[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","_id":"11999","article_type":"original","title":"Inserting one edge into a simple drawing is hard","oa":1,"publication_status":"published","acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","department":[{"_id":"UlWa"}],"ec_funded":1,"abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"status":"public","has_accepted_license":"1","day":"01","intvolume":"        69","citation":{"mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>, vol. 69, Springer Nature, 2023, pp. 745–770, doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>.","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” <i>Discrete and Computational Geometry</i>, vol. 69. Springer Nature, pp. 745–770, 2023.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., &#38; Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. 2023;69:745–770. doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770."},"publisher":"Springer Nature","doi":"10.1007/s00454-022-00394-9","file_date_updated":"2022-08-29T11:23:15Z","type":"journal_article","language":[{"iso":"eng"}],"arxiv":1,"date_published":"2023-04-01T00:00:00Z","oa_version":"Published Version","external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"ddc":["510"],"author":[{"last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670"},{"first_name":"Fabian","full_name":"Klute, Fabian","last_name":"Klute"},{"last_name":"Parada","first_name":"Irene","full_name":"Parada, Irene"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"},{"first_name":"Raimund","full_name":"Seidel, Raimund","last_name":"Seidel"},{"first_name":"Tilo","full_name":"Wiedera, Tilo","last_name":"Wiedera"}],"publication":"Discrete and Computational Geometry","date_updated":"2023-08-14T12:51:25Z","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","page":"745–770","year":"2023","date_created":"2022-08-28T22:02:01Z","volume":69,"file":[{"file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","access_level":"open_access","date_updated":"2022-08-29T11:23:15Z","success":1,"content_type":"application/pdf","file_id":"12006","date_created":"2022-08-29T11:23:15Z","checksum":"def7ae3b28d9fd6aec16450e40090302","relation":"main_file","creator":"alisjak","file_size":1002218}],"isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]}},{"isi":1,"file":[{"file_size":911017,"creator":"dernst","relation":"main_file","checksum":"71685ca5121f4c837f40c3f8eb50c915","date_created":"2023-01-20T10:02:48Z","file_id":"12322","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2023-01-20T10:02:48Z","file_name":"2023_Algorithmica_Edelsbrunner.pdf"}],"volume":85,"date_created":"2022-09-11T22:01:57Z","year":"2023","page":"277-295","quality_controlled":"1","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_updated":"2023-06-27T12:53:43Z","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2023-01-20T10:02:48Z","doi":"10.1007/s00453-022-01027-6","publisher":"Springer Nature","publication":"Algorithmica","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","first_name":"Georg F","last_name":"Osang"}],"ddc":["510"],"oa_version":"Published Version","external_id":{"isi":["000846967100001"]},"date_published":"2023-01-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}],"ec_funded":1,"citation":{"apa":"Edelsbrunner, H., &#38; Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>, vol. 85, Springer Nature, 2023, pp. 277–95, doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>.","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” <i>Algorithmica</i>, vol. 85. Springer Nature, pp. 277–295, 2023.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. 2023;85:277-295. doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>"},"intvolume":"        85","day":"01","has_accepted_license":"1","publication_status":"published","oa":1,"title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","article_type":"original","_id":"12086","month":"01","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","department":[{"_id":"HeEd"}]},{"day":"01","has_accepted_license":"1","intvolume":"        24","citation":{"ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” <i>Annales Henri Poincare</i>, vol. 24. Springer Nature, pp. 717–750, 2023.","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>, vol. 24, Springer Nature, 2023, pp. 717–50, doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>.","ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","apa":"Wirth, M., &#38; Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>","chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>.","ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. 2023;24:717-750. doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750."},"ec_funded":1,"status":"public","abstract":[{"text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups.","lang":"eng"}],"department":[{"_id":"JaMa"}],"acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","month":"03","_id":"12087","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","article_type":"original","article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"issn":["1424-0637"]},"scopus_import":"1","year":"2023","date_created":"2022-09-11T22:01:57Z","quality_controlled":"1","page":"717-750","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"M03337","name":"Curvature-dimension in noncommutative analysis","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6"},{"call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"date_updated":"2023-08-14T11:39:28Z","isi":1,"file":[{"file_size":554871,"creator":"dernst","relation":"main_file","checksum":"8c7b185eba5ccd92ef55c120f654222c","date_created":"2023-08-14T11:38:28Z","content_type":"application/pdf","file_id":"14051","success":1,"access_level":"open_access","date_updated":"2023-08-14T11:38:28Z","file_name":"2023_AnnalesHenriPoincare_Wirth.pdf"}],"volume":24,"oa_version":"Published Version","external_id":{"arxiv":["2105.08303"],"isi":["000837499800002"]},"date_published":"2023-03-01T00:00:00Z","publication":"Annales Henri Poincare","author":[{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","last_name":"Wirth","full_name":"Wirth, Melchior","first_name":"Melchior"},{"id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","last_name":"Zhang","full_name":"Zhang, Haonan","first_name":"Haonan"}],"ddc":["510"],"doi":"10.1007/s00023-022-01220-x","publisher":"Springer Nature","arxiv":1,"language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2023-08-14T11:38:28Z"},{"acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","department":[{"_id":"JaMa"}],"month":"01","_id":"12104","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","publication_status":"published","oa":1,"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","has_accepted_license":"1","day":"01","intvolume":"        23","citation":{"short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. 2023;23(1). doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>","apa":"Dello Schiavo, L., &#38; Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>.","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” <i>Journal of Evolution Equations</i>, vol. 23, no. 1. Springer Nature, 2023.","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>, vol. 23, no. 1, 9, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>."},"ec_funded":1,"abstract":[{"text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.","lang":"eng"}],"status":"public","article_number":"9","date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000906214600004"]},"oa_version":"Published Version","author":[{"last_name":"Dello Schiavo","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E"},{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","first_name":"Melchior","last_name":"Wirth"}],"ddc":["510"],"publication":"Journal of Evolution Equations","issue":"1","publisher":"Springer Nature","doi":"10.1007/s00028-022-00859-7","type":"journal_article","file_date_updated":"2023-01-20T10:45:06Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces","grant_number":"E208"},{"grant_number":"ESP156_N","name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"date_updated":"2023-06-28T11:54:35Z","year":"2023","date_created":"2023-01-08T23:00:53Z","quality_controlled":"1","file":[{"content_type":"application/pdf","file_id":"12325","date_created":"2023-01-20T10:45:06Z","success":1,"access_level":"open_access","date_updated":"2023-01-20T10:45:06Z","file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","file_size":422612,"creator":"dernst","relation":"main_file","checksum":"1f34f3e2cb521033de6154f274ea3a4e"}],"isi":1,"volume":23},{"isi":1,"file":[{"checksum":"9224f987caefe5dd85a70814d3cce65c","relation":"main_file","creator":"dernst","file_size":1931647,"file_name":"2023_JourFluidMechanics_Marensi.pdf","success":1,"date_updated":"2023-02-02T12:34:54Z","access_level":"open_access","file_id":"12489","date_created":"2023-02-02T12:34:54Z","content_type":"application/pdf"}],"volume":954,"year":"2023","date_created":"2023-01-08T23:00:53Z","quality_controlled":"1","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"date_updated":"2023-08-01T12:53:23Z","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","arxiv":1,"language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2023-02-02T12:34:54Z","doi":"10.1017/jfm.2022.1001","publisher":"Cambridge University Press","publication":"Journal of Fluid Mechanics","author":[{"id":"0BE7553A-1004-11EA-B805-18983DDC885E","last_name":"Marensi","first_name":"Elena","full_name":"Marensi, Elena"},{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312","last_name":"Yalniz","full_name":"Yalniz, Gökhan","first_name":"Gökhan"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","last_name":"Budanur","full_name":"Budanur, Nazmi B","first_name":"Nazmi B"}],"ddc":["530"],"external_id":{"arxiv":["2101.07516"],"isi":["000903336600001"]},"oa_version":"Published Version","date_published":"2023-01-10T00:00:00Z","status":"public","article_number":"A10","abstract":[{"lang":"eng","text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion."}],"citation":{"ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. <i>Journal of Fluid Mechanics</i>. 2023;954. doi:<a href=\"https://doi.org/10.1017/jfm.2022.1001\">10.1017/jfm.2022.1001</a>","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023).","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” <i>Journal of Fluid Mechanics</i>, vol. 954. Cambridge University Press, 2023.","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” <i>Journal of Fluid Mechanics</i>, vol. 954, A10, Cambridge University Press, 2023, doi:<a href=\"https://doi.org/10.1017/jfm.2022.1001\">10.1017/jfm.2022.1001</a>.","chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.1017/jfm.2022.1001\">https://doi.org/10.1017/jfm.2022.1001</a>.","apa":"Marensi, E., Yalniz, G., Hof, B., &#38; Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2022.1001\">https://doi.org/10.1017/jfm.2022.1001</a>","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10."},"intvolume":"       954","day":"10","has_accepted_license":"1","publication_status":"published","title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","oa":1,"article_type":"original","month":"01","_id":"12105","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BjHo"}],"acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH)."},{"volume":41,"isi":1,"file":[{"file_id":"14066","date_created":"2023-08-16T11:30:45Z","content_type":"application/pdf","access_level":"open_access","success":1,"date_updated":"2023-08-16T11:30:45Z","file_name":"2023_NatureBioTech_Yeung.pdf","file_size":12040976,"creator":"dernst","relation":"main_file","checksum":"668447a1c8d360b68f8aaf9e08ed644f"}],"quality_controlled":"1","page":"813–823","year":"2023","date_created":"2023-01-08T23:00:53Z","date_updated":"2023-08-16T11:32:33Z","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","language":[{"iso":"eng"}],"file_date_updated":"2023-08-16T11:30:45Z","type":"journal_article","doi":"10.1038/s41587-022-01560-3","publisher":"Springer Nature","publication":"Nature Biotechnology","ddc":["570"],"author":[{"id":"123012b2-db30-11eb-b4d8-a35840c0551b","orcid":"0000-0003-1732-1559","first_name":"Jake","full_name":"Yeung, Jake","last_name":"Yeung"},{"last_name":"Florescu","full_name":"Florescu, Maria","first_name":"Maria"},{"last_name":"Zeller","full_name":"Zeller, Peter","first_name":"Peter"},{"full_name":"De Barbanson, Buys Anton","first_name":"Buys Anton","last_name":"De Barbanson"},{"last_name":"Wellenstein","first_name":"Max D.","full_name":"Wellenstein, Max D."},{"last_name":"Van Oudenaarden","first_name":"Alexander","full_name":"Van Oudenaarden, Alexander"}],"oa_version":"Published Version","external_id":{"isi":["000909067600003"]},"date_published":"2023-06-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells."}],"intvolume":"        41","citation":{"apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., &#38; Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>.","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” <i>Nature Biotechnology</i>, vol. 41. Springer Nature, pp. 813–823, 2023.","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>, vol. 41, Springer Nature, 2023, pp. 813–823, doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. 2023;41:813–823. doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>"},"day":"01","has_accepted_license":"1","title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","oa":1,"publication_status":"published","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","_id":"12106","department":[{"_id":"ScienComp"}],"acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society."},{"day":"15","keyword":["Surfaces","Coatings and Films","Condensed Matter Physics","Surfaces and Interfaces","General Physics and Astronomy","General Chemistry"],"intvolume":"       613","citation":{"ama":"Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. <i>Applied Surface Science</i>. 2023;613. doi:<a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">10.1016/j.apsusc.2022.156101</a>","short":"L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H. Wang, Applied Surface Science 613 (2023).","ieee":"L. Zhang <i>et al.</i>, “Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient,” <i>Applied Surface Science</i>, vol. 613. Elsevier, 2023.","mla":"Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” <i>Applied Surface Science</i>, vol. 613, 156101, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">10.1016/j.apsusc.2022.156101</a>.","ista":"Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 613, 156101.","chicago":"Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” <i>Applied Surface Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">https://doi.org/10.1016/j.apsusc.2022.156101</a>.","apa":"Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. <i>Applied Surface Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">https://doi.org/10.1016/j.apsusc.2022.156101</a>"},"article_number":"156101","status":"public","abstract":[{"text":"The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices.","lang":"eng"}],"department":[{"_id":"MaIb"}],"acknowledgement":"Scientific Research Program Funded by Shaanxi Provincial Education Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi (Grant No.2022JZ-31), Young Talent fund of University Association for Science and Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation (Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology (Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry and Technology for Chemical Industry, Ministry of Education, Shaanxi University of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology, Shaanxi University of Science and Technology (Grant No. KFKT2022-15).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12113","month":"03","title":"Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient","publication_status":"epub_ahead","article_type":"original","article_processing_charge":"No","publication_identifier":{"issn":["0169-4332"]},"scopus_import":"1","quality_controlled":"1","year":"2023","date_created":"2023-01-12T11:55:02Z","date_updated":"2023-08-14T11:47:06Z","volume":613,"isi":1,"oa_version":"None","external_id":{"isi":["000911497000001"]},"date_published":"2023-03-15T00:00:00Z","publication":"Applied Surface Science","author":[{"last_name":"Zhang","full_name":"Zhang, Li","first_name":"Li"},{"last_name":"Liu","first_name":"Xingyu","full_name":"Liu, Xingyu"},{"last_name":"Wu","full_name":"Wu, Ting","first_name":"Ting"},{"id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f","last_name":"Xu","full_name":"Xu, Shengduo","first_name":"Shengduo"},{"full_name":"Suo, Guoquan","first_name":"Guoquan","last_name":"Suo"},{"last_name":"Ye","first_name":"Xiaohui","full_name":"Ye, Xiaohui"},{"first_name":"Xiaojiang","full_name":"Hou, Xiaojiang","last_name":"Hou"},{"last_name":"Yang","first_name":"Yanling","full_name":"Yang, Yanling"},{"full_name":"Liu, Qingfeng","first_name":"Qingfeng","last_name":"Liu"},{"last_name":"Wang","full_name":"Wang, Hongqiang","first_name":"Hongqiang"}],"doi":"10.1016/j.apsusc.2022.156101","publisher":"Elsevier","language":[{"iso":"eng"}],"type":"journal_article"},{"publication":"Journal of Structural Biology: X","author":[{"first_name":"Diego F.","full_name":"Gauto, Diego F.","last_name":"Gauto"},{"first_name":"Olga O.","full_name":"Lebedenko, Olga O.","last_name":"Lebedenko"},{"first_name":"Lea Marie","full_name":"Becker, Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151"},{"last_name":"Ayala","first_name":"Isabel","full_name":"Ayala, Isabel"},{"last_name":"Lichtenecker","first_name":"Roman","full_name":"Lichtenecker, Roman"},{"last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R."},{"last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"ddc":["570"],"oa_version":"Published Version","external_id":{"pmid":["36578472"]},"date_published":"2023-01-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2023-08-16T09:36:28Z","doi":"10.1016/j.yjsbx.2022.100079","publisher":"Elsevier","publication_identifier":{"issn":["2590-1524"]},"pmid":1,"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"No","file":[{"file_id":"14064","content_type":"application/pdf","date_created":"2023-08-16T09:36:28Z","access_level":"open_access","success":1,"date_updated":"2023-08-16T09:36:28Z","file_name":"2023_JourStrucBiologyX_Gauto.pdf","file_size":5132322,"creator":"dernst","relation":"main_file","checksum":"b4b1c10a31018aafe053b7d55a470e54"}],"volume":7,"date_created":"2023-01-12T11:55:38Z","year":"2023","quality_controlled":"1","date_updated":"2023-08-16T09:37:25Z","acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","department":[{"_id":"PaSc"}],"publication_status":"published","title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","oa":1,"article_type":"original","month":"01","_id":"12114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Structural Biology"],"citation":{"short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. 2023;7. doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., &#38; Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>.","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","ieee":"D. F. Gauto <i>et al.</i>, “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” <i>Journal of Structural Biology: X</i>, vol. 7. Elsevier, 2023.","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>, vol. 7, 100079, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>."},"intvolume":"         7","day":"01","has_accepted_license":"1","status":"public","article_number":"100079","abstract":[{"lang":"eng","text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects."}]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1245/s10434-022-12681-z"}],"scopus_import":"1","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"article_processing_charge":"No","isi":1,"volume":30,"date_updated":"2023-09-05T15:18:36Z","year":"2023","date_created":"2023-01-12T11:56:22Z","page":"46-47","quality_controlled":"1","author":[{"last_name":"Glajzer","full_name":"Glajzer, Jacek","first_name":"Jacek"},{"last_name":"Castillo-Tong","full_name":"Castillo-Tong, Dan Cacsire","first_name":"Dan Cacsire"},{"last_name":"Richter","full_name":"Richter, Rolf","first_name":"Rolf"},{"first_name":"Ignace","full_name":"Vergote, Ignace","last_name":"Vergote"},{"last_name":"Kulbe","first_name":"Hagen","full_name":"Kulbe, Hagen"},{"last_name":"Vanderstichele","full_name":"Vanderstichele, Adriaan","first_name":"Adriaan"},{"full_name":"Ruscito, Ilary","first_name":"Ilary","last_name":"Ruscito"},{"last_name":"Trillsch","full_name":"Trillsch, Fabian","first_name":"Fabian"},{"last_name":"Mustea","full_name":"Mustea, Alexander","first_name":"Alexander"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","first_name":"Caroline","full_name":"Kreuzinger, Caroline"},{"last_name":"Gourley","full_name":"Gourley, Charlie","first_name":"Charlie"},{"first_name":"Hani","full_name":"Gabra, Hani","last_name":"Gabra"},{"last_name":"Taube","full_name":"Taube, Eliane T.","first_name":"Eliane T."},{"last_name":"Dorigo","full_name":"Dorigo, Oliver","first_name":"Oliver"},{"full_name":"Horst, David","first_name":"David","last_name":"Horst"},{"full_name":"Keunecke, Carlotta","first_name":"Carlotta","last_name":"Keunecke"},{"first_name":"Joanna","full_name":"Baum, Joanna","last_name":"Baum"},{"last_name":"Angelotti","full_name":"Angelotti, Timothy","first_name":"Timothy"},{"last_name":"Sehouli","full_name":"Sehouli, Jalid","first_name":"Jalid"},{"last_name":"Braicu","full_name":"Braicu, Elena Ioana","first_name":"Elena Ioana"}],"publication":"Annals of Surgical Oncology","date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000879151800001"]},"oa_version":"Published Version","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Springer Nature","doi":"10.1245/s10434-022-12681-z","citation":{"ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. <i>Annals of Surgical Oncology</i>. 2023;30:46-47. doi:<a href=\"https://doi.org/10.1245/s10434-022-12681-z\">10.1245/s10434-022-12681-z</a>","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","ieee":"J. Glajzer <i>et al.</i>, “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” <i>Annals of Surgical Oncology</i>, vol. 30. Springer Nature, pp. 46–47, 2023.","mla":"Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of Surgical Oncology</i>, vol. 30, Springer Nature, 2023, pp. 46–47, doi:<a href=\"https://doi.org/10.1245/s10434-022-12681-z\">10.1245/s10434-022-12681-z</a>.","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. <i>Annals of Surgical Oncology</i>. Springer Nature. <a href=\"https://doi.org/10.1245/s10434-022-12681-z\">https://doi.org/10.1245/s10434-022-12681-z</a>","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of Surgical Oncology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1245/s10434-022-12681-z\">https://doi.org/10.1245/s10434-022-12681-z</a>."},"intvolume":"        30","keyword":["Oncology","Surgery"],"day":"01","status":"public","acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","department":[{"_id":"JoDa"}],"article_type":"original","publication_status":"published","related_material":{"record":[{"relation":"other","status":"public","id":"12205"}]},"title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","oa":1,"month":"01","_id":"12115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"abstract":[{"text":"We study the time evolution of the Nelson model in a mean-field limit in which N nonrelativistic bosons weakly couple (with respect to the particle number) to a positive or zero mass quantized scalar field. Our main result is the derivation of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove the convergence of the approximate wave function to the many-body wave function in norm, with a convergence rate proportional to the number of corrections taken into account in the approximation. We prove an analogous result for the unitary propagator. As an application, we derive a simple system of partial differential equations describing the time evolution of the first- and second-order approximations to the one-particle reduced density matrices of the particles and the quantum field, respectively.","lang":"eng"}],"status":"public","article_number":"2350006","intvolume":"        35","citation":{"ama":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. <i>Reviews in Mathematical Physics</i>. 2023;35(4). doi:<a href=\"https://doi.org/10.1142/S0129055X2350006X\">10.1142/S0129055X2350006X</a>","short":"M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical Physics 35 (2023).","mla":"Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” <i>Reviews in Mathematical Physics</i>, vol. 35, no. 4, 2350006, World Scientific Publishing, 2023, doi:<a href=\"https://doi.org/10.1142/S0129055X2350006X\">10.1142/S0129055X2350006X</a>.","ieee":"M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov dynamics and higher-order corrections for the regularized Nelson model,” <i>Reviews in Mathematical Physics</i>, vol. 35, no. 4. World Scientific Publishing, 2023.","ista":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 35(4), 2350006.","chicago":"Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2023. <a href=\"https://doi.org/10.1142/S0129055X2350006X\">https://doi.org/10.1142/S0129055X2350006X</a>.","apa":"Falconi, M., Leopold, N. K., Mitrouskas, D. J., &#38; Petrat, S. P. (2023). Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129055X2350006X\">https://doi.org/10.1142/S0129055X2350006X</a>"},"day":"09","article_type":"original","publication_status":"published","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","das_tickbox":"1","oa":1,"month":"01","_id":"12430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"isi":1,"volume":35,"date_updated":"2026-06-18T07:59:24Z","year":"2023","date_created":"2023-01-29T23:00:59Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2110.00458"}],"scopus_import":"1","publication_identifier":{"issn":["0129-055X"]},"article_processing_charge":"No","type":"journal_article","arxiv":1,"language":[{"iso":"eng"}],"publisher":"World Scientific Publishing","doi":"10.1142/S0129055X2350006X","author":[{"full_name":"Falconi, Marco","first_name":"Marco","last_name":"Falconi"},{"full_name":"Leopold, Nikolai K","first_name":"Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822"},{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas"},{"id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P","first_name":"Sören P","last_name":"Petrat"}],"ddc":["510"],"issue":"4","publication":"Reviews in Mathematical Physics","date_published":"2023-01-09T00:00:00Z","oa_version":"Preprint","external_id":{"isi":["000909760300001"],"arxiv":["2110.00458"]}},{"publication":"Frontiers in Neural Circuits","ddc":["570"],"author":[{"first_name":"Giuditta","full_name":"Gambino, Giuditta","last_name":"Gambino"},{"last_name":"Bhik-Ghanie","full_name":"Bhik-Ghanie, Rebecca","first_name":"Rebecca"},{"full_name":"Giglia, Giuseppe","first_name":"Giuseppe","last_name":"Giglia"},{"last_name":"Puig","full_name":"Puig, M. Victoria","first_name":"M. Victoria"},{"id":"44B06F76-F248-11E8-B48F-1D18A9856A87","last_name":"Ramirez Villegas","full_name":"Ramirez Villegas, Juan F","first_name":"Juan F"},{"full_name":"Zaldivar, Daniel","first_name":"Daniel","last_name":"Zaldivar"}],"external_id":{"isi":["000886671400001"]},"oa_version":"Published Version","date_published":"2022-10-26T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2023-01-24T10:10:43Z","type":"journal_article","doi":"10.3389/fncir.2022.1028154","publisher":"Frontiers Media","publication_identifier":{"issn":["1662-5110"]},"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","volume":16,"isi":1,"file":[{"checksum":"457aa00e1800847abb340853058531de","relation":"main_file","creator":"dernst","file_size":110031,"file_name":"2022_FrontiersNeuralCircuits_Gambino.pdf","access_level":"open_access","date_updated":"2023-01-24T10:10:43Z","success":1,"content_type":"application/pdf","date_created":"2023-01-24T10:10:43Z","file_id":"12357"}],"quality_controlled":"1","year":"2022","date_created":"2023-01-12T12:07:39Z","date_updated":"2023-08-04T09:01:06Z","project":[{"call_identifier":"H2020","grant_number":"841301","name":"The Brainstem-Hippocampus Network Uncovered: Dynamics, Reactivation and Memory Consolidation","_id":"26BAE2E4-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"JoCs"}],"acknowledgement":"This work was supported by a DFG grant ZA990/1 to DZ. This work was supported by the MSCA EU proposal 841301 - DREAM, European Commission; Horizon 2020 - Research and Innovation Framework Programme to JFRV.","oa":1,"title":"Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels","publication_status":"published","article_type":"letter_note","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"10","_id":"12149","keyword":["Cellular and Molecular Neuroscience","Cognitive Neuroscience","Sensory Systems","Neuroscience (miscellaneous)"],"intvolume":"        16","citation":{"ieee":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M. V. Puig, J. F. Ramirez Villegas, and D. Zaldivar, “Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels,” <i>Frontiers in Neural Circuits</i>, vol. 16. Frontiers Media, 2022.","mla":"Gambino, Giuditta, et al. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” <i>Frontiers in Neural Circuits</i>, vol. 16, 1028154, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fncir.2022.1028154\">10.3389/fncir.2022.1028154</a>.","chicago":"Gambino, Giuditta, Rebecca Bhik-Ghanie, Giuseppe Giglia, M. Victoria Puig, Juan F Ramirez Villegas, and Daniel Zaldivar. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” <i>Frontiers in Neural Circuits</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fncir.2022.1028154\">https://doi.org/10.3389/fncir.2022.1028154</a>.","apa":"Gambino, G., Bhik-Ghanie, R., Giglia, G., Puig, M. V., Ramirez Villegas, J. F., &#38; Zaldivar, D. (2022). Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. <i>Frontiers in Neural Circuits</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncir.2022.1028154\">https://doi.org/10.3389/fncir.2022.1028154</a>","ista":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. 2022. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. Frontiers in Neural Circuits. 16, 1028154.","ama":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. <i>Frontiers in Neural Circuits</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fncir.2022.1028154\">10.3389/fncir.2022.1028154</a>","short":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M.V. Puig, J.F. Ramirez Villegas, D. Zaldivar, Frontiers in Neural Circuits 16 (2022)."},"day":"26","has_accepted_license":"1","article_number":"1028154","status":"public","abstract":[{"lang":"eng","text":"Editorial on the Research Topic"}],"ec_funded":1},{"citation":{"ama":"Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for nonadditive systems. <i>Physical Review B</i>. 2022;106(15). doi:<a href=\"https://doi.org/10.1103/physrevb.106.155127\">10.1103/physrevb.106.155127</a>","short":"W. Rzadkowski, M. Lemeshko, J.H. Mentink, Physical Review B 106 (2022).","mla":"Rzadkowski, Wojciech, et al. “Artificial Neural Network States for Nonadditive Systems.” <i>Physical Review B</i>, vol. 106, no. 15, 155127, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.106.155127\">10.1103/physrevb.106.155127</a>.","ieee":"W. Rzadkowski, M. Lemeshko, and J. H. Mentink, “Artificial neural network states for nonadditive systems,” <i>Physical Review B</i>, vol. 106, no. 15. American Physical Society, 2022.","apa":"Rzadkowski, W., Lemeshko, M., &#38; Mentink, J. H. (2022). Artificial neural network states for nonadditive systems. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.106.155127\">https://doi.org/10.1103/physrevb.106.155127</a>","ista":"Rzadkowski W, Lemeshko M, Mentink JH. 2022. Artificial neural network states for nonadditive systems. Physical Review B. 106(15), 155127.","chicago":"Rzadkowski, Wojciech, Mikhail Lemeshko, and Johan H. Mentink. “Artificial Neural Network States for Nonadditive Systems.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.106.155127\">https://doi.org/10.1103/physrevb.106.155127</a>."},"intvolume":"       106","day":"15","abstract":[{"text":"Methods inspired from machine learning have recently attracted great interest in the computational study of quantum many-particle systems. So far, however, it has proven challenging to deal with microscopic models in which the total number of particles is not conserved. To address this issue, we propose a variant of neural network states, which we term neural coherent states. Taking the Fröhlich impurity model as a case study, we show that neural coherent states can learn the ground state of nonadditive systems very well. In particular, we recover exact diagonalization in all regimes tested and observe substantial improvement over the standard coherent state estimates in the most challenging intermediate-coupling regime. Our approach is generic and does not assume specific details of the system, suggesting wide applications.","lang":"eng"}],"status":"public","article_number":"155127","ec_funded":1,"acknowledgement":"We acknowledge fruitful discussions with G. Bighin, G. Fabiani, A. Ghazaryan, C. Lampert, and A. Volosniev at various stages of this work. W.R. acknowledges support through a DOC Fellowship of the Austrian Academy of Sciences and has received funding from the EU Horizon 2020 programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. M.L. and J.H.M. acknowledge support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON) and Synergy Grant No. 856538 (3D-MAGiC), respectively. This work is part of the Shell-NWO/FOMinitiative “Computational sciences for energy research” of Shell and Chemical Sciences, Earth and Life Sciences, Physical Sciences, FOM and STW. ","department":[{"_id":"MiLe"}],"article_type":"original","publication_status":"published","oa":1,"title":"Artificial neural network states for nonadditive systems","_id":"12150","month":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.15193","open_access":"1"}],"scopus_import":"1","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"article_processing_charge":"No","isi":1,"volume":106,"project":[{"name":"Analytic and machine learning approaches to composite quantum impurities","grant_number":"25681","_id":"05A235A0-7A3F-11EA-A408-12923DDC885E"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"date_updated":"2023-08-04T09:01:48Z","date_created":"2023-01-12T12:07:49Z","year":"2022","quality_controlled":"1","author":[{"full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"last_name":"Mentink","full_name":"Mentink, Johan H.","first_name":"Johan H."}],"publication":"Physical Review B","issue":"15","date_published":"2022-10-15T00:00:00Z","external_id":{"arxiv":["2105.15193"],"isi":["000875189100005"]},"oa_version":"Preprint","type":"journal_article","arxiv":1,"language":[{"iso":"eng"}],"publisher":"American Physical Society","doi":"10.1103/physrevb.106.155127"},{"language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2023-01-24T10:45:01Z","doi":"10.1371/journal.pcbi.1010586","publisher":"Public Library of Science","publication":"PLOS Computational Biology","issue":"10","author":[{"last_name":"Jiang","full_name":"Jiang, Xiuyun","first_name":"Xiuyun"},{"last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena","first_name":"Lena"},{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo","first_name":"Christian Eduardo","last_name":"Vanhille-Campos"},{"last_name":"Pfitzner","first_name":"Anna-Katharina","full_name":"Pfitzner, Anna-Katharina"},{"full_name":"Lominadze, Elene","first_name":"Elene","last_name":"Lominadze"},{"last_name":"Roux","full_name":"Roux, Aurélien","first_name":"Aurélien"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"},{"last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"ddc":["570"],"external_id":{"isi":["000924885500005"]},"oa_version":"Published Version","date_published":"2022-10-17T00:00:00Z","file":[{"creator":"dernst","file_size":2641067,"checksum":"bada6a7865e470cf42bbdfa67dd471d2","relation":"main_file","date_updated":"2023-01-24T10:45:01Z","access_level":"open_access","success":1,"date_created":"2023-01-24T10:45:01Z","content_type":"application/pdf","file_id":"12359","file_name":"2022_PLoSCompBio_Jiang.pdf"}],"isi":1,"volume":18,"year":"2022","date_created":"2023-01-12T12:08:10Z","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","grant_number":"96752","name":"The evolution of trafficking: from archaea to eukaryotes"}],"date_updated":"2023-08-04T09:03:21Z","publication_identifier":{"issn":["1553-7358"]},"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","publication_status":"published","oa":1,"title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","related_material":{"link":[{"url":"https://github.com/sharonJXY/3-filament-model","relation":"software"}]},"article_type":"original","_id":"12152","month":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"AnSa"}],"acknowledgement":"A.S . received an award from European Research Council (https://erc.europa.eu, “NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org, UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open, Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation, Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc, MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research (https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and an award from the European Research Council\r\nConsolidator (https://erc.europa.eu, 311536). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","status":"public","article_number":"e1010586","abstract":[{"text":"ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.","lang":"eng"}],"ec_funded":1,"keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"intvolume":"        18","citation":{"mla":"Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>, vol. 18, no. 10, e1010586, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>.","ieee":"X. Jiang <i>et al.</i>, “Modelling membrane reshaping by staged polymerization of ESCRT-III filaments,” <i>PLOS Computational Biology</i>, vol. 18, no. 10. Public Library of Science, 2022.","apa":"Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K., Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>","chicago":"Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>.","ista":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.","ama":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. 2022;18(10). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>","short":"X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E. Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022)."},"day":"17","has_accepted_license":"1"},{"citation":{"short":"L. Salasnich, A. Cappellaro, K. Furutani, A. Tononi, G. Bighin, Symmetry 14 (2022).","ama":"Salasnich L, Cappellaro A, Furutani K, Tononi A, Bighin G. First and second sound in two-dimensional bosonic and fermionic superfluids. <i>Symmetry</i>. 2022;14(10). doi:<a href=\"https://doi.org/10.3390/sym14102182\">10.3390/sym14102182</a>","ista":"Salasnich L, Cappellaro A, Furutani K, Tononi A, Bighin G. 2022. First and second sound in two-dimensional bosonic and fermionic superfluids. Symmetry. 14(10), 2182.","chicago":"Salasnich, Luca, Alberto Cappellaro, Koichiro Furutani, Andrea Tononi, and Giacomo Bighin. “First and Second Sound in Two-Dimensional Bosonic and Fermionic Superfluids.” <i>Symmetry</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/sym14102182\">https://doi.org/10.3390/sym14102182</a>.","apa":"Salasnich, L., Cappellaro, A., Furutani, K., Tononi, A., &#38; Bighin, G. (2022). First and second sound in two-dimensional bosonic and fermionic superfluids. <i>Symmetry</i>. MDPI. <a href=\"https://doi.org/10.3390/sym14102182\">https://doi.org/10.3390/sym14102182</a>","ieee":"L. Salasnich, A. Cappellaro, K. Furutani, A. Tononi, and G. Bighin, “First and second sound in two-dimensional bosonic and fermionic superfluids,” <i>Symmetry</i>, vol. 14, no. 10. MDPI, 2022.","mla":"Salasnich, Luca, et al. “First and Second Sound in Two-Dimensional Bosonic and Fermionic Superfluids.” <i>Symmetry</i>, vol. 14, no. 10, 2182, MDPI, 2022, doi:<a href=\"https://doi.org/10.3390/sym14102182\">10.3390/sym14102182</a>."},"intvolume":"        14","keyword":["Physics and Astronomy (miscellaneous)","General Mathematics","Chemistry (miscellaneous)","Computer Science (miscellaneous)"],"has_accepted_license":"1","day":"17","abstract":[{"text":"We review our theoretical results of the sound propagation in two-dimensional (2D) systems of ultracold fermionic and bosonic atoms. In the superfluid phase, characterized by the spontaneous symmetry breaking of the U(1) symmetry, there is the coexistence of first and second sound. In the case of weakly-interacting repulsive bosons, we model the recent measurements of the sound velocities of 39K atoms in 2D obtained in the weakly-interacting regime and around the Berezinskii–Kosterlitz–Thouless (BKT) superfluid-to-normal transition temperature. In particular, we perform a quite accurate computation of the superfluid density and show that it is reasonably consistent with the experimental results. For superfluid attractive fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover. In the low-temperature regime, we reproduce the recent measurements of first-sound speed with 6Li atoms. We also predict that there is mixing between sound modes only in the finite-temperature BEC regime.","lang":"eng"}],"article_number":"2182","status":"public","department":[{"_id":"MiLe"}],"acknowledgement":"This research is partially supported by University of Padova, BIRD grant “Ultracold atoms\r\nin curved geometries”. KF is supported by Fondazione CARIPARO with a PhD fellowship. AT is\r\npartially supported by French National Research Agency ANR Grant Droplets N. ANR-19-CE30-0003-02. LS thanks Herwig Ott and Sandro Wimberger for their kind invitation to the\r\nInternational Workshop “Quantum Transport with ultracold atoms” (2022).","article_type":"original","title":"First and second sound in two-dimensional bosonic and fermionic superfluids","oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"10","_id":"12154","scopus_import":"1","publication_identifier":{"issn":["2073-8994"]},"article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":14,"isi":1,"file":[{"relation":"main_file","checksum":"9b6bd0e484834dd76d7b26e3c5fba8bd","file_size":843723,"creator":"dernst","file_name":"2022_Symmetry_Salsnich.pdf","date_created":"2023-01-24T10:56:12Z","content_type":"application/pdf","file_id":"12361","date_updated":"2023-01-24T10:56:12Z","access_level":"open_access","success":1}],"date_updated":"2023-08-09T10:13:17Z","quality_controlled":"1","year":"2022","date_created":"2023-01-12T12:08:31Z","ddc":["530"],"author":[{"full_name":"Salasnich, Luca","first_name":"Luca","last_name":"Salasnich"},{"orcid":"0000-0001-6110-2359","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","full_name":"Cappellaro, Alberto","first_name":"Alberto"},{"last_name":"Furutani","full_name":"Furutani, Koichiro","first_name":"Koichiro"},{"first_name":"Andrea","full_name":"Tononi, Andrea","last_name":"Tononi"},{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","full_name":"Bighin, Giacomo","last_name":"Bighin"}],"issue":"10","publication":"Symmetry","date_published":"2022-10-17T00:00:00Z","oa_version":"Published Version","external_id":{"isi":["000875039200001"]},"file_date_updated":"2023-01-24T10:56:12Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"MDPI","doi":"10.3390/sym14102182"},{"month":"09","_id":"12156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","publication_status":"published","oa":1,"title":"Eukaryotic gene regulation at equilibrium, or non?","department":[{"_id":"GaTk"}],"acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","abstract":[{"text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.","lang":"eng"}],"status":"public","article_number":"100435","has_accepted_license":"1","day":"01","intvolume":"        31","citation":{"short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>","mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>.","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022."},"keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"publisher":"Elsevier","doi":"10.1016/j.coisb.2022.100435","type":"journal_article","file_date_updated":"2023-01-24T12:14:10Z","language":[{"iso":"eng"}],"date_published":"2022-09-01T00:00:00Z","oa_version":"Published Version","author":[{"last_name":"Zoller","first_name":"Benjamin","full_name":"Zoller, Benjamin"},{"last_name":"Gregor","full_name":"Gregor, Thomas","first_name":"Thomas"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1"}],"ddc":["570"],"issue":"9","publication":"Current Opinion in Systems Biology","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"date_updated":"2023-02-13T09:20:34Z","date_created":"2023-01-12T12:08:51Z","year":"2022","quality_controlled":"1","file":[{"relation":"main_file","checksum":"97ef01e0cc60cdc84f45640a0f248fb0","file_size":2214944,"creator":"dernst","file_name":"2022_CurrentBiology_Zoller.pdf","file_id":"12362","content_type":"application/pdf","date_created":"2023-01-24T12:14:10Z","access_level":"open_access","date_updated":"2023-01-24T12:14:10Z","success":1}],"volume":31,"article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","publication_identifier":{"issn":["2452-3100"]}},{"oa_version":"Published Version","external_id":{"isi":["000890735600001"]},"date_published":"2022-09-26T00:00:00Z","publication":"eLife","ddc":["570"],"author":[{"id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","first_name":"Laura","full_name":"Hayward, Laura","last_name":"Hayward"},{"full_name":"Sella, Guy","first_name":"Guy","last_name":"Sella"}],"doi":"10.7554/elife.66697","publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"file_date_updated":"2023-01-24T12:21:32Z","type":"journal_article","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["2050-084X"]},"scopus_import":"1","quality_controlled":"1","year":"2022","date_created":"2023-01-12T12:09:00Z","date_updated":"2023-08-04T09:04:58Z","volume":11,"isi":1,"file":[{"checksum":"28de155b231ac1c8d4501c98b2fb359a","relation":"main_file","creator":"dernst","file_size":18935612,"file_name":"2022_eLife_Hayward.pdf","date_updated":"2023-01-24T12:21:32Z","access_level":"open_access","success":1,"file_id":"12363","content_type":"application/pdf","date_created":"2023-01-24T12:21:32Z"}],"acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","department":[{"_id":"NiBa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"09","_id":"12157","oa":1,"title":"Polygenic adaptation after a sudden change in environment","publication_status":"published","article_type":"original","day":"26","has_accepted_license":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"citation":{"ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>, vol. 11, 66697, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>.","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","apa":"Hayward, L., &#38; Sella, G. (2022). Polygenic adaptation after a sudden change in environment. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>.","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>","short":"L. Hayward, G. Sella, ELife 11 (2022)."},"intvolume":"        11","article_number":"66697","status":"public","abstract":[{"text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.","lang":"eng"}]},{"department":[{"_id":"ElKo"}],"publication_status":"published","title":"Hierarchical consensus: A horizontal scaling framework for blockchains","_id":"12160","month":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"De la Rocha A, Kokoris Kogias E, Soares JM, Vukolic M. 2022. Hierarchical consensus: A horizontal scaling framework for blockchains. 42nd International Conference on Distributed Computing Systems Workshops. ICDCSW: International Conference on Distributed Computing Systems Workshop vol. 2022, 45–52.","apa":"De la Rocha, A., Kokoris Kogias, E., Soares, J. M., &#38; Vukolic, M. (2022). Hierarchical consensus: A horizontal scaling framework for blockchains. In <i>42nd International Conference on Distributed Computing Systems Workshops</i> (Vol. 2022, pp. 45–52). Bologna, Italy: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/icdcsw56584.2022.00018\">https://doi.org/10.1109/icdcsw56584.2022.00018</a>","chicago":"De la Rocha, Alfonso, Eleftherios Kokoris Kogias, Jorge M. Soares, and Marko Vukolic. “Hierarchical Consensus: A Horizontal Scaling Framework for Blockchains.” In <i>42nd International Conference on Distributed Computing Systems Workshops</i>, 2022:45–52. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/icdcsw56584.2022.00018\">https://doi.org/10.1109/icdcsw56584.2022.00018</a>.","mla":"De la Rocha, Alfonso, et al. “Hierarchical Consensus: A Horizontal Scaling Framework for Blockchains.” <i>42nd International Conference on Distributed Computing Systems Workshops</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 45–52, doi:<a href=\"https://doi.org/10.1109/icdcsw56584.2022.00018\">10.1109/icdcsw56584.2022.00018</a>.","ieee":"A. De la Rocha, E. Kokoris Kogias, J. M. Soares, and M. Vukolic, “Hierarchical consensus: A horizontal scaling framework for blockchains,” in <i>42nd International Conference on Distributed Computing Systems Workshops</i>, Bologna, Italy, 2022, vol. 2022, pp. 45–52.","short":"A. De la Rocha, E. Kokoris Kogias, J.M. Soares, M. Vukolic, in:, 42nd International Conference on Distributed Computing Systems Workshops, Institute of Electrical and Electronics Engineers, 2022, pp. 45–52.","ama":"De la Rocha A, Kokoris Kogias E, Soares JM, Vukolic M. Hierarchical consensus: A horizontal scaling framework for blockchains. In: <i>42nd International Conference on Distributed Computing Systems Workshops</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:45-52. doi:<a href=\"https://doi.org/10.1109/icdcsw56584.2022.00018\">10.1109/icdcsw56584.2022.00018</a>"},"intvolume":"      2022","day":"29","status":"public","abstract":[{"lang":"eng","text":"We present the Filecoin Hierarchical Consensus framework, which aims to overcome the throughput challenges of blockchain consensus by horizontally scaling the network. Unlike traditional sharding designs, based on partitioning the state of the network, our solution centers on the concept of subnets -which are organized hierarchically- and can be spawned on-demand to manage new state. Child sub nets are firewalled from parent subnets, have their own specific policies, and run a different consensus algorithm, increasing the network capacity and enabling new applications. Moreover, they benefit from the security of parent subnets by periodically checkpointing state. In this paper, we introduce the overall system architecture, our detailed designs for cross-net transaction handling, and the open questions that we are still exploring."}],"publication":"42nd International Conference on Distributed Computing Systems Workshops","author":[{"last_name":"De la Rocha","first_name":"Alfonso","full_name":"De la Rocha, Alfonso"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"last_name":"Soares","first_name":"Jorge M.","full_name":"Soares, Jorge M."},{"full_name":"Vukolic, Marko","first_name":"Marko","last_name":"Vukolic"}],"external_id":{"isi":["000895984800009"]},"oa_version":"None","conference":{"start_date":"2022-07-10","name":"ICDCSW: International Conference on Distributed Computing Systems Workshop","end_date":"2022-07-10","location":"Bologna, Italy"},"date_published":"2022-11-29T00:00:00Z","language":[{"iso":"eng"}],"type":"conference","doi":"10.1109/icdcsw56584.2022.00018","publisher":"Institute of Electrical and Electronics Engineers","publication_identifier":{"eisbn":["9781665488792"],"eissn":["2332-5666"]},"scopus_import":"1","article_processing_charge":"No","isi":1,"volume":2022,"year":"2022","date_created":"2023-01-12T12:09:28Z","quality_controlled":"1","page":"45-52","date_updated":"2023-08-04T09:06:02Z"},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.05181","open_access":"1"}],"publication_identifier":{"eissn":["2831-7475"],"eisbn":["9781665490627"]},"article_processing_charge":"No","volume":2022,"isi":1,"date_updated":"2023-08-04T09:06:34Z","quality_controlled":"1","page":"2128-2134","year":"2022","date_created":"2023-01-12T12:09:38Z","author":[{"first_name":"Paulina","full_name":"Tomaszewska, Paulina","last_name":"Tomaszewska"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph"}],"publication":"26th International Conference on Pattern Recognition","date_published":"2022-11-29T00:00:00Z","conference":{"location":"Montreal, Canada","end_date":"2022-08-25","name":"ICPR: International Conference on Pattern Recognition","start_date":"2022-08-21"},"external_id":{"arxiv":["2206.05181"],"isi":["000897707602018"]},"oa_version":"Preprint","type":"conference","arxiv":1,"language":[{"iso":"eng"}],"publisher":"Institute of Electrical and Electronics Engineers","doi":"10.1109/icpr56361.2022.9956195","intvolume":"      2022","citation":{"short":"P. Tomaszewska, C. Lampert, in:, 26th International Conference on Pattern Recognition, Institute of Electrical and Electronics Engineers, 2022, pp. 2128–2134.","ama":"Tomaszewska P, Lampert C. Lightweight conditional model extrapolation for streaming data under class-prior shift. In: <i>26th International Conference on Pattern Recognition</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:2128-2134. doi:<a href=\"https://doi.org/10.1109/icpr56361.2022.9956195\">10.1109/icpr56361.2022.9956195</a>","ista":"Tomaszewska P, Lampert C. 2022. Lightweight conditional model extrapolation for streaming data under class-prior shift. 26th International Conference on Pattern Recognition. ICPR: International Conference on Pattern Recognition vol. 2022, 2128–2134.","chicago":"Tomaszewska, Paulina, and Christoph Lampert. “Lightweight Conditional Model Extrapolation for Streaming Data under Class-Prior Shift.” In <i>26th International Conference on Pattern Recognition</i>, 2022:2128–34. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/icpr56361.2022.9956195\">https://doi.org/10.1109/icpr56361.2022.9956195</a>.","apa":"Tomaszewska, P., &#38; Lampert, C. (2022). Lightweight conditional model extrapolation for streaming data under class-prior shift. In <i>26th International Conference on Pattern Recognition</i> (Vol. 2022, pp. 2128–2134). Montreal, Canada: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/icpr56361.2022.9956195\">https://doi.org/10.1109/icpr56361.2022.9956195</a>","ieee":"P. Tomaszewska and C. Lampert, “Lightweight conditional model extrapolation for streaming data under class-prior shift,” in <i>26th International Conference on Pattern Recognition</i>, Montreal, Canada, 2022, vol. 2022, pp. 2128–2134.","mla":"Tomaszewska, Paulina, and Christoph Lampert. “Lightweight Conditional Model Extrapolation for Streaming Data under Class-Prior Shift.” <i>26th International Conference on Pattern Recognition</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 2128–34, doi:<a href=\"https://doi.org/10.1109/icpr56361.2022.9956195\">10.1109/icpr56361.2022.9956195</a>."},"day":"29","abstract":[{"text":"We introduce LIMES, a new method for learning with non-stationary streaming data, inspired by the recent success of meta-learning. The main idea is not to attempt to learn a single classifier that would have to work well across all occurring data distributions, nor many separate classifiers, but to exploit a hybrid strategy: we learn a single set of model parameters from which a specific classifier for any specific data distribution is derived via classifier adaptation. Assuming a multiclass classification setting with class-prior shift, the adaptation step can be performed analytically with only the classifier’s bias terms being affected. Another contribution of our work is an extrapolation step that predicts suitable adaptation parameters for future time steps based on the previous data. In combination, we obtain a lightweight procedure for learning from streaming data with varying class distribution that adds no trainable parameters and almost no memory or computational overhead compared to training a single model. Experiments on a set of exemplary tasks using Twitter data show that LIMES achieves higher accuracy than alternative approaches, especially with respect to the relevant real-world metric of lowest within-day accuracy.","lang":"eng"}],"status":"public","department":[{"_id":"ChLa"}],"title":"Lightweight conditional model extrapolation for streaming data under class-prior shift","oa":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12161","month":"11"},{"date_published":"2022-11-28T00:00:00Z","oa_version":"Published Version","external_id":{"isi":["000892168800001"]},"author":[{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"publication":"Molecular Ecology","issue":"1","publisher":"Wiley","doi":"10.1111/mec.16779","type":"journal_article","language":[{"iso":"eng"}],"article_processing_charge":"No","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.16779"}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"date_updated":"2023-08-04T09:09:15Z","quality_controlled":"1","page":"26-29","year":"2022","date_created":"2023-01-12T12:10:28Z","volume":32,"isi":1,"department":[{"_id":"NiBa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","_id":"12166","article_type":"letter_note","oa":1,"title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize","publication_status":"published","day":"28","citation":{"chicago":"Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>.","ista":"Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","apa":"Westram, A. M., &#38; Butlin, R. (2022). Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>","ieee":"A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize,” <i>Molecular Ecology</i>, vol. 32, no. 1. Wiley, pp. 26–29, 2022.","mla":"Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>, vol. 32, no. 1, Wiley, 2022, pp. 26–29, doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>.","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.","ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. 2022;32(1):26-29. doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>"},"intvolume":"        32","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"abstract":[{"lang":"eng","text":"Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings."}],"status":"public"},{"abstract":[{"text":"Payment channels effectively move the transaction load off-chain thereby successfully addressing the inherent scalability problem most cryptocurrencies face. A major drawback of payment channels is the need to “top up” funds on-chain when a channel is depleted. Rebalancing was proposed to alleviate this issue, where parties with depleting channels move their funds along a cycle to replenish their channels off-chain. Protocols for rebalancing so far either introduce local solutions or compromise privacy.\r\nIn this work, we present an opt-in rebalancing protocol that is both private and globally optimal, meaning our protocol maximizes the total amount of rebalanced funds. We study rebalancing from the framework of linear programming. To obtain full privacy guarantees, we leverage multi-party computation in solving the linear program, which is executed by selected participants to maintain efficiency. Finally, we efficiently decompose the rebalancing solution into incentive-compatible cycles which conserve user balances when executed atomically.","lang":"eng"}],"status":"public","intvolume":"     13411","citation":{"mla":"Avarikioti, Georgia, et al. “Hide &#38; Seek: Privacy-Preserving Rebalancing on Payment Channel Networks.” <i>Financial Cryptography and Data Security</i>, vol. 13411, Springer Nature, 2022, pp. 358–73, doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_17\">10.1007/978-3-031-18283-9_17</a>.","ieee":"G. Avarikioti, K. Z. Pietrzak, I. Salem, S. Schmid, S. Tiwari, and M. X. Yeo, “Hide &#38; Seek: Privacy-preserving rebalancing on payment channel networks,” in <i>Financial Cryptography and Data Security</i>, Grenada, 2022, vol. 13411, pp. 358–373.","apa":"Avarikioti, G., Pietrzak, K. Z., Salem, I., Schmid, S., Tiwari, S., &#38; Yeo, M. X. (2022). Hide &#38; Seek: Privacy-preserving rebalancing on payment channel networks. In <i>Financial Cryptography and Data Security</i> (Vol. 13411, pp. 358–373). Grenada: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_17\">https://doi.org/10.1007/978-3-031-18283-9_17</a>","chicago":"Avarikioti, Georgia, Krzysztof Z Pietrzak, Iosif Salem, Stefan Schmid, Samarth Tiwari, and Michelle X Yeo. “Hide &#38; Seek: Privacy-Preserving Rebalancing on Payment Channel Networks.” In <i>Financial Cryptography and Data Security</i>, 13411:358–73. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_17\">https://doi.org/10.1007/978-3-031-18283-9_17</a>.","ista":"Avarikioti G, Pietrzak KZ, Salem I, Schmid S, Tiwari S, Yeo MX. 2022. Hide &#38; Seek: Privacy-preserving rebalancing on payment channel networks. Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13411, 358–373.","ama":"Avarikioti G, Pietrzak KZ, Salem I, Schmid S, Tiwari S, Yeo MX. Hide &#38; Seek: Privacy-preserving rebalancing on payment channel networks. In: <i>Financial Cryptography and Data Security</i>. Vol 13411. Springer Nature; 2022:358-373. doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_17\">10.1007/978-3-031-18283-9_17</a>","short":"G. Avarikioti, K.Z. Pietrzak, I. Salem, S. Schmid, S. Tiwari, M.X. Yeo, in:, Financial Cryptography and Data Security, Springer Nature, 2022, pp. 358–373."},"day":"22","oa":1,"title":"Hide & Seek: Privacy-preserving rebalancing on payment channel networks","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"12167","month":"10","alternative_title":["LNCS"],"department":[{"_id":"KrPi"}],"volume":13411,"date_updated":"2023-09-05T15:10:57Z","page":"358-373","quality_controlled":"1","year":"2022","date_created":"2023-01-12T12:10:38Z","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2110.08848","open_access":"1"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031182822"],"eisbn":["9783031182839"]},"article_processing_charge":"No","type":"conference","arxiv":1,"language":[{"iso":"eng"}],"publisher":"Springer Nature","doi":"10.1007/978-3-031-18283-9_17","author":[{"id":"c20482a0-3b89-11eb-9862-88cf6404b88c","full_name":"Avarikioti, Georgia","first_name":"Georgia","last_name":"Avarikioti"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"full_name":"Salem, Iosif","first_name":"Iosif","last_name":"Salem"},{"last_name":"Schmid","full_name":"Schmid, Stefan","first_name":"Stefan"},{"full_name":"Tiwari, Samarth","first_name":"Samarth","last_name":"Tiwari"},{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","first_name":"Michelle X","last_name":"Yeo"}],"publication":"Financial Cryptography and Data Security","date_published":"2022-10-22T00:00:00Z","conference":{"name":"FC: Financial Cryptography and Data Security","start_date":"2022-05-02","location":"Grenada","end_date":"2022-05-06"},"oa_version":"Preprint","external_id":{"arxiv":["2110.08848"]}}]