal and orbital angular momenta of the impurity as a consequence of the phonon exchange. We interpret the coupling as a phonon-mediated spin-orbit coupling and quantify it by using a correlation function between the internal and the orbital angular momentum operators. The strong-coupling regime is investigated within the Pekar approach, and it is shown that the correlation function of the ground state shows a kink at a critical coupling, that is explained by a sharp transition from the noninteracting state to the states that exhibit strong interaction with the surroundings. The results might find applications in such fields as spintronics or topological insulators where spin-orbit coupling is of crucial importance.","lang":"eng"}],"scopus_import":"1","issue":"18","month":"05","_id":"7933","external_id":{"isi":["000530754700003"],"arxiv":["1912.03092"]},"date_created":"2020-06-07T22:00:52Z","publication_status":"published"},{"citation":{"short":"H. Edelsbrunner, A. Nikitenko, K. Ölsböck, P. Synak, in:, Topological Data Analysis, Springer Nature, 2020, pp. 181–218.","apa":"Edelsbrunner, H., Nikitenko, A., Ölsböck, K., &#38; Synak, P. (2020). Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. In <i>Topological Data Analysis</i> (Vol. 15, pp. 181–218). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">https://doi.org/10.1007/978-3-030-43408-3_8</a>","ama":"Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. In: <i>Topological Data Analysis</i>. Vol 15. Springer Nature; 2020:181-218. doi:<a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">10.1007/978-3-030-43408-3_8</a>","ieee":"H. Edelsbrunner, A. Nikitenko, K. Ölsböck, and P. Synak, “Radius functions on Poisson–Delaunay mosaics and related complexes experimentally,” in <i>Topological Data Analysis</i>, 2020, vol. 15, pp. 181–218.","mla":"Edelsbrunner, Herbert, et al. “Radius Functions on Poisson–Delaunay Mosaics and Related Complexes Experimentally.” <i>Topological Data Analysis</i>, vol. 15, Springer Nature, 2020, pp. 181–218, doi:<a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">10.1007/978-3-030-43408-3_8</a>.","ista":"Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. 2020. Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. Topological Data Analysis. , Abel Symposia, vol. 15, 181–218.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, Katharina Ölsböck, and Peter Synak. “Radius Functions on Poisson–Delaunay Mosaics and Related Complexes Experimentally.” In <i>Topological Data Analysis</i>, 15:181–218. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">https://doi.org/10.1007/978-3-030-43408-3_8</a>."},"abstract":[{"text":"Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics.","lang":"eng"}],"type":"conference","quality_controlled":"1","volume":15,"department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","date_created":"2020-07-19T22:00:59Z","alternative_title":["Abel Symposia"],"external_id":{"isi":["001321861000008"]},"_id":"8135","month":"06","scopus_import":"1","file":[{"date_created":"2020-10-08T08:56:14Z","file_name":"2020-B-01-PoissonExperimentalSurvey.pdf","success":1,"creator":"dernst","file_size":2207071,"access_level":"open_access","date_updated":"2020-10-08T08:56:14Z","file_id":"8628","content_type":"application/pdf","checksum":"7b5e0de10675d787a2ddb2091370b8d8","relation":"main_file"}],"oa":1,"day":"22","doi":"10.1007/978-3-030-43408-3_8","date_published":"2020-06-22T00:00:00Z","intvolume":"        15","year":"2020","publication_identifier":{"isbn":["9783030434076"],"eissn":["2197-8549"],"issn":["2193-2808"]},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 78818 Alpha and No 638176). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","ec_funded":1,"isi":1,"publication":"Topological Data Analysis","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"ddc":["510"],"oa_version":"Submitted Version","title":"Radius functions on Poisson–Delaunay mosaics and related complexes experimentally","author":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anton","orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4672-8297","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","last_name":"Ölsböck","full_name":"Ölsböck, Katharina","first_name":"Katharina"},{"first_name":"Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87","full_name":"Synak, Peter","last_name":"Synak"}],"page":"181-218","date_updated":"2026-04-07T12:35:47Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19630"}]},"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-10-08T08:56:14Z"},{"month":"08","scopus_import":"1","issue":"6","_id":"8308","external_id":{"arxiv":["2005.02999"],"isi":["000562628300001"]},"publication_status":"published","date_created":"2020-08-26T19:27:42Z","publisher":"American Physical Society","corr_author":"1","volume":102,"department":[{"_id":"MaSe"}],"OA_type":"green","citation":{"short":"P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020).","chicago":"Brighi, Pietro, Dmitry A. Abanin, and Maksym Serbyn. “Stability of Mobility Edges in Disordered Interacting Systems.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.060202\">https://doi.org/10.1103/physrevb.102.060202</a>.","ista":"Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered interacting systems. Physical Review B. 102(6), 060202(R).","mla":"Brighi, Pietro, et al. “Stability of Mobility Edges in Disordered Interacting Systems.” <i>Physical Review B</i>, vol. 102, no. 6, 060202(R), American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.060202\">10.1103/physrevb.102.060202</a>.","ama":"Brighi P, Abanin DA, Serbyn M. Stability of mobility edges in disordered interacting systems. <i>Physical Review B</i>. 2020;102(6). doi:<a href=\"https://doi.org/10.1103/physrevb.102.060202\">10.1103/physrevb.102.060202</a>","ieee":"P. Brighi, D. A. Abanin, and M. Serbyn, “Stability of mobility edges in disordered interacting systems,” <i>Physical Review B</i>, vol. 102, no. 6. American Physical Society, 2020.","apa":"Brighi, P., Abanin, D. A., &#38; Serbyn, M. (2020). Stability of mobility edges in disordered interacting systems. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.060202\">https://doi.org/10.1103/physrevb.102.060202</a>"},"abstract":[{"text":"Many-body localization provides a mechanism to avoid thermalization in isolated interacting quantum systems. The breakdown of thermalization may be complete, when all eigenstates in the many-body spectrum become localized, or partial, when the so-called many-body mobility edge separates localized and delocalized parts of the spectrum. Previously, De Roeck et al. [Phys. Rev. B 93, 014203 (2016)] suggested a possible instability of the many-body mobility edge in energy density. The local ergodic regions—so-called “bubbles”—resonantly spread throughout the system, leading to delocalization. In order to study such instability mechanism, in this work we design a model featuring many-body mobility edge in particle density: the states at small particle density are localized, while increasing the density of particles leads to delocalization. Using numerical simulations with matrix product states, we demonstrate the stability of many-body localization with respect to small bubbles in large dilute systems for experimentally relevant timescales. In addition, we demonstrate that processes where the bubble spreads are favored over processes that lead to resonant tunneling, suggesting a possible mechanism behind the observed stability of many-body mobility edge. We conclude by proposing experiments to probe particle density mobility edge in the Bose-Hubbard model.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-08-26T19:29:00Z","author":[{"first_name":"Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","full_name":"Brighi, Pietro"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A.","first_name":"Dmitry A."},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"title":"Stability of mobility edges in disordered interacting systems","related_material":{"record":[{"status":"public","id":"12732","relation":"dissertation_contains"}]},"date_updated":"2026-04-07T13:26:31Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"ddc":["530"],"OA_place":"repository","isi":1,"publication":"Physical Review B","arxiv":1,"article_number":"060202(R)","article_type":"original","acknowledgement":"Acknowledgments. We acknowledge useful discussions with W. De Roeck and A. Michailidis. P.B. was supported by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 665385. D.A. was supported by the Swiss National Science Foundation. M.S. was supported by European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). This work benefited from visits to KITP, supported by the National Science Foundation under Grant No. NSF PHY-1748958 and from the program “Thermalization, Many Body Localization and Hydrodynamics” at International Centre for Theoretical Sciences (Code: ICTS/hydrodynamics2019/11).","year":"2020","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"ec_funded":1,"oa":1,"file":[{"date_updated":"2020-08-26T19:28:55Z","file_id":"8309","content_type":"application/pdf","checksum":"716442fa7861323fcc80b93718ca009c","relation":"main_file","creator":"mserbyn","file_size":488825,"file_name":"PhysRevB.102.060202.pdf","date_created":"2020-08-26T19:28:55Z","success":1,"access_level":"open_access"},{"file_size":711405,"creator":"mserbyn","date_created":"2020-08-26T19:29:00Z","file_name":"Supplementary-mbme.pdf","success":1,"access_level":"open_access","file_id":"8310","date_updated":"2020-08-26T19:29:00Z","relation":"main_file","content_type":"application/pdf","checksum":"be0abdc8f60fe065ea6dc92e08487122"}],"doi":"10.1103/physrevb.102.060202","day":"26","date_published":"2020-08-26T00:00:00Z","intvolume":"       102"},{"year":"2020","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_type":"original","ec_funded":1,"date_published":"2020-05-26T00:00:00Z","intvolume":"       117","oa":1,"day":"26","doi":"10.1073/pnas.1913716117","project":[{"grant_number":"I04188","name":"Instabilities in pulsating pipe flow in complex fluids","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","arxiv":1,"oa_version":"Preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","related_material":{"link":[{"url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"12726","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"14530"}]},"page":"11233-11239","date_updated":"2026-04-07T13:29:13Z","author":[{"first_name":"Duo","last_name":"Xu","full_name":"Xu, Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul","last_name":"Varshney"},{"orcid":"0000-0002-0179-9737","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87","last_name":"Ma","full_name":"Ma, Xingyu","first_name":"Xingyu"},{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"first_name":"Michael","full_name":"Riedl, Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","quality_controlled":"1","citation":{"short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239.","ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(21):11233-11239. doi:<a href=\"https://doi.org/10.1073/pnas.1913716117\">10.1073/pnas.1913716117</a>","apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., &#38; Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. <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.1913716117\">https://doi.org/10.1073/pnas.1913716117</a>","ieee":"D. Xu <i>et al.</i>, “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020.","chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” <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.1913716117\">https://doi.org/10.1073/pnas.1913716117</a>.","ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239.","mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:<a href=\"https://doi.org/10.1073/pnas.1913716117\">10.1073/pnas.1913716117</a>."},"abstract":[{"text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer.","lang":"eng"}],"pmid":1,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.11190"}],"publisher":"National Academy of Sciences","department":[{"_id":"BjHo"}],"volume":117,"external_id":{"arxiv":["2005.11190"],"isi":["000536797100014"],"pmid":["32393637"]},"date_created":"2020-06-07T22:00:51Z","publication_status":"published","scopus_import":"1","issue":"21","month":"05","_id":"7932"},{"citation":{"short":"K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025.","mla":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” <i>Annales Henri Poincare</i>, vol. 21, no. 12, Springer Nature, 2020, pp. 4003–25, doi:<a href=\"https://doi.org/10.1007/s00023-020-00969-3\">10.1007/s00023-020-00969-3</a>.","chicago":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” <i>Annales Henri Poincare</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00023-020-00969-3\">https://doi.org/10.1007/s00023-020-00969-3</a>.","ista":"Mysliwy K, Seiringer R. 2020. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 21(12), 4003–4025.","apa":"Mysliwy, K., &#38; Seiringer, R. (2020). Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-020-00969-3\">https://doi.org/10.1007/s00023-020-00969-3</a>","ieee":"K. Mysliwy and R. Seiringer, “Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit,” <i>Annales Henri Poincare</i>, vol. 21, no. 12. Springer Nature, pp. 4003–4025, 2020.","ama":"Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. <i>Annales Henri Poincare</i>. 2020;21(12):4003-4025. doi:<a href=\"https://doi.org/10.1007/s00023-020-00969-3\">10.1007/s00023-020-00969-3</a>"},"abstract":[{"text":"We consider the quantum mechanical many-body problem of a single impurity particle immersed in a weakly interacting Bose gas. The impurity interacts with the bosons via a two-body potential. We study the Hamiltonian of this system in the mean-field limit and rigorously show that, at low energies, the problem is well described by the Fröhlich polaron model.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Springer Nature","corr_author":"1","volume":21,"department":[{"_id":"RoSe"}],"external_id":{"arxiv":["2003.12371"],"isi":["000578111800002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2020-10-25T23:01:19Z","month":"12","issue":"12","scopus_import":"1","_id":"8705","year":"2020","publication_identifier":{"issn":["1424-0637"]},"article_type":"original","acknowledgement":"Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie Grant agreement No. 665386 (K.M.) is gratefully acknowledged. Funding Open access funding provided by Institute of Science and Technology (IST Austria)","ec_funded":1,"oa":1,"file":[{"date_updated":"2020-10-27T12:49:04Z","file_id":"8711","content_type":"application/pdf","checksum":"c12c9c1e6f08def245e42f3cb1d83827","relation":"main_file","success":1,"date_created":"2020-10-27T12:49:04Z","file_name":"2020_Annales_Mysliwy.pdf","creator":"cziletti","file_size":469831,"access_level":"open_access"}],"doi":"10.1007/s00023-020-00969-3","day":"01","date_published":"2020-12-01T00:00:00Z","intvolume":"        21","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"isi":1,"publication":"Annales Henri Poincare","arxiv":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2020-10-27T12:49:04Z","author":[{"first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","full_name":"Mysliwy, Krzysztof","last_name":"Mysliwy"},{"first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"title":"Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit","related_material":{"record":[{"id":"11473","relation":"dissertation_contains","status":"public"}]},"page":"4003-4025","date_updated":"2026-04-07T14:14:51Z"},{"month":"04","scopus_import":"1","issue":"4","_id":"7465","external_id":{"isi":["000520609800009"],"pmid":["32081263"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2020-02-09T23:00:50Z","publisher":"Elsevier","corr_author":"1","volume":293,"department":[{"_id":"JiFr"}],"citation":{"short":"E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020).","mla":"Mazur, Ewa, et al. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>, vol. 293, no. 4, 110414, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>.","ista":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. 2020. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 293(4), 110414.","chicago":"Mazur, Ewa, Michelle C Gallei, Maciek Adamowski, Huibin Han, Hélène S. Robert, and Jiří Friml. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>.","ama":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. 2020;293(4). doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>","ieee":"E. Mazur, M. C. Gallei, M. Adamowski, H. Han, H. S. Robert, and J. Friml, “Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis,” <i>Plant Science</i>, vol. 293, no. 4. Elsevier, 2020.","apa":"Mazur, E., Gallei, M. C., Adamowski, M., Han, H., Robert, H. S., &#38; Friml, J. (2020). Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>"},"type":"journal_article","pmid":1,"abstract":[{"lang":"eng","text":"The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization."}],"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:59Z","title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","author":[{"full_name":"Mazur, Ewa","last_name":"Mazur","first_name":"Ewa"},{"orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","full_name":"Gallei, Michelle C","first_name":"Michelle C"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","first_name":"Maciek"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin"},{"last_name":"Robert","full_name":"Robert, Hélène S.","first_name":"Hélène S."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"date_updated":"2026-04-07T14:18:57Z","related_material":{"record":[{"relation":"dissertation_contains","id":"11626","status":"public"}]},"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"ddc":["580"],"isi":1,"publication":"Plant Science","article_number":"110414","article_type":"original","year":"2020","publication_identifier":{"eissn":["1873-2259"],"issn":["0168-9452"]},"ec_funded":1,"file":[{"date_updated":"2020-07-14T12:47:59Z","file_id":"7471","content_type":"application/pdf","checksum":"f7f27c6a8fea985ceb9279be2204461c","relation":"main_file","creator":"dernst","file_size":3499069,"file_name":"2020_PlantScience_Mazur.pdf","date_created":"2020-02-10T08:59:36Z","access_level":"open_access"}],"oa":1,"day":"01","doi":"10.1016/j.plantsci.2020.110414","date_published":"2020-04-01T00:00:00Z","intvolume":"       293"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"}],"ddc":["580"],"publication":"Nature Communications","isi":1,"ec_funded":1,"acknowledgement":"We are grateful to David Nelson for providing published materials and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful discussions. The research leading to these results has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (742985). This work was also supported by the Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, the National Natural Science Foundation of China (31370309), CEITEC 2020 (LQ1601) project with financial contribution made by the Ministry of Education, Youth and Sports of the Czech Republic within special support paid from the National Program of Sustainability II funds, Australian Research Council (FT180100081), and China Postdoctoral Science Foundation (2019M660864).","article_type":"original","publication_identifier":{"issn":["2041-1723"]},"year":"2020","day":"14","doi":"10.1038/s41467-020-17252-y","oa":1,"file":[{"access_level":"open_access","file_size":1759490,"creator":"dernst","date_created":"2020-07-22T08:32:55Z","success":1,"file_name":"2020_NatureComm_Zhang.pdf","relation":"main_file","content_type":"application/pdf","file_id":"8148","date_updated":"2020-07-22T08:32:55Z"}],"intvolume":"        11","date_published":"2020-07-14T00:00:00Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2020-07-22T08:32:55Z","article_processing_charge":"No","has_accepted_license":"1","title":"Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization","author":[{"last_name":"Zhang","full_name":"Zhang, J","first_name":"J"},{"first_name":"E","last_name":"Mazur","full_name":"Mazur, E"},{"last_name":"Balla","full_name":"Balla, J","first_name":"J"},{"first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","full_name":"Gallei, Michelle C"},{"last_name":"Kalousek","full_name":"Kalousek, P","first_name":"P"},{"last_name":"Medveďová","full_name":"Medveďová, Z","first_name":"Z"},{"last_name":"Li","full_name":"Li, Y","first_name":"Y"},{"first_name":"Y","full_name":"Wang, Y","last_name":"Wang"},{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","full_name":"Prat, Tomas","last_name":"Prat","first_name":"Tomas"},{"last_name":"Vasileva","full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K"},{"first_name":"V","last_name":"Reinöhl","full_name":"Reinöhl, V"},{"full_name":"Procházka, S","last_name":"Procházka","first_name":"S"},{"last_name":"Halouzka","full_name":"Halouzka, R","first_name":"R"},{"last_name":"Tarkowski","full_name":"Tarkowski, P","first_name":"P"},{"full_name":"Luschnig, C","last_name":"Luschnig","first_name":"C"},{"first_name":"PB","last_name":"Brewer","full_name":"Brewer, PB"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"date_updated":"2026-04-07T14:18:57Z","related_material":{"record":[{"relation":"dissertation_contains","id":"11626","status":"public"}]},"page":"3508","oa_version":"Published Version","corr_author":"1","publisher":"Springer Nature","volume":11,"department":[{"_id":"JiFr"}],"pmid":1,"type":"journal_article","abstract":[{"lang":"eng","text":"Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration."}],"citation":{"short":"J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y. Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P. Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.","apa":"Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z., … Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17252-y\">https://doi.org/10.1038/s41467-020-17252-y</a>","ieee":"J. Zhang <i>et al.</i>, “Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization,” <i>Nature Communications</i>, vol. 11, no. 1. Springer Nature, p. 3508, 2020.","ama":"Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. <i>Nature Communications</i>. 2020;11(1):3508. doi:<a href=\"https://doi.org/10.1038/s41467-020-17252-y\">10.1038/s41467-020-17252-y</a>","mla":"Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” <i>Nature Communications</i>, vol. 11, no. 1, Springer Nature, 2020, p. 3508, doi:<a href=\"https://doi.org/10.1038/s41467-020-17252-y\">10.1038/s41467-020-17252-y</a>.","ista":"Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 11(1), 3508.","chicago":"Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová, Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17252-y\">https://doi.org/10.1038/s41467-020-17252-y</a>."},"quality_controlled":"1","month":"07","scopus_import":"1","issue":"1","_id":"8138","external_id":{"pmid":["32665554"],"isi":["000550062200004"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2020-07-21T08:58:07Z"},{"_id":"7142","month":"02","issue":"2","scopus_import":"1","publication_status":"published","date_created":"2019-12-02T12:05:26Z","external_id":{"isi":["000521120600007"],"pmid":["31760231"]},"volume":53,"department":[{"_id":"JiFr"}],"corr_author":"1","publisher":"Elsevier","citation":{"ama":"Gallei MC, Luschnig C, Friml J. Auxin signalling in growth: Schrödinger’s cat out of the bag. <i>Current Opinion in Plant Biology</i>. 2020;53(2):43-49. doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.10.003\">10.1016/j.pbi.2019.10.003</a>","apa":"Gallei, M. C., Luschnig, C., &#38; Friml, J. (2020). Auxin signalling in growth: Schrödinger’s cat out of the bag. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2019.10.003\">https://doi.org/10.1016/j.pbi.2019.10.003</a>","ieee":"M. C. Gallei, C. Luschnig, and J. Friml, “Auxin signalling in growth: Schrödinger’s cat out of the bag,” <i>Current Opinion in Plant Biology</i>, vol. 53, no. 2. Elsevier, pp. 43–49, 2020.","mla":"Gallei, Michelle C., et al. “Auxin Signalling in Growth: Schrödinger’s Cat out of the Bag.” <i>Current Opinion in Plant Biology</i>, vol. 53, no. 2, Elsevier, 2020, pp. 43–49, doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.10.003\">10.1016/j.pbi.2019.10.003</a>.","ista":"Gallei MC, Luschnig C, Friml J. 2020. Auxin signalling in growth: Schrödinger’s cat out of the bag. Current Opinion in Plant Biology. 53(2), 43–49.","chicago":"Gallei, Michelle C, Christian Luschnig, and Jiří Friml. “Auxin Signalling in Growth: Schrödinger’s Cat out of the Bag.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.pbi.2019.10.003\">https://doi.org/10.1016/j.pbi.2019.10.003</a>.","short":"M.C. Gallei, C. Luschnig, J. Friml, Current Opinion in Plant Biology 53 (2020) 43–49."},"type":"journal_article","pmid":1,"abstract":[{"text":"The phytohormone auxin acts as an amazingly versatile coordinator of plant growth and development. With its morphogen-like properties, auxin controls sites and timing of differentiation and/or growth responses both, in quantitative and qualitative terms. Specificity in the auxin response depends largely on distinct modes of signal transmission, by which individual cells perceive and convert auxin signals into a remarkable diversity of responses. The best understood, or so-called canonical mechanism of auxin perception ultimately results in variable adjustments of the cellular transcriptome, via a short, nuclear signal transduction pathway. Additional findings that accumulated over decades implied that an additional, presumably, cell surface-based auxin perception mechanism mediates very rapid cellular responses and decisively contributes to the cell's overall hormonal response. Recent investigations into both, nuclear and cell surface auxin signalling challenged this assumed partition of roles for different auxin signalling pathways and revealed an unexpected complexity in transcriptional and non-transcriptional cellular responses mediated by auxin.","lang":"eng"}],"quality_controlled":"1","author":[{"first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","full_name":"Gallei, Michelle C"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Auxin signalling in growth: Schrödinger's cat out of the bag","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"}]},"page":"43-49","date_updated":"2026-04-07T14:18:57Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"None","isi":1,"publication":"Current Opinion in Plant Biology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"}],"day":"01","doi":"10.1016/j.pbi.2019.10.003","date_published":"2020-02-01T00:00:00Z","intvolume":"        53","year":"2020","article_type":"original","publication_identifier":{"issn":["1369-5266"],"eissn":["1879-0356"]},"acknowledgement":"Research in J.F. laboratory is funded by the European Union's Horizon 2020 program (ERC grant agreement n° 742985); C.L. is supported by the Austrian Science Fund (FWF grant P 31493).","ec_funded":1}]