[{"title":"Persistent homology as a new method of the assessment of heart rate variability","_id":"9821","issue":"7","year":"2021","oa_version":"Published Version","pmid":1,"month":"07","article_processing_charge":"Yes","ddc":["006"],"acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","date_published":"2021-07-01T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode."}],"status":"public","isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_updated":"2021-08-09T09:25:41Z","file_name":"2021_PLoSONE_Graff.pdf","checksum":"0277aa155d5db1febd2cb384768bba5f","success":1,"relation":"main_file","file_size":2706919,"file_id":"9832","access_level":"open_access","date_created":"2021-08-09T09:25:41Z","creator":"asandaue","content_type":"application/pdf"}],"oa":1,"publication_status":"published","article_type":"original","author":[{"last_name":"Graff","full_name":"Graff, Grzegorz","first_name":"Grzegorz"},{"full_name":"Graff, Beata","first_name":"Beata","last_name":"Graff"},{"first_name":"Pawel","full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk"},{"full_name":"Jablonski, Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","first_name":"Grzegorz","orcid":"0000-0002-3536-9866","last_name":"Jablonski"},{"last_name":"Gąsecki","full_name":"Gąsecki, Dariusz","first_name":"Dariusz"},{"full_name":"Narkiewicz, Krzysztof","first_name":"Krzysztof","last_name":"Narkiewicz"}],"doi":"10.1371/journal.pone.0253851","day":"01","publisher":"Public Library of Science","type":"journal_article","citation":{"ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., &#38; Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>","ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851.","mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021).","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>.","ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>"},"volume":16,"publication":"PLoS ONE","has_accepted_license":"1","date_updated":"2026-04-02T13:56:42Z","external_id":{"pmid":["34292957"],"isi":["000678124900050"]},"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        16","publication_identifier":{"eissn":["1932-6203"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-08-08T22:01:28Z","file_date_updated":"2021-08-09T09:25:41Z","department":[{"_id":"HeEd"}],"article_number":"e0253851"},{"scopus_import":"1","date_published":"2021-09-29T00:00:00Z","abstract":[{"text":"In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features.","lang":"eng"}],"status":"public","acknowledgement":"We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n","ddc":["570"],"arxiv":1,"article_type":"original","publication_status":"published","author":[{"first_name":"Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","full_name":"Sahu, Preeti","last_name":"Sahu"},{"first_name":"J. M.","full_name":"Schwarz, J. M.","last_name":"Schwarz"},{"last_name":"Manning","first_name":"M. Lisa","full_name":"Manning, M. Lisa"}],"file":[{"checksum":"ace603e8f0962b3ba55f23fa34f57764","success":1,"date_updated":"2021-10-28T12:06:01Z","file_name":"2021_NewJPhys_Sahu.pdf","access_level":"open_access","creator":"cziletti","date_created":"2021-10-28T12:06:01Z","content_type":"application/pdf","file_size":2215016,"relation":"main_file","file_id":"10193"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"oa":1,"year":"2021","_id":"10178","issue":"9","oa_version":"Published Version","title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","article_processing_charge":"Yes","month":"09","intvolume":"        23","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1367-2630"]},"date_updated":"2026-04-02T13:54:56Z","has_accepted_license":"1","external_id":{"isi":["000702042400001"],"arxiv":["2102.05397"]},"date_created":"2021-10-24T22:01:34Z","file_date_updated":"2021-10-28T12:06:01Z","article_number":"093043","department":[{"_id":"EdHa"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” <i>New Journal of Physics</i>, vol. 23, no. 9. IOP Publishing, 2021.","mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>.","ista":"Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043.","apa":"Sahu, P., Schwarz, J. M., &#38; Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>","ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. 2021;23(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>","chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>."},"volume":23,"publisher":"IOP Publishing","day":"29","doi":"10.1088/1367-2630/ac23f1","type":"journal_article","publication":"New Journal of Physics"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"JiFr"}],"article_number":"1141","date_created":"2021-08-15T22:01:28Z","file_date_updated":"2021-08-16T09:02:40Z","external_id":{"isi":["000690558000001"]},"has_accepted_license":"1","date_updated":"2026-04-02T13:57:06Z","publication_identifier":{"eissn":["2073-4425"]},"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        12","publication":"Genes","type":"journal_article","publisher":"MDPI","day":"27","doi":"10.3390/genes12081141","volume":12,"citation":{"short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>, vol. 12, no. 8, 1141, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>.","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","ieee":"Y. Zeng <i>et al.</i>, “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>","chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>."},"oa":1,"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"relation":"main_file","file_size":1340305,"file_id":"9919","access_level":"open_access","date_created":"2021-08-16T09:02:40Z","creator":"asandaue","content_type":"application/pdf","date_updated":"2021-08-16T09:02:40Z","file_name":"2021_Genes_Zeng.pdf","checksum":"3d99535618cf9a5b14d264408fa52e97","success":1}],"author":[{"full_name":"Zeng, Yinwei","first_name":"Yinwei","last_name":"Zeng"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","first_name":"Inge"},{"first_name":"Hoang Khai","full_name":"Trinh, Hoang Khai","last_name":"Trinh"},{"last_name":"Heugebaert","full_name":"Heugebaert, Thomas","first_name":"Thomas"},{"last_name":"Stevens","first_name":"Christian V.","full_name":"Stevens, Christian V."},{"first_name":"Irene","full_name":"Garcia-Maquilon, Irene","last_name":"Garcia-Maquilon"},{"first_name":"Pedro L.","full_name":"Rodriguez, Pedro L.","last_name":"Rodriguez"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Danny","full_name":"Geelen, Danny","last_name":"Geelen"}],"article_type":"original","publication_status":"published","ddc":["580","570"],"acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","status":"public","abstract":[{"lang":"eng","text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition."}],"scopus_import":"1","date_published":"2021-07-27T00:00:00Z","month":"07","article_processing_charge":"Yes","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","oa_version":"Published Version","issue":"8","_id":"9909","year":"2021"},{"publication":"Letters in Mathematical Physics","type":"journal_article","doi":"10.1007/s11005-021-01380-7","publisher":"Springer Nature","day":"05","volume":111,"citation":{"ama":"Mitrouskas DJ. A note on the Fröhlich dynamics in the strong coupling limit. <i>Letters in Mathematical Physics</i>. 2021;111. doi:<a href=\"https://doi.org/10.1007/s11005-021-01380-7\">10.1007/s11005-021-01380-7</a>","chicago":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11005-021-01380-7\">https://doi.org/10.1007/s11005-021-01380-7</a>.","short":"D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021).","ieee":"D. J. Mitrouskas, “A note on the Fröhlich dynamics in the strong coupling limit,” <i>Letters in Mathematical Physics</i>, vol. 111. Springer Nature, 2021.","ista":"Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 111, 45.","apa":"Mitrouskas, D. J. (2021). A note on the Fröhlich dynamics in the strong coupling limit. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-021-01380-7\">https://doi.org/10.1007/s11005-021-01380-7</a>","mla":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” <i>Letters in Mathematical Physics</i>, vol. 111, 45, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11005-021-01380-7\">10.1007/s11005-021-01380-7</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"45","department":[{"_id":"RoSe"}],"file_date_updated":"2021-04-19T10:40:01Z","date_created":"2021-04-18T22:01:41Z","external_id":{"isi":["000637359300002"]},"date_updated":"2026-04-02T13:58:00Z","has_accepted_license":"1","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"intvolume":"       111","quality_controlled":"1","language":[{"iso":"eng"}],"month":"04","article_processing_charge":"No","title":"A note on the Fröhlich dynamics in the strong coupling limit","oa_version":"Published Version","year":"2021","_id":"9333","oa":1,"file":[{"checksum":"be56c0845a43c0c5c772ee0b5053f7d7","success":1,"date_updated":"2021-04-19T10:40:01Z","file_name":"2021_LettersMathPhysics_Mitrouskas.pdf","access_level":"open_access","date_created":"2021-04-19T10:40:01Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":438084,"file_id":"9341"}],"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Mitrouskas","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"}],"publication_status":"published","article_type":"original","acknowledgement":"I thank Marcel Griesemer for many interesting discussions about the Fröhlich polaron and also for valuable comments on this manuscript. Helpful discussions with Nikolai Leopold and Robert Seiringer are also gratefully acknowledged. This work was partially supported by the Deutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral Theory and Dynamics of Quantum Systems. Open Access funding enabled and organized by Projekt DEAL.","ddc":["510"],"status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"We revise a previous result about the Fröhlich dynamics in the strong coupling limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα, where φ0 is the electron ground state of the Pekar energy functional and ξα the associated coherent state of the phonons, can be approximated by a global phase for times small compared to α2. In the present note we prove that a similar approximation holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons that is generated by an operator proportional to α−2 and quadratic in creation and annihilation operators. Our result implies that the electron ground state remains close to its initial state for times of order α2, while the phonon fluctuations around the coherent state ξα can be described by a time-dependent Bogoliubov transformation."}],"date_published":"2021-04-05T00:00:00Z"},{"author":[{"last_name":"Hankeova","full_name":"Hankeova, Simona","first_name":"Simona"},{"first_name":"Jakub","full_name":"Salplachta, Jakub","last_name":"Salplachta"},{"last_name":"Zikmund","first_name":"Tomas","full_name":"Zikmund, Tomas"},{"first_name":"Michaela","full_name":"Kavkova, Michaela","last_name":"Kavkova"},{"last_name":"Van Hul","full_name":"Van Hul, Noémi","first_name":"Noémi"},{"first_name":"Adam","full_name":"Brinek, Adam","last_name":"Brinek"},{"last_name":"Smekalova","first_name":"Veronika","full_name":"Smekalova, Veronika"},{"full_name":"Laznovsky, Jakub","first_name":"Jakub","last_name":"Laznovsky"},{"full_name":"Dawit, Feven","first_name":"Feven","last_name":"Dawit"},{"first_name":"Josef","full_name":"Jaros, Josef","last_name":"Jaros"},{"full_name":"Bryja, Vítězslav","first_name":"Vítězslav","last_name":"Bryja"},{"last_name":"Lendahl","first_name":"Urban","full_name":"Lendahl, Urban"},{"last_name":"Ellis","first_name":"Ewa","full_name":"Ellis, Ewa"},{"last_name":"Nemeth","full_name":"Nemeth, Antal","first_name":"Antal"},{"last_name":"Fischler","first_name":"Björn","full_name":"Fischler, Björn"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"full_name":"Kaiser, Jozef","first_name":"Jozef","last_name":"Kaiser"},{"first_name":"Emma Rachel","full_name":"Andersson, Emma Rachel","last_name":"Andersson"}],"article_type":"original","publication_status":"published","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"}],"oa":1,"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"checksum":"20ccf4dfe46c48cf986794c8bf4fd1cb","success":1,"date_updated":"2021-03-22T08:50:33Z","file_name":"2021_eLife_Hankeova.pdf","access_level":"open_access","date_created":"2021-03-22T08:50:33Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":9259690,"file_id":"9271"}],"status":"public","abstract":[{"lang":"eng","text":"Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models."}],"date_published":"2021-02-26T00:00:00Z","scopus_import":"1","ddc":["570"],"acknowledgement":"Work in ERA lab is supported by the Swedish Research Council, the Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated to this project. The funders have no role in the design or interpretation of the work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m Foundation Scholarship. We are grateful for support from Tornspiran foundation to NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II and CzechNanoLab Research Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged. JJ: The work was supported by the Grant Agency of Masaryk University (project no. MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise and help regarding bile duct cannulation and their laboratory hospitality. We also thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion. We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics (SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242. We thank Goncalo M Brito for all illustrations. This work was supported by the European Union (European Research Council Starting grant 851288 to E.H.).","article_processing_charge":"No","month":"02","pmid":1,"oa_version":"Published Version","_id":"9244","year":"2021","title":"DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome","department":[{"_id":"EdHa"}],"article_number":"e60916","date_created":"2021-03-14T23:01:34Z","file_date_updated":"2021-03-22T08:50:33Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        10","external_id":{"isi":["000625357100001"],"pmid":["33635272"]},"has_accepted_license":"1","date_updated":"2026-04-02T14:00:00Z","publication":"eLife","volume":10,"citation":{"chicago":"Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>.","ama":"Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>","ista":"Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 10, e60916.","mla":"Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>, vol. 10, e60916, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>.","apa":"Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek, A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>","ieee":"S. Hankeova <i>et al.</i>, “DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek, V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis, A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021)."},"ec_funded":1,"type":"journal_article","doi":"10.7554/eLife.60916","publisher":"eLife Sciences Publications","day":"26"},{"oa_version":"Published Version","year":"2021","_id":"9306","issue":"4","title":"Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation","article_processing_charge":"No","month":"03","pmid":1,"status":"public","abstract":[{"text":"Assemblies of actin and its regulators underlie the dynamic morphology of all eukaryotic cells. To understand how actin regulatory proteins work together to generate actin-rich structures such as filopodia, we analyzed the localization of diverse actin regulators within filopodia in Drosophila embryos and in a complementary in vitro system of filopodia-like structures (FLSs). We found that the composition of the regulatory protein complex where actin is incorporated (the filopodial tip complex) is remarkably heterogeneous both in vivo and in vitro. Our data reveal that different pairs of proteins correlate with each other and with actin bundle length, suggesting the presence of functional subcomplexes. This is consistent with a theoretical framework where three or more redundant subcomplexes join the tip complex stochastically, with any two being sufficient to drive filopodia formation. We provide an explanation for the observed heterogeneity and suggest that a mechanism based on multiple components allows stereotypical filopodial dynamics to arise from diverse upstream signaling pathways.","lang":"eng"}],"scopus_import":"1","date_published":"2021-03-19T00:00:00Z","acknowledgement":"This work was supported by European Research Council grant 281971, Wellcome Trust Research Career Development Fellowship WT095829AIA and Wellcome Trust Senior Research\r\nFellowship 219482/Z/19/Z to J.L. Gallop, a Wellcome Trust Senior Investigator Award 098357 to B.D. Simons, and an Austrian Science Fund grant (P31639) to E. Hannezo. We acknowledge\r\ncore funding by the Wellcome Trust (092096) and Cancer Research UK (C6946/A14492). U. Dobramysl was supported by a Wellcome Trust Junior Interdisciplinary Fellowship grant\r\n(105602/Z/14/Z) and a Herchel Smith Postdoctoral Fellowship. H. Shimo was supported by a Funai Foundation Overseas scholarship.","ddc":["576"],"author":[{"first_name":"Ulrich","full_name":"Dobramysl, Ulrich","last_name":"Dobramysl"},{"full_name":"Jarsch, Iris Katharina","first_name":"Iris Katharina","last_name":"Jarsch"},{"full_name":"Inoue, Yoshiko","first_name":"Yoshiko","last_name":"Inoue"},{"full_name":"Shimo, Hanae","first_name":"Hanae","last_name":"Shimo"},{"first_name":"Benjamin","full_name":"Richier, Benjamin","last_name":"Richier"},{"last_name":"Gadsby","first_name":"Jonathan R.","full_name":"Gadsby, Jonathan R."},{"full_name":"Mason, Julia","first_name":"Julia","last_name":"Mason"},{"last_name":"Szałapak","full_name":"Szałapak, Alicja","first_name":"Alicja"},{"last_name":"Ioannou","first_name":"Pantelis Savvas","full_name":"Ioannou, Pantelis Savvas"},{"first_name":"Guilherme Pereira","full_name":"Correia, Guilherme Pereira","last_name":"Correia"},{"last_name":"Walrant","first_name":"Astrid","full_name":"Walrant, Astrid"},{"first_name":"Richard","full_name":"Butler, Richard","last_name":"Butler"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"full_name":"Gallop, Jennifer L.","first_name":"Jennifer L.","last_name":"Gallop"}],"project":[{"call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"}],"publication_status":"published","article_type":"original","oa":1,"file":[{"file_name":"2021_JCB_Dobramysl.pdf","date_updated":"2021-04-06T10:39:08Z","checksum":"4739ffd90f2c7e05ac5b00f057c58aa2","success":1,"file_size":9019720,"relation":"main_file","file_id":"9310","creator":"dernst","date_created":"2021-04-06T10:39:08Z","access_level":"open_access","content_type":"application/pdf"}],"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":220,"citation":{"ista":"Dobramysl U, Jarsch IK, Inoue Y, Shimo H, Richier B, Gadsby JR, Mason J, Szałapak A, Ioannou PS, Correia GP, Walrant A, Butler R, Hannezo EB, Simons BD, Gallop JL. 2021. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. 220(4), e202003052.","apa":"Dobramysl, U., Jarsch, I. K., Inoue, Y., Shimo, H., Richier, B., Gadsby, J. R., … Gallop, J. L. (2021). Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202003052\">https://doi.org/10.1083/jcb.202003052</a>","mla":"Dobramysl, Ulrich, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” <i>Journal of Cell Biology</i>, vol. 220, no. 4, e202003052, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202003052\">10.1083/jcb.202003052</a>.","ieee":"U. Dobramysl <i>et al.</i>, “Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation,” <i>Journal of Cell Biology</i>, vol. 220, no. 4. Rockefeller University Press, 2021.","short":"U. Dobramysl, I.K. Jarsch, Y. Inoue, H. Shimo, B. Richier, J.R. Gadsby, J. Mason, A. Szałapak, P.S. Ioannou, G.P. Correia, A. Walrant, R. Butler, E.B. Hannezo, B.D. Simons, J.L. Gallop, Journal of Cell Biology 220 (2021).","chicago":"Dobramysl, Ulrich, Iris Katharina Jarsch, Yoshiko Inoue, Hanae Shimo, Benjamin Richier, Jonathan R. Gadsby, Julia Mason, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202003052\">https://doi.org/10.1083/jcb.202003052</a>.","ama":"Dobramysl U, Jarsch IK, Inoue Y, et al. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. <i>Journal of Cell Biology</i>. 2021;220(4). doi:<a href=\"https://doi.org/10.1083/jcb.202003052\">10.1083/jcb.202003052</a>"},"type":"journal_article","publisher":"Rockefeller University Press","day":"19","doi":"10.1083/jcb.202003052","publication":"Journal of Cell Biology","publication_identifier":{"eissn":["1540-8140"]},"intvolume":"       220","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000663160600002"],"pmid":["33740033"]},"date_updated":"2026-04-02T13:59:43Z","has_accepted_license":"1","article_number":"e202003052","department":[{"_id":"EdHa"}],"date_created":"2021-04-04T22:01:21Z","file_date_updated":"2021-04-06T10:39:08Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"oa_version":"Published Version","year":"2021","issue":"3","_id":"9205","title":"Cryo-EM grid optimization for membrane proteins","article_processing_charge":"No","month":"03","pmid":1,"status":"public","date_published":"2021-03-19T00:00:00Z","abstract":[{"lang":"eng","text":"Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins."}],"scopus_import":"1","acknowledgement":"We thank the Electron Microscopy Facilities at the Institute of Science and Technology Austria and at the Vienna Biocenter for providing access and training for the electron microscopes. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385 .","ddc":["570"],"author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen","last_name":"Kampjut","orcid":"0000-0002-6018-3422"},{"last_name":"Steiner","orcid":"0000-0003-0493-3775","first_name":"Julia","full_name":"Steiner, Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"article_type":"original","publication_status":"published","oa":1,"file":[{"date_updated":"2021-03-03T07:38:14Z","file_name":"2021_iScience_Kampjut.pdf","checksum":"50585447386fe5842f07ab9b3a66e7e9","success":1,"file_size":7431411,"relation":"main_file","file_id":"9219","access_level":"open_access","creator":"dernst","date_created":"2021-03-03T07:38:14Z","content_type":"application/pdf"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"volume":24,"citation":{"chicago":"Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>.","ama":"Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins. <i>iScience</i>. 2021;24(3). doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>","ieee":"D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for membrane proteins,” <i>iScience</i>, vol. 24, no. 3. Elsevier, 2021.","apa":"Kampjut, D., Steiner, J., &#38; Sazanov, L. A. (2021). Cryo-EM grid optimization for membrane proteins. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>","mla":"Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>, vol. 24, no. 3, 102139, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>.","ista":"Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane proteins. iScience. 24(3), 102139.","short":"D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021)."},"ec_funded":1,"type":"journal_article","doi":"10.1016/j.isci.2021.102139","day":"19","publisher":"Elsevier","publication":"iScience","publication_identifier":{"eissn":["2589-0042"]},"intvolume":"        24","language":[{"iso":"eng"}],"quality_controlled":"1","external_id":{"pmid":["33665558"],"isi":["000631646000012"]},"date_updated":"2026-04-02T14:00:19Z","has_accepted_license":"1","article_number":"102139","department":[{"_id":"LeSa"}],"date_created":"2021-02-28T23:01:24Z","file_date_updated":"2021-03-03T07:38:14Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"}},{"ddc":["530"],"acknowledgement":"G.Á.-P. and J.T.-G. acknowledge support through the Severo Ochoa Program from the government of the Principality of Asturias (grant nos. PA20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). K.V.V. and V.S.V. acknowledge the Ministry of Science and Higher Education of the Russian Federation (no. 0714-2020-0002). J. M.-S. acknowledges financial support through the Ramón y Cajal Program from the government of Spain and FSE (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT201788358-C3-3-R), and the Basque Department of Education (PIBA-2020-1-0014). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA. ","scopus_import":"1","abstract":[{"lang":"eng","text":"Polaritons with directional in-plane propagation and ultralow losses in van der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale. However, these polaritons present a crucial limitation: their directional propagation is intrinsically determined by the crystal structure of the host material, imposing forbidden directions of propagation. Here, we demonstrate that directional polaritons (in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide) can be directed along forbidden directions by inducing an optical topological transition, which emerges when the slab is placed on a substrate with a given negative permittivity (4H–silicon carbide). By visualizing the transition in real space, we observe exotic polaritonic states between mutually orthogonal hyperbolic regimes, which unveil the topological origin of the transition: a gap opening in the dispersion. This work provides insights into optical topological transitions in vdW crystals, which introduce a route to direct light at the nanoscale."}],"date_published":"2021-04-02T00:00:00Z","status":"public","isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_updated":"2021-04-19T11:17:29Z","file_name":"2021_ScienceAdv_Duan.pdf","checksum":"4b383d4a1d484a71bbc64ecf401bbdbb","success":1,"relation":"main_file","file_size":717489,"file_id":"9343","access_level":"open_access","creator":"dernst","date_created":"2021-04-19T11:17:29Z","content_type":"application/pdf"}],"oa":1,"publication_status":"published","article_type":"original","author":[{"last_name":"Duan","full_name":"Duan, J.","first_name":"J."},{"last_name":"Álvarez-Pérez","first_name":"G.","full_name":"Álvarez-Pérez, G."},{"full_name":"Voronin, K. V.","first_name":"K. V.","last_name":"Voronin"},{"orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez","first_name":"Ivan","full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"J.","full_name":"Taboada-Gutiérrez, J.","last_name":"Taboada-Gutiérrez"},{"full_name":"Volkov, V. S.","first_name":"V. S.","last_name":"Volkov"},{"full_name":"Martín-Sánchez, J.","first_name":"J.","last_name":"Martín-Sánchez"},{"last_name":"Nikitin","first_name":"A. Y.","full_name":"Nikitin, A. Y."},{"last_name":"Alonso-González","first_name":"P.","full_name":"Alonso-González, P."}],"title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","issue":"14","_id":"9334","year":"2021","oa_version":"Published Version","pmid":1,"month":"04","article_processing_charge":"No","has_accepted_license":"1","date_updated":"2026-04-02T13:58:21Z","external_id":{"pmid":["33811076"],"isi":["000636455600027"]},"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"         7","publication_identifier":{"eissn":["2375-2548"]},"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"date_created":"2021-04-18T22:01:42Z","file_date_updated":"2021-04-19T11:17:29Z","department":[{"_id":"NanoFab"}],"article_number":"eabf2690","doi":"10.1126/sciadv.abf2690","publisher":"AAAS","day":"02","type":"journal_article","citation":{"apa":"Duan, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., Taboada-Gutiérrez, J., Volkov, V. S., … Alonso-González, P. (2021). Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.abf2690\">https://doi.org/10.1126/sciadv.abf2690</a>","ista":"Duan J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Taboada-Gutiérrez J, Volkov VS, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2021. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 7(14), eabf2690.","mla":"Duan, J., et al. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” <i>Science Advances</i>, vol. 7, no. 14, eabf2690, AAAS, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abf2690\">10.1126/sciadv.abf2690</a>.","ieee":"J. Duan <i>et al.</i>, “Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition,” <i>Science Advances</i>, vol. 7, no. 14. AAAS, 2021.","short":"J. Duan, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, J. Taboada-Gutiérrez, V.S. Volkov, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","chicago":"Duan, J., G. Álvarez-Pérez, K. V. Voronin, Ivan Prieto Gonzalez, J. Taboada-Gutiérrez, V. S. Volkov, J. Martín-Sánchez, A. Y. Nikitin, and P. Alonso-González. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” <i>Science Advances</i>. AAAS, 2021. <a href=\"https://doi.org/10.1126/sciadv.abf2690\">https://doi.org/10.1126/sciadv.abf2690</a>.","ama":"Duan J, Álvarez-Pérez G, Voronin KV, et al. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. <i>Science Advances</i>. 2021;7(14). doi:<a href=\"https://doi.org/10.1126/sciadv.abf2690\">10.1126/sciadv.abf2690</a>"},"volume":7,"publication":"Science Advances"},{"citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. <i>Electronic Journal of Probability</i>. 2021;26. doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2021. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021).","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” <i>Electronic Journal of Probability</i>, vol. 26. Institute of Mathematical Statistics, 2021.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24.","mla":"Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” <i>Electronic Journal of Probability</i>, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>"},"volume":26,"publisher":"Institute of Mathematical Statistics","day":"23","doi":"10.1214/21-EJP591","type":"journal_article","ec_funded":1,"publication":"Electronic Journal of Probability","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        26","publication_identifier":{"eissn":["1083-6489"]},"has_accepted_license":"1","date_updated":"2026-04-02T14:00:37Z","external_id":{"arxiv":["2002.02438"],"isi":["000641855600001"]},"file_date_updated":"2021-05-25T13:24:19Z","date_created":"2021-05-23T22:01:44Z","department":[{"_id":"LaEr"}],"article_number":"24","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9412","year":"2021","oa_version":"Published Version","title":"Fluctuation around the circular law for random matrices with real entries","article_processing_charge":"No","month":"03","abstract":[{"lang":"eng","text":"We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness."}],"date_published":"2021-03-23T00:00:00Z","scopus_import":"1","status":"public","arxiv":1,"ddc":["510"],"publication_status":"published","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"author":[{"orcid":"0000-0002-4901-7992","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","first_name":"Giorgio"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder","orcid":"0000-0002-2904-1856"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"file":[{"date_updated":"2021-05-25T13:24:19Z","file_name":"2021_EJP_Cipolloni.pdf","success":1,"checksum":"864ab003ad4cffea783f65aa8c2ba69f","file_id":"9423","relation":"main_file","file_size":865148,"content_type":"application/pdf","access_level":"open_access","creator":"kschuh","date_created":"2021-05-25T13:24:19Z"}],"oa":1},{"publisher":"American Society for Microbiology","doi":"10.1128/mSphere.01024-20","day":"14","type":"journal_article","citation":{"apa":"Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., &#38; Plattet, P. (2021). Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>MSphere</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>","ista":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 6(2), e01024-20.","mla":"Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>.","ieee":"M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein,” <i>mSphere</i>, vol. 6, no. 2. American Society for Microbiology, 2021.","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","chicago":"Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>. American Society for Microbiology, 2021. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>.","ama":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>mSphere</i>. 2021;6(2). doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>"},"volume":6,"publication":"mSphere","date_updated":"2026-04-02T13:58:38Z","has_accepted_license":"1","external_id":{"pmid":["33853875"],"isi":["000663823400025"]},"intvolume":"         6","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["2379-5042"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-05-02T22:01:28Z","file_date_updated":"2021-05-04T12:41:38Z","article_number":"e01024-20","department":[{"_id":"Bio"}],"title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","year":"2021","issue":"2","_id":"9361","oa_version":"Published Version","pmid":1,"month":"04","article_processing_charge":"No","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","ddc":["570"],"date_published":"2021-04-14T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM."}],"status":"public","file":[{"file_size":3379349,"relation":"main_file","file_id":"9370","access_level":"open_access","date_created":"2021-05-04T12:41:38Z","creator":"kschuh","content_type":"application/pdf","date_updated":"2021-05-04T12:41:38Z","file_name":"2021_mSphere_Gast.pdf","checksum":"310748d140c8838335c1314431095898","success":1}],"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"publication_status":"published","author":[{"full_name":"Gast, Matthieu","first_name":"Matthieu","last_name":"Gast"},{"first_name":"Nicole P.","full_name":"Kadzioch, Nicole P.","last_name":"Kadzioch"},{"first_name":"Doreen","id":"384050BC-F248-11E8-B48F-1D18A9856A87","full_name":"Milius, Doreen","last_name":"Milius"},{"last_name":"Origgi","first_name":"Francesco","full_name":"Origgi, Francesco"},{"last_name":"Plattet","first_name":"Philippe","full_name":"Plattet, Philippe"}]},{"volume":16,"citation":{"short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” <i>PLoS ONE</i>, vol. 16, no. 4. Public Library of Science, 2021.","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>.","apa":"Chalk, M. J., Tkačik, G., &#38; Marre, O. (2021). Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. 2021;16(4). doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>."},"type":"journal_article","doi":"10.1371/journal.pone.0248940","publisher":"Public Library of Science","day":"15","publication":"PLoS ONE","publication_identifier":{"eissn":["1932-6203"]},"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        16","external_id":{"pmid":["33857170"],"isi":["000641474900072"]},"has_accepted_license":"1","date_updated":"2026-04-02T13:58:56Z","department":[{"_id":"GaTk"}],"article_number":"e0248940","date_created":"2021-05-02T22:01:28Z","file_date_updated":"2021-05-04T13:22:19Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","_id":"9362","issue":"4","year":"2021","title":"Inferring the function performed by a recurrent neural network","article_processing_charge":"No","month":"04","pmid":1,"status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"date_published":"2021-04-15T00:00:00Z","ddc":["570"],"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","author":[{"last_name":"Chalk","orcid":"0000-0001-7782-4436","first_name":"Matthew J","full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"}],"publication_status":"published","article_type":"original","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"file":[{"creator":"kschuh","date_created":"2021-05-04T13:22:19Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":2768282,"file_id":"9371","checksum":"c52da133850307d2031f552d998f00e8","success":1,"file_name":"2021_pone_Chalk.pdf","date_updated":"2021-05-04T13:22:19Z"}]},{"date_updated":"2026-04-02T13:59:25Z","external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"corr_author":"1","intvolume":"        31","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"date_created":"2021-05-16T22:01:46Z","department":[{"_id":"NiBa"}],"page":"R428-R429","doi":"10.1016/j.cub.2021.03.060","publisher":"Cell Press","day":"10","type":"journal_article","citation":{"ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. <i>Current Biology</i>. 2021;31(9):R428-R429. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>.","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","apa":"Stankowski, S., &#38; Ravinet, M. (2021). Quantifying the use of species concepts. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” <i>Current Biology</i>, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021."},"volume":31,"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"publication":"Current Biology","acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","abstract":[{"lang":"eng","text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not."}],"scopus_import":"1","date_published":"2021-05-10T00:00:00Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"oa":1,"article_type":"original","publication_status":"published","author":[{"last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"}],"title":"Quantifying the use of species concepts","year":"2021","_id":"9392","issue":"9","oa_version":"Published Version","pmid":1,"month":"05","article_processing_charge":"No"},{"month":"06","article_processing_charge":"Yes","title":"Morphology of three-body quantum states from machine learning","oa_version":"Published Version","year":"2021","_id":"9679","issue":"6","oa":1,"file":[{"access_level":"open_access","creator":"cziletti","date_created":"2021-07-19T11:47:16Z","content_type":"application/pdf","relation":"main_file","file_size":3868445,"file_id":"9690","checksum":"e39164ce7ea228d287cf8924e1a0f9fe","success":1,"date_updated":"2021-07-19T11:47:16Z","file_name":"2021_NewJPhys_Huber.pdf"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"author":[{"last_name":"Huber","first_name":"David","full_name":"Huber, David"},{"last_name":"Marchukov","full_name":"Marchukov, Oleksandr V.","first_name":"Oleksandr V."},{"last_name":"Hammer","full_name":"Hammer, Hans Werner","first_name":"Hans Werner"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"publication_status":"published","article_type":"original","acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","arxiv":1,"ddc":["530"],"status":"public","abstract":[{"text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.","lang":"eng"}],"scopus_import":"1","date_published":"2021-06-23T00:00:00Z","publication":"New Journal of Physics","ec_funded":1,"type":"journal_article","day":"23","publisher":"IOP Publishing","doi":"10.1088/1367-2630/ac0576","volume":23,"citation":{"ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” <i>New Journal of Physics</i>, vol. 23, no. 6. IOP Publishing, 2021.","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>.","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., &#38; Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>.","ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. 2021;23(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"065009","department":[{"_id":"MiLe"}],"file_date_updated":"2021-07-19T11:47:16Z","date_created":"2021-07-18T22:01:22Z","external_id":{"arxiv":["2102.04961"],"isi":["000664736300001"]},"date_updated":"2026-04-02T14:01:49Z","has_accepted_license":"1","publication_identifier":{"eissn":["1367-2630"]},"intvolume":"        23","quality_controlled":"1","language":[{"iso":"eng"}]},{"_id":"9410","issue":"5","year":"2021","oa_version":"Published Version","title":"Adaptation at different points along antibiotic concentration gradients","article_processing_charge":"No","pmid":1,"month":"05","date_published":"2021-05-12T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains."}],"status":"public","ddc":["570"],"acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","publication_status":"published","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"author":[{"first_name":"Mato","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator"},{"orcid":"0000-0001-9435-2813","last_name":"Uecker","first_name":"Hildegard","full_name":"Uecker, Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paul","full_name":"Neve, Paul","last_name":"Neve"}],"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_name":"2021_BiologyLetters_Lagator.pdf","date_updated":"2021-05-25T14:09:03Z","checksum":"9c13c1f5af7609c97c741f11d293188a","success":1,"relation":"main_file","file_size":726759,"file_id":"9425","creator":"kschuh","date_created":"2021-05-25T14:09:03Z","access_level":"open_access","content_type":"application/pdf"}],"oa":1,"citation":{"short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","apa":"Lagator, M., Uecker, H., &#38; Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. <i>Biology Letters</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsbl.2020.0913\">https://doi.org/10.1098/rsbl.2020.0913</a>","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” <i>Biology Letters</i>, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:<a href=\"https://doi.org/10.1098/rsbl.2020.0913\">10.1098/rsbl.2020.0913</a>.","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” <i>Biology letters</i>, vol. 17, no. 5. Royal Society of London, 2021.","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. <i>Biology letters</i>. 2021;17(5). doi:<a href=\"https://doi.org/10.1098/rsbl.2020.0913\">10.1098/rsbl.2020.0913</a>","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” <i>Biology Letters</i>. Royal Society of London, 2021. <a href=\"https://doi.org/10.1098/rsbl.2020.0913\">https://doi.org/10.1098/rsbl.2020.0913</a>."},"volume":17,"publisher":"Royal Society of London","day":"12","doi":"10.1098/rsbl.2020.0913","ec_funded":1,"type":"journal_article","publication":"Biology letters","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        17","publication_identifier":{"eissn":["1744-957X"]},"has_accepted_license":"1","date_updated":"2026-04-02T14:02:44Z","corr_author":"1","external_id":{"pmid":[" 33975485"],"isi":["000651501400001"]},"date_created":"2021-05-23T22:01:43Z","file_date_updated":"2021-05-25T14:09:03Z","department":[{"_id":"NiBa"}],"article_number":"20200913","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"title":"Edge universality for non-Hermitian random matrices","oa_version":"Published Version","_id":"8601","year":"2021","month":"02","article_processing_charge":"Yes (via OA deal)","arxiv":1,"ddc":["510"],"status":"public","scopus_import":"1","date_published":"2021-02-01T00:00:00Z","abstract":[{"text":"We consider large non-Hermitian real or complex random matrices X with independent, identically distributed centred entries. We prove that their local eigenvalue statistics near the spectral edge, the unit circle, coincide with those of the Ginibre ensemble, i.e. when the matrix elements of X are Gaussian. This result is the non-Hermitian counterpart of the universality of the Tracy–Widom distribution at the spectral edges of the Wigner ensemble.","lang":"eng"}],"oa":1,"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"checksum":"611ae28d6055e1e298d53a57beb05ef4","success":1,"file_name":"2020_ProbTheory_Cipolloni.pdf","date_updated":"2020-10-05T14:53:40Z","creator":"dernst","date_created":"2020-10-05T14:53:40Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":497032,"file_id":"8612"}],"author":[{"orcid":"0000-0002-4901-7992","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","first_name":"Giorgio"},{"orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","last_name":"Schröder","orcid":"0000-0002-2904-1856"}],"publication_status":"published","article_type":"original","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"ec_funded":1,"type":"journal_article","day":"01","publisher":"Springer Nature","doi":"10.1007/s00440-020-01003-7","citation":{"ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian random matrices,” <i>Probability Theory and Related Fields</i>. Springer Nature, 2021.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Edge universality for non-Hermitian random matrices. <i>Probability Theory and Related Fields</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00440-020-01003-7\">https://doi.org/10.1007/s00440-020-01003-7</a>","mla":"Cipolloni, Giorgio, et al. “Edge Universality for Non-Hermitian Random Matrices.” <i>Probability Theory and Related Fields</i>, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00440-020-01003-7\">10.1007/s00440-020-01003-7</a>.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2021).","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Edge Universality for Non-Hermitian Random Matrices.” <i>Probability Theory and Related Fields</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00440-020-01003-7\">https://doi.org/10.1007/s00440-020-01003-7</a>.","ama":"Cipolloni G, Erdös L, Schröder DJ. Edge universality for non-Hermitian random matrices. <i>Probability Theory and Related Fields</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s00440-020-01003-7\">10.1007/s00440-020-01003-7</a>"},"publication":"Probability Theory and Related Fields","corr_author":"1","external_id":{"arxiv":["1908.00969"],"isi":["000572724600002"]},"has_accepted_license":"1","date_updated":"2026-04-02T14:03:52Z","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"language":[{"iso":"eng"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"LaEr"}],"date_created":"2020-10-04T22:01:37Z","file_date_updated":"2020-10-05T14:53:40Z"},{"oa_version":"Published Version","_id":"9318","year":"2021","title":"Asymptotic expansion of low-energy excitations for weakly interacting bosons","article_processing_charge":"Yes (via OA deal)","month":"03","status":"public","abstract":[{"lang":"eng","text":"We consider a system of N bosons in the mean-field scaling regime for a class of interactions including the repulsive Coulomb potential. We derive an asymptotic expansion of the low-energy eigenstates and the corresponding energies, which provides corrections to Bogoliubov theory to any order in 1/N."}],"date_published":"2021-03-26T00:00:00Z","scopus_import":"1","ddc":["510"],"acknowledgement":"The first author gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411. The third author was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227).","author":[{"full_name":"Bossmann, Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","orcid":"0000-0002-6854-1343","last_name":"Bossmann"},{"orcid":"0000-0002-9166-5889","last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P","first_name":"Sören P"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"publication_status":"published","article_type":"original","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"oa":1,"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"checksum":"17a3e6786d1e930cf0c14a880a6d7e92","success":1,"file_name":"2021_ForumMath_Bossmann.pdf","date_updated":"2021-04-12T07:15:58Z","date_created":"2021-04-12T07:15:58Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":883851,"file_id":"9319"}],"volume":9,"citation":{"ama":"Bossmann L, Petrat SP, Seiringer R. Asymptotic expansion of low-energy excitations for weakly interacting bosons. <i>Forum of Mathematics, Sigma</i>. 2021;9. doi:<a href=\"https://doi.org/10.1017/fms.2021.22\">10.1017/fms.2021.22</a>","chicago":"Bossmann, Lea, Sören P Petrat, and Robert Seiringer. “Asymptotic Expansion of Low-Energy Excitations for Weakly Interacting Bosons.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/fms.2021.22\">https://doi.org/10.1017/fms.2021.22</a>.","short":"L. Bossmann, S.P. Petrat, R. Seiringer, Forum of Mathematics, Sigma 9 (2021).","ista":"Bossmann L, Petrat SP, Seiringer R. 2021. Asymptotic expansion of low-energy excitations for weakly interacting bosons. Forum of Mathematics, Sigma. 9, e28.","mla":"Bossmann, Lea, et al. “Asymptotic Expansion of Low-Energy Excitations for Weakly Interacting Bosons.” <i>Forum of Mathematics, Sigma</i>, vol. 9, e28, Cambridge University Press, 2021, doi:<a href=\"https://doi.org/10.1017/fms.2021.22\">10.1017/fms.2021.22</a>.","apa":"Bossmann, L., Petrat, S. P., &#38; Seiringer, R. (2021). Asymptotic expansion of low-energy excitations for weakly interacting bosons. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2021.22\">https://doi.org/10.1017/fms.2021.22</a>","ieee":"L. Bossmann, S. P. Petrat, and R. Seiringer, “Asymptotic expansion of low-energy excitations for weakly interacting bosons,” <i>Forum of Mathematics, Sigma</i>, vol. 9. Cambridge University Press, 2021."},"type":"journal_article","ec_funded":1,"doi":"10.1017/fms.2021.22","day":"26","publisher":"Cambridge University Press","publication":"Forum of Mathematics, Sigma","publication_identifier":{"eissn":["2050-5094"]},"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"         9","external_id":{"isi":["000634006900001"]},"has_accepted_license":"1","date_updated":"2026-04-02T14:02:29Z","department":[{"_id":"RoSe"}],"article_number":"e28","date_created":"2021-04-11T22:01:15Z","file_date_updated":"2021-04-12T07:15:58Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"main_file_link":[{"url":"https://arxiv.org/abs/2007.14879","open_access":"1"}],"publication":"Physical Review B","type":"journal_article","ec_funded":1,"day":"21","doi":"10.1103/PhysRevB.103.214204","publisher":"American Physical Society","volume":103,"citation":{"ista":"Diringer AA, Gulden T. 2021. Impact of drive harmonics on the stability of Floquet many-body localization. Physical Review B. 103(21), 214204.","mla":"Diringer, Asaf A., and Tobias Gulden. “Impact of Drive Harmonics on the Stability of Floquet Many-Body Localization.” <i>Physical Review B</i>, vol. 103, no. 21, 214204, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">10.1103/PhysRevB.103.214204</a>.","apa":"Diringer, A. A., &#38; Gulden, T. (2021). Impact of drive harmonics on the stability of Floquet many-body localization. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">https://doi.org/10.1103/PhysRevB.103.214204</a>","ieee":"A. A. Diringer and T. Gulden, “Impact of drive harmonics on the stability of Floquet many-body localization,” <i>Physical Review B</i>, vol. 103, no. 21. American Physical Society, 2021.","short":"A.A. Diringer, T. Gulden, Physical Review B 103 (2021).","chicago":"Diringer, Asaf A., and Tobias Gulden. “Impact of Drive Harmonics on the Stability of Floquet Many-Body Localization.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">https://doi.org/10.1103/PhysRevB.103.214204</a>.","ama":"Diringer AA, Gulden T. Impact of drive harmonics on the stability of Floquet many-body localization. <i>Physical Review B</i>. 2021;103(21). doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">10.1103/PhysRevB.103.214204</a>"},"department":[{"_id":"MaSe"}],"article_number":"214204","date_created":"2020-08-04T13:03:40Z","external_id":{"isi":["000664429700005"],"arxiv":["2007.14879"]},"date_updated":"2026-04-02T14:02:07Z","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       103","month":"06","article_processing_charge":"No","title":"Impact of drive harmonics on the stability of Floquet many-body localization","oa_version":"Preprint","issue":"21","_id":"8198","year":"2021","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"author":[{"last_name":"Diringer","full_name":"Diringer, Asaf A.","first_name":"Asaf A."},{"first_name":"Tobias","full_name":"Gulden, Tobias","id":"1083E038-9F73-11E9-A4B5-532AE6697425","last_name":"Gulden","orcid":"0000-0001-6814-7541"}],"article_type":"original","publication_status":"published","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"acknowledgement":"We thank Y. Bar Lev, T. Biadse, and, particularly, E. Bairey and B. Katzir for illuminating discussions and their many insights and help. The authors thank N. Lindner for his support throughout this project. We are further grateful to M. Serbyn, A. Kamenev, A. Turner, and S. de Nicola for reading the manuscript and providing good feedback and suggestions. We acknowledge financial support from the Defense Advanced Research Projects Agency through the DRINQS program, Grant No. D18AC00025. T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 research and innovation program under Marie SkłodowskaCurie Grant Agreement No. 754411.under the Marie Skłodowska-Curie Grant Agreement No.754411.","status":"public","scopus_import":"1","date_published":"2021-06-21T00:00:00Z","abstract":[{"text":"We investigate how the critical driving amplitude at the Floquet many-body localized (MBL) to ergodic phase transition differs between smooth and nonsmooth drives. To this end, we numerically study a disordered spin-1/2 chain which is periodically driven by a sine or square-wave drive over a wide range of driving frequencies. In both cases the critical driving amplitude increases monotonically with the frequency, and at large frequencies it is identical for the two drives. However, at low and intermediate frequencies the critical amplitude of the square-wave drive depends strongly on the frequency, while that of the sinusoidal drive is almost constant over a wide frequency range. By analyzing the density of drive-induced resonances we conclude that this difference is due to resonances induced by the higher harmonics which are present (absent) in the Fourier spectrum of the square-wave (sine) drive. Furthermore, we suggest a numerically efficient method for estimating the frequency dependence of the critical driving amplitudes for different drives which is based on calculating the density of drive-induced resonances. We conclude that delocalization occurs once the density of drive-induced resonances reaches a critical value determined only by the static system.","lang":"eng"}]},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"article_number":"109274","file_date_updated":"2021-06-28T14:06:24Z","date_created":"2021-06-27T22:01:48Z","external_id":{"pmid":["34161767"],"isi":["000664463600016"]},"has_accepted_license":"1","date_updated":"2026-04-02T14:04:28Z","publication_identifier":{"eissn":["2211-1247"]},"language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        35","publication":"Cell Reports","ec_funded":1,"type":"journal_article","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/"}]},"day":"22","doi":"10.1016/j.celrep.2021.109274","publisher":"Cell Press","volume":35,"citation":{"short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>, vol. 35, no. 12, 109274, Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>.","ieee":"X. Contreras <i>et al.</i>, “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” <i>Cell Reports</i>, vol. 35, no. 12. Cell Press, 2021.","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. 2021;35(12). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>","chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>."},"oa":1,"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"access_level":"open_access","creator":"asandaue","date_created":"2021-06-28T14:06:24Z","content_type":"application/pdf","relation":"main_file","file_size":7653149,"file_id":"9613","checksum":"d49520fdcbbb5c2f883bddb67cee5d77","success":1,"date_updated":"2021-06-28T14:06:24Z","file_name":"2021_CellReports_Contreras.pdf"}],"author":[{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207"},{"last_name":"Davaatseren","first_name":"Amarbayasgalan","id":"70ADC922-B424-11E9-99E3-BA18E6697425","full_name":"Davaatseren, Amarbayasgalan"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen"},{"first_name":"Johanna","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","full_name":"Sonntag, Johanna","last_name":"Sonntag"},{"full_name":"Andersen, Lill","first_name":"Lill","last_name":"Andersen"},{"last_name":"Bernthaler","first_name":"Tina","full_name":"Bernthaler, Tina"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"last_name":"Heger","full_name":"Heger, Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena"},{"first_name":"Randy L.","full_name":"Johnson, Randy L.","last_name":"Johnson"},{"first_name":"Lindsay A.","full_name":"Schwarz, Lindsay A.","last_name":"Schwarz"},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"},{"full_name":"Rülicke, Thomas","first_name":"Thomas","last_name":"Rülicke"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"publication_status":"published","article_type":"original","project":[{"name":"Molecular mechanisms of radial neuronal migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"ddc":["570"],"acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.","status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division."}],"date_published":"2021-06-22T00:00:00Z","month":"06","pmid":1,"article_processing_charge":"No","title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","oa_version":"Published Version","_id":"9603","issue":"12","year":"2021"},{"external_id":{"pmid":["33857132"],"isi":["000640606700001"]},"date_updated":"2026-04-02T14:07:10Z","has_accepted_license":"1","publication_identifier":{"eissn":["1553-7404"]},"intvolume":"        17","language":[{"iso":"eng"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"file_date_updated":"2021-05-04T09:05:27Z","date_created":"2021-05-02T22:01:29Z","type":"journal_article","page":"e1009479","doi":"10.1371/journal.pgen.1009479","day":"01","publisher":"Public Library of Science","volume":17,"citation":{"ista":"Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M, Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 17(4), e1009479.","apa":"Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N., Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1009479\">https://doi.org/10.1371/journal.pgen.1009479</a>","mla":"Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” <i>PLoS Genetics</i>, vol. 17, no. 4, Public Library of Science, 2021, p. e1009479, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1009479\">10.1371/journal.pgen.1009479</a>.","ieee":"Á. Inglés Prieto <i>et al.</i>, “Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease,” <i>PLoS genetics</i>, vol. 17, no. 4. Public Library of Science, p. e1009479, 2021.","short":"Á. Inglés Prieto, N. Furthmann, S.H. Crossman, A.M. Tichy, N. Hoyer, M. Petersen, V. Zheden, J. Bicher, E. Gschaider-Reichhart, A. György, D.E. Siekhaus, P. Soba, K.F. Winklhofer, H.L. Janovjak, PLoS Genetics 17 (2021) e1009479.","chicago":"Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” <i>PLoS Genetics</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pgen.1009479\">https://doi.org/10.1371/journal.pgen.1009479</a>.","ama":"Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS genetics</i>. 2021;17(4):e1009479. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1009479\">10.1371/journal.pgen.1009479</a>"},"publication":"PLoS genetics","acknowledgement":"We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice, S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for help with statistical analysis.","ddc":["570"],"status":"public","date_published":"2021-04-01T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Optogenetics has been harnessed to shed new mechanistic light on current and future therapeutic strategies. This has been to date achieved by the regulation of ion flow and electrical signals in neuronal cells and neural circuits that are known to be affected by disease. In contrast, the optogenetic delivery of trophic biochemical signals, which support cell survival and are implicated in degenerative disorders, has never been demonstrated in an animal model of disease. Here, we reengineered the human and Drosophila melanogaster REarranged during Transfection (hRET and dRET) receptors to be activated by light, creating one-component optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation, these receptors robustly induced the MAPK/ERK proliferative signaling pathway in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD), light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results demonstrate that a light-activated receptor can ameliorate disease hallmarks in a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific and reversible and thus has the potential to inspire novel strategies towards a spatio-temporal regulation of tissue repair."}],"oa":1,"file":[{"file_name":"2021_PLOS_Ingles-Prieto.pdf","date_updated":"2021-05-04T09:05:27Z","success":1,"checksum":"82a74668f863e8dfb22fdd4f845c92ce","file_id":"9369","relation":"main_file","file_size":3072764,"content_type":"application/pdf","creator":"kschuh","date_created":"2021-05-04T09:05:27Z","access_level":"open_access"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"author":[{"last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","full_name":"Inglés Prieto, Álvaro","first_name":"Álvaro"},{"last_name":"Furthmann","first_name":"Nikolas","full_name":"Furthmann, Nikolas"},{"full_name":"Crossman, Samuel H.","first_name":"Samuel H.","last_name":"Crossman"},{"last_name":"Tichy","full_name":"Tichy, Alexandra Madelaine","first_name":"Alexandra Madelaine"},{"full_name":"Hoyer, Nina","first_name":"Nina","last_name":"Hoyer"},{"full_name":"Petersen, Meike","first_name":"Meike","last_name":"Petersen"},{"orcid":"0000-0002-9438-4783","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","first_name":"Vanessa"},{"last_name":"Bicher","first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","full_name":"Bicher, Julia"},{"id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","full_name":"Gschaider-Reichhart, Eva","first_name":"Eva","last_name":"Gschaider-Reichhart","orcid":"0000-0002-7218-7738"},{"orcid":"0000-0002-1819-198X","last_name":"György","first_name":"Attila","full_name":"György, Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus"},{"first_name":"Peter","full_name":"Soba, Peter","last_name":"Soba"},{"full_name":"Winklhofer, Konstanze F.","first_name":"Konstanze F.","last_name":"Winklhofer"},{"last_name":"Janovjak","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"publication_status":"published","title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","oa_version":"Published Version","year":"2021","issue":"4","_id":"9363","month":"04","pmid":1,"article_processing_charge":"No"},{"acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","ddc":["510"],"status":"public","abstract":[{"lang":"eng","text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed."}],"scopus_import":"1","date_published":"2021-06-29T00:00:00Z","oa":1,"file":[{"file_name":"2021_NatCoom_Tkadlec.pdf","date_updated":"2021-07-19T13:02:20Z","success":1,"checksum":"5767418926a7f7fb76151de29473dae0","file_id":"9692","file_size":628992,"relation":"main_file","content_type":"application/pdf","creator":"cziletti","date_created":"2021-07-19T13:02:20Z","access_level":"open_access"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"author":[{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"publication_status":"published","article_type":"original","title":"Fast and strong amplifiers of natural selection","oa_version":"Published Version","year":"2021","issue":"1","_id":"9640","month":"06","pmid":1,"article_processing_charge":"No","external_id":{"pmid":["34188036"],"isi":["000671752100003"]},"date_updated":"2026-04-02T14:04:10Z","has_accepted_license":"1","publication_identifier":{"eissn":["2041-1723"]},"intvolume":"        12","quality_controlled":"1","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"4009","department":[{"_id":"KrCh"}],"file_date_updated":"2021-07-19T13:02:20Z","date_created":"2021-07-11T22:01:15Z","type":"journal_article","ec_funded":1,"doi":"10.1038/s41467-021-24271-w","day":"29","publisher":"Springer Nature","volume":12,"citation":{"short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009.","mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>."},"publication":"Nature Communications"}]