[{"oa":1,"day":"01","doi":"10.15227/orgsyn.100.0271","date_published":"2023-07-01T00:00:00Z","intvolume":"       100","year":"2023","article_type":"original","publication_identifier":{"issn":["0078-6209"],"eissn":["2333-3553"]},"publication":"Organic Syntheses","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","author":[{"first_name":"Amiera","last_name":"Madani","full_name":"Madani, Amiera"},{"first_name":"Eric T.","last_name":"Sletten","full_name":"Sletten, Eric T."},{"first_name":"Cristian","last_name":"Cavedon","full_name":"Cavedon, Cristian"},{"last_name":"Seeberger","full_name":"Seeberger, Peter H.","first_name":"Peter H."},{"first_name":"Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus","last_name":"Pieber"}],"title":"Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose","page":"271-286","date_updated":"2024-10-09T21:06:16Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"short":"A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses 100 (2023) 271–286.","apa":"Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., &#38; Pieber, B. (2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. <i>Organic Syntheses</i>. Organic Syntheses. <a href=\"https://doi.org/10.15227/orgsyn.100.0271\">https://doi.org/10.15227/orgsyn.100.0271</a>","ieee":"A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,” <i>Organic Syntheses</i>, vol. 100. Organic Syntheses, pp. 271–286, 2023.","ama":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. <i>Organic Syntheses</i>. 2023;100:271-286. doi:<a href=\"https://doi.org/10.15227/orgsyn.100.0271\">10.15227/orgsyn.100.0271</a>","mla":"Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” <i>Organic Syntheses</i>, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:<a href=\"https://doi.org/10.15227/orgsyn.100.0271\">10.15227/orgsyn.100.0271</a>.","ista":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 100, 271–286.","chicago":"Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger, and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” <i>Organic Syntheses</i>. Organic Syntheses, 2023. <a href=\"https://doi.org/10.15227/orgsyn.100.0271\">https://doi.org/10.15227/orgsyn.100.0271</a>."},"type":"journal_article","quality_controlled":"1","volume":100,"department":[{"_id":"BaPi"}],"corr_author":"1","publisher":"Organic Syntheses","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15227/orgsyn.100.0271"}],"publication_status":"published","date_created":"2023-08-06T22:01:11Z","_id":"13970","month":"07","scopus_import":"1"},{"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"publication":"Nature Physics","isi":1,"ec_funded":1,"acknowledgement":"D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa for providing the E. coli strains. This material is based upon work supported by the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411.","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"year":"2023","article_type":"original","intvolume":"        19","date_published":"2023-11-01T00:00:00Z","day":"01","doi":"10.1038/s41567-023-02136-x","oa":1,"file":[{"access_level":"open_access","date_created":"2024-01-30T12:26:08Z","success":1,"file_name":"2023_NaturePhysics_Grober.pdf","creator":"dernst","file_size":6365607,"checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","content_type":"application/pdf","relation":"main_file","date_updated":"2024-01-30T12:26:08Z","file_id":"14906"}],"file_date_updated":"2024-01-30T12:26:08Z","has_accepted_license":"1","article_processing_charge":"Yes","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-04-14T07:43:56Z","page":"1680-1688","author":[{"first_name":"Daniel","full_name":"Grober, Daniel","last_name":"Grober","id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99"},{"orcid":" 0000-0002-8843-9485 ","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","full_name":"Palaia, Ivan","first_name":"Ivan"},{"first_name":"Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","full_name":"Palacci, Jérémie A","first_name":"Jérémie A"}],"title":"Unconventional colloidal aggregation in chiral bacterial baths","oa_version":"Published Version","corr_author":"1","publisher":"Springer Nature","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"volume":19,"quality_controlled":"1","abstract":[{"text":"When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases.","lang":"eng"}],"type":"journal_article","citation":{"ieee":"D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci, “Unconventional colloidal aggregation in chiral bacterial baths,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1680–1688, 2023.","ama":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. 2023;19:1680-1688. doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>","apa":"Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., &#38; Palacci, J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>","ista":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.","chicago":"Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić, and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>.","mla":"Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>.","short":"D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688."},"scopus_import":"1","month":"11","_id":"13971","external_id":{"isi":["001037346400005"]},"date_created":"2023-08-06T22:01:11Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"corr_author":"1","publisher":"Wiley","main_file_link":[{"url":"https://doi.org/10.1002/cctc.202300683","open_access":"1"}],"volume":15,"department":[{"_id":"BaPi"}],"abstract":[{"lang":"eng","text":"This Special Collection is dedicated to the field of photocatalytic synthesis and contains a diverse selection of original research contributions. It includes studies on catalyst development, mechanistic investigations, method development and the use of enabling technologies, illustrating the many facets of state-of-the-art research in photocatalytic synthesis. Further, emerging topics are surveyed and discussed in three reviews and a concept article."}],"type":"journal_article","citation":{"mla":"Næsborg, Line, et al. “Special Collection: Photocatalytic Synthesis.” <i>ChemCatChem</i>, vol. 15, no. 17, e202300683, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/cctc.202300683\">10.1002/cctc.202300683</a>.","chicago":"Næsborg, Line, Bartholomäus Pieber, and Oliver S. Wenger. “Special Collection: Photocatalytic Synthesis.” <i>ChemCatChem</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/cctc.202300683\">https://doi.org/10.1002/cctc.202300683</a>.","ista":"Næsborg L, Pieber B, Wenger OS. 2023. Special Collection: Photocatalytic synthesis. ChemCatChem. 15(17), e202300683.","ieee":"L. Næsborg, B. Pieber, and O. S. Wenger, “Special Collection: Photocatalytic synthesis,” <i>ChemCatChem</i>, vol. 15, no. 17. Wiley, 2023.","ama":"Næsborg L, Pieber B, Wenger OS. Special Collection: Photocatalytic synthesis. <i>ChemCatChem</i>. 2023;15(17). doi:<a href=\"https://doi.org/10.1002/cctc.202300683\">10.1002/cctc.202300683</a>","apa":"Næsborg, L., Pieber, B., &#38; Wenger, O. S. (2023). Special Collection: Photocatalytic synthesis. <i>ChemCatChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cctc.202300683\">https://doi.org/10.1002/cctc.202300683</a>","short":"L. Næsborg, B. Pieber, O.S. Wenger, ChemCatChem 15 (2023)."},"quality_controlled":"1","month":"09","scopus_import":"1","issue":"17","_id":"13972","external_id":{"isi":["001037859900001"]},"publication_status":"published","date_created":"2023-08-06T22:01:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"ChemCatChem","isi":1,"article_number":"e202300683","article_type":"letter_note","year":"2023","publication_identifier":{"issn":["1867-3880"],"eissn":["1867-3899"]},"day":"08","doi":"10.1002/cctc.202300683","oa":1,"intvolume":"        15","date_published":"2023-09-08T00:00:00Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"last_name":"Næsborg","full_name":"Næsborg, Line","first_name":"Line"},{"orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus"},{"last_name":"Wenger","full_name":"Wenger, Oliver S.","first_name":"Oliver S."}],"title":"Special Collection: Photocatalytic synthesis","date_updated":"2024-07-16T07:35:15Z","oa_version":"Published Version"},{"volume":73,"department":[{"_id":"TiBr"}],"corr_author":"1","publisher":"Association des Annales de l'Institut Fourier","citation":{"mla":"Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle on Log K3 Surfaces.” <i>Annales de l’Institut Fourier</i>, vol. 73, no. 2, Association des Annales de l’Institut Fourier, 2023, pp. 447–78, doi:<a href=\"https://doi.org/10.5802/aif.3529\">10.5802/aif.3529</a>.","ista":"Lyczak J. 2023. Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. 73(2), 447–478.","chicago":"Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle on Log K3 Surfaces.” <i>Annales de l’Institut Fourier</i>. Association des Annales de l’Institut Fourier, 2023. <a href=\"https://doi.org/10.5802/aif.3529\">https://doi.org/10.5802/aif.3529</a>.","ieee":"J. Lyczak, “Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces,” <i>Annales de l’Institut Fourier</i>, vol. 73, no. 2. Association des Annales de l’Institut Fourier, pp. 447–478, 2023.","apa":"Lyczak, J. (2023). Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. <i>Annales de l’Institut Fourier</i>. Association des Annales de l’Institut Fourier. <a href=\"https://doi.org/10.5802/aif.3529\">https://doi.org/10.5802/aif.3529</a>","ama":"Lyczak J. Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. <i>Annales de l’Institut Fourier</i>. 2023;73(2):447-478. doi:<a href=\"https://doi.org/10.5802/aif.3529\">10.5802/aif.3529</a>","short":"J. Lyczak, Annales de l’Institut Fourier 73 (2023) 447–478."},"type":"journal_article","abstract":[{"lang":"eng","text":"We construct families of log K3 surfaces and study the arithmetic of their members. We use this to produce explicit surfaces with an order 5 Brauer–Manin obstruction to the integral Hasse principle."}],"quality_controlled":"1","_id":"13973","month":"05","scopus_import":"1","issue":"2","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png"},"publication_status":"published","date_created":"2023-08-06T22:01:12Z","external_id":{"isi":["001000279500001"],"arxiv":["2005.14013"]},"isi":1,"arxiv":1,"publication":"Annales de l'Institut Fourier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"ddc":["510"],"file":[{"date_updated":"2023-08-07T07:19:42Z","file_id":"13977","content_type":"application/pdf","checksum":"daf53fc614c894422e4c0fb3d2a2ae3e","relation":"main_file","creator":"dernst","file_size":1529821,"success":1,"file_name":"2023_AnnalesFourier_Lyczak.pdf","date_created":"2023-08-07T07:19:42Z","access_level":"open_access"}],"oa":1,"day":"12","doi":"10.5802/aif.3529","date_published":"2023-05-12T00:00:00Z","intvolume":"        73","year":"2023","article_type":"original","acknowledgement":"This paper was completed as part of a project which received funding from the\r\nEuropean Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie grant agreement No. 754411.","publication_identifier":{"issn":["0373-0956"]},"ec_funded":1,"title":"Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces","author":[{"id":"3572849A-F248-11E8-B48F-1D18A9856A87","last_name":"Lyczak","full_name":"Lyczak, Julian","first_name":"Julian"}],"page":"447-478","date_updated":"2025-04-14T07:43:56Z","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2023-08-07T07:19:42Z","oa_version":"Published Version"},{"title":"Scientists without borders: Lessons from Ukraine","author":[{"full_name":"Wolfsberger, Walter","last_name":"Wolfsberger","first_name":"Walter"},{"full_name":"Chhugani, Karishma","last_name":"Chhugani","first_name":"Karishma"},{"full_name":"Shchubelka, Khrystyna","last_name":"Shchubelka","first_name":"Khrystyna"},{"first_name":"Alina","last_name":"Frolova","full_name":"Frolova, Alina"},{"first_name":"Yuriy","last_name":"Salyha","full_name":"Salyha, Yuriy"},{"last_name":"Zlenko","full_name":"Zlenko, Oksana","first_name":"Oksana"},{"first_name":"Mykhailo","last_name":"Arych","full_name":"Arych, Mykhailo"},{"first_name":"Dmytro","full_name":"Dziuba, Dmytro","last_name":"Dziuba"},{"first_name":"Andrii","full_name":"Parkhomenko, Andrii","last_name":"Parkhomenko"},{"last_name":"Smolanka","full_name":"Smolanka, Volodymyr","first_name":"Volodymyr"},{"full_name":"Gümüş, Zeynep H.","last_name":"Gümüş","first_name":"Zeynep H."},{"full_name":"Sezgin, Efe","last_name":"Sezgin","first_name":"Efe"},{"first_name":"Alondra","last_name":"Diaz-Lameiro","full_name":"Diaz-Lameiro, Alondra"},{"last_name":"Toth","full_name":"Toth, Viktor R.","first_name":"Viktor R."},{"first_name":"Megi","last_name":"Maci","full_name":"Maci, Megi"},{"first_name":"Eric","last_name":"Bortz","full_name":"Bortz, Eric"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"last_name":"Morton","full_name":"Morton, Patricia M.","first_name":"Patricia M."},{"first_name":"Paweł P.","full_name":"Łabaj, Paweł P.","last_name":"Łabaj"},{"last_name":"Romero","full_name":"Romero, Veronika","first_name":"Veronika"},{"full_name":"Hlávka, Jakub","last_name":"Hlávka","first_name":"Jakub"},{"first_name":"Serghei","last_name":"Mangul","full_name":"Mangul, Serghei"},{"full_name":"Oleksyk, Taras K.","last_name":"Oleksyk","first_name":"Taras K."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/gigascience/giad066"}]},"date_updated":"2025-05-14T11:07:17Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"Yes","oa_version":"Published Version","isi":1,"publication":"GigaScience","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"doi":"10.1093/gigascience/giad045","day":"27","date_published":"2023-07-27T00:00:00Z","intvolume":"        12","article_number":"giad045","year":"2023","acknowledgement":"Our article is dedicated to all freedom-loving people around the world and to the people of Ukraine who fight for our freedom. Special thanks to Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful review, valuable criticism, and useful suggestions while preparing this manuscript, and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered their time. No funding supported work on this article.","article_type":"review","publication_identifier":{"eissn":["2047-217X"]},"_id":"13976","month":"07","scopus_import":"1","publication_status":"published","date_created":"2023-08-06T22:01:13Z","external_id":{"pmid":["37496156"],"isi":["001081086100001"]},"volume":12,"department":[{"_id":"FyKo"}],"publisher":"Oxford University Press","main_file_link":[{"url":"https://doi.org/10.1093/gigascience/giad045","open_access":"1"}],"citation":{"chicago":"Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova, Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders: Lessons from Ukraine.” <i>GigaScience</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/gigascience/giad045\">https://doi.org/10.1093/gigascience/giad045</a>.","ista":"Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience. 12, giad045.","mla":"Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.” <i>GigaScience</i>, vol. 12, giad045, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/gigascience/giad045\">10.1093/gigascience/giad045</a>.","ieee":"W. Wolfsberger <i>et al.</i>, “Scientists without borders: Lessons from Ukraine,” <i>GigaScience</i>, vol. 12. Oxford University Press, 2023.","ama":"Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders: Lessons from Ukraine. <i>GigaScience</i>. 2023;12. doi:<a href=\"https://doi.org/10.1093/gigascience/giad045\">10.1093/gigascience/giad045</a>","apa":"Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko, O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine. <i>GigaScience</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gigascience/giad045\">https://doi.org/10.1093/gigascience/giad045</a>","short":"W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko, M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro, V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero, J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023)."},"type":"journal_article","abstract":[{"text":"Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades’ worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.","lang":"eng"}],"pmid":1,"quality_controlled":"1"},{"oa_version":"Published Version","keyword":["General Engineering","General Materials Science","General Computer Science","Electrical and Electronic Engineering"],"page":"8651-8662","date_updated":"2024-10-09T21:06:38Z","author":[{"orcid":"0000-0001-7227-8309","last_name":"Neiheiser","full_name":"Neiheiser, Ray","id":"f09651b9-fec0-11ec-b5d8-934aff0e52a4","first_name":"Ray"},{"first_name":"Gustavo","full_name":"Inacio, Gustavo","last_name":"Inacio"},{"first_name":"Luciana","full_name":"Rech, Luciana","last_name":"Rech"},{"last_name":"Montez","full_name":"Montez, Carlos","first_name":"Carlos"},{"first_name":"Miguel","last_name":"Matos","full_name":"Matos, Miguel"},{"full_name":"Rodrigues, Luis","last_name":"Rodrigues","first_name":"Luis"}],"title":"Practical limitations of Ethereum’s layer-2","article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2023-08-22T06:37:48Z","language":[{"iso":"eng"}],"status":"public","date_published":"2023-08-01T00:00:00Z","intvolume":"        11","oa":1,"file":[{"access_level":"open_access","date_created":"2023-08-22T06:37:48Z","success":1,"file_name":"2023_IEEEAccess_Neiheiser.pdf","file_size":1289285,"creator":"dernst","relation":"main_file","content_type":"application/pdf","checksum":"4b80b0ff212edf7e5842fbdd53784432","file_id":"14166","date_updated":"2023-08-22T06:37:48Z"}],"day":"01","doi":"10.1109/access.2023.3237897","year":"2023","article_type":"original","publication_identifier":{"issn":["2169-3536"]},"acknowledgement":"This work was supported in part by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior (CAPES)—Brazil (CAPES), in part by the Fundação para a Ciência e Tecnologia (FCT) under Project UIDB/50021/2020 and Grant 2020.05270.BD, in part by the Project COSMOS (via the Orçamento de Estado (OE) with ref. PTDC/EEI-COM/29271/2017 and via the ‘‘Programa Operacional Regional de Lisboa na sua componente Fundo Europeu de Desenvolvimento Regional (FEDER)’’ with ref. Lisboa-01-0145-FEDER-029271), and in part by the project Angainor with reference LISBOA-01-0145-FEDER-031456 as well as supported by Meta Platforms for the project key Transparency at Scale.","isi":1,"publication":"IEEE Access","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-09T12:09:57Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"isi":["000927831000001"]},"_id":"13988","scopus_import":"1","month":"08","quality_controlled":"1","citation":{"short":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, L. Rodrigues, IEEE Access 11 (2023) 8651–8662.","mla":"Neiheiser, Ray, et al. “Practical Limitations of Ethereum’s Layer-2.” <i>IEEE Access</i>, vol. 11, Institute of Electrical and Electronics Engineers, 2023, pp. 8651–62, doi:<a href=\"https://doi.org/10.1109/access.2023.3237897\">10.1109/access.2023.3237897</a>.","ista":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. 2023. Practical limitations of Ethereum’s layer-2. IEEE Access. 11, 8651–8662.","chicago":"Neiheiser, Ray, Gustavo Inacio, Luciana Rech, Carlos Montez, Miguel Matos, and Luis Rodrigues. “Practical Limitations of Ethereum’s Layer-2.” <i>IEEE Access</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/access.2023.3237897\">https://doi.org/10.1109/access.2023.3237897</a>.","ieee":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, and L. Rodrigues, “Practical limitations of Ethereum’s layer-2,” <i>IEEE Access</i>, vol. 11. Institute of Electrical and Electronics Engineers, pp. 8651–8662, 2023.","ama":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. Practical limitations of Ethereum’s layer-2. <i>IEEE Access</i>. 2023;11:8651-8662. doi:<a href=\"https://doi.org/10.1109/access.2023.3237897\">10.1109/access.2023.3237897</a>","apa":"Neiheiser, R., Inacio, G., Rech, L., Montez, C., Matos, M., &#38; Rodrigues, L. (2023). Practical limitations of Ethereum’s layer-2. <i>IEEE Access</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/access.2023.3237897\">https://doi.org/10.1109/access.2023.3237897</a>"},"type":"journal_article","abstract":[{"lang":"eng","text":"Most permissionless blockchains inherently suffer from throughput limitations. Layer-2 systems, such as side-chains or Rollups, have been proposed as a possible strategy to overcome this limitation. Layer-2 systems interact with the main-chain in two ways. First, users can move funds from/to the main-chain to/from the layer-2. Second, layer-2 systems periodically synchronize with the main-chain to keep some form of log of their activity on the main-chain - this log is key for security. Due to this interaction with the main-chain, which is necessary and recurrent, layer-2 systems impose some load on the main-chain. The impact of such load on the main-chain has been, so far, poorly understood. In addition to that, layer-2 approaches typically sacrifice decentralization and security in favor of higher throughput. This paper presents an experimental study that analyzes the current state of Ethereum layer-2 projects. Our goal is to assess the load they impose on Ethereum and to understand their scalability potential in the long-run. Our analysis shows that the impact of any given layer-2 on the main-chain is the result of both technical aspects (how state is logged on the main-chain) and user behavior (how often users decide to transfer funds between the layer-2 and the main-chain). Based on our observations, we infer that without efficient mechanisms that allow users to transfer funds in a secure and fast manner directly from one layer-2 project to another, current layer-2 systems will not be able to scale Ethereum effectively, regardless of their technical solutions. Furthermore, from our results, we conclude that the layer-2 systems that offer similar security guarantees as Ethereum have limited scalability potential, while approaches that offer better performance, sacrifice security and lead to an increase in centralization which runs against the end-goals of permissionless blockchains."}],"department":[{"_id":"ElKo"}],"volume":11,"publisher":"Institute of Electrical and Electronics Engineers","corr_author":"1"},{"date_created":"2023-08-09T13:06:59Z","publication_status":"published","external_id":{"arxiv":["2209.02283"],"pmid":["37316515"]},"_id":"13989","scopus_import":"1","month":"06","quality_controlled":"1","type":"journal_article","pmid":1,"abstract":[{"text":"Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements.","lang":"eng"}],"extern":"1","citation":{"short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023).","mla":"Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>, vol. 14, 3512, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38540-3\">10.1038/s41467-023-38540-3</a>.","chicago":"Hales, Jordyn, Utkarsh Bajpai, Tongtong Liu, Denitsa Rangelova Baykusheva, Mingda Li, Matteo Mitrano, and Yao Wang. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38540-3\">https://doi.org/10.1038/s41467-023-38540-3</a>.","ista":"Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 14, 3512.","ieee":"J. Hales <i>et al.</i>, “Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ama":"Hales J, Bajpai U, Liu T, et al. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38540-3\">10.1038/s41467-023-38540-3</a>","apa":"Hales, J., Bajpai, U., Liu, T., Baykusheva, D. R., Li, M., Mitrano, M., &#38; Wang, Y. (2023). Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38540-3\">https://doi.org/10.1038/s41467-023-38540-3</a>"},"volume":14,"main_file_link":[{"url":"https://doi.org/10.1038/s41467-023-38540-3","open_access":"1"}],"publisher":"Springer Nature","oa_version":"Published Version","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"date_updated":"2023-08-22T06:50:04Z","author":[{"first_name":"Jordyn","full_name":"Hales, Jordyn","last_name":"Hales"},{"last_name":"Bajpai","full_name":"Bajpai, Utkarsh","first_name":"Utkarsh"},{"full_name":"Liu, Tongtong","last_name":"Liu","first_name":"Tongtong"},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"first_name":"Mingda","last_name":"Li","full_name":"Li, Mingda"},{"first_name":"Matteo","full_name":"Mitrano, Matteo","last_name":"Mitrano"},{"first_name":"Yao","last_name":"Wang","full_name":"Wang, Yao"}],"title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","intvolume":"        14","date_published":"2023-06-14T00:00:00Z","day":"14","doi":"10.1038/s41467-023-38540-3","oa":1,"publication_identifier":{"eissn":["2041-1723"]},"year":"2023","article_type":"original","article_number":"3512","arxiv":1,"publication":"Nature Communications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","citation":{"short":"D.R. Baykusheva, M.H. Kalthoff, D. Hofmann, M. Claassen, D.M. Kennes, M.A. Sentef, M. Mitrano, Physical Review Letters 130 (2023).","ama":"Baykusheva DR, Kalthoff MH, Hofmann D, et al. Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain. <i>Physical Review Letters</i>. 2023;130(10). doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106902\">10.1103/physrevlett.130.106902</a>","ieee":"D. R. Baykusheva <i>et al.</i>, “Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain,” <i>Physical Review Letters</i>, vol. 130, no. 10. American Physical Society, 2023.","apa":"Baykusheva, D. R., Kalthoff, M. H., Hofmann, D., Claassen, M., Kennes, D. M., Sentef, M. A., &#38; Mitrano, M. (2023). Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.130.106902\">https://doi.org/10.1103/physrevlett.130.106902</a>","mla":"Baykusheva, Denitsa Rangelova, et al. “Witnessing Nonequilibrium Entanglement Dynamics in a Strongly Correlated Fermionic Chain.” <i>Physical Review Letters</i>, vol. 130, no. 10, 106902, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106902\">10.1103/physrevlett.130.106902</a>.","ista":"Baykusheva DR, Kalthoff MH, Hofmann D, Claassen M, Kennes DM, Sentef MA, Mitrano M. 2023. Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain. Physical Review Letters. 130(10), 106902.","chicago":"Baykusheva, Denitsa Rangelova, Mona H. Kalthoff, Damian Hofmann, Martin Claassen, Dante M. Kennes, Michael A. Sentef, and Matteo Mitrano. “Witnessing Nonequilibrium Entanglement Dynamics in a Strongly Correlated Fermionic Chain.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.130.106902\">https://doi.org/10.1103/physrevlett.130.106902</a>."},"pmid":1,"type":"journal_article","abstract":[{"lang":"eng","text":"Many-body entanglement in condensed matter systems can be diagnosed from equilibrium response functions through the use of entanglement witnesses and operator-specific quantum bounds. Here, we investigate the applicability of this approach for detecting entangled states in quantum systems driven out of equilibrium. We use a multipartite entanglement witness, the quantum Fisher information, to study the dynamics of a paradigmatic fermion chain undergoing a time-dependent change of the Coulomb interaction. Our results show that the quantum Fisher information is able to witness distinct signatures of multipartite entanglement both near and far from equilibrium that are robust against decoherence. We discuss implications of these findings for probing entanglement in light-driven quantum materials with time-resolved optical and x-ray scattering methods."}],"extern":"1","volume":130,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2209.02081"}],"publisher":"American Physical Society","date_created":"2023-08-09T13:07:24Z","publication_status":"published","external_id":{"pmid":["36962013"],"arxiv":["2209.02081"]},"_id":"13990","scopus_import":"1","issue":"10","month":"03","date_published":"2023-03-10T00:00:00Z","intvolume":"       130","oa":1,"day":"10","doi":"10.1103/physrevlett.130.106902","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"article_type":"original","year":"2023","article_number":"106902","publication":"Physical Review Letters","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","keyword":["General Physics and Astronomy"],"date_updated":"2024-10-14T12:23:16Z","title":"Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain","author":[{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"first_name":"Mona H.","full_name":"Kalthoff, Mona H.","last_name":"Kalthoff"},{"last_name":"Hofmann","full_name":"Hofmann, Damian","first_name":"Damian"},{"full_name":"Claassen, Martin","last_name":"Claassen","first_name":"Martin"},{"full_name":"Kennes, Dante M.","last_name":"Kennes","first_name":"Dante M."},{"full_name":"Sentef, Michael A.","last_name":"Sentef","first_name":"Michael A."},{"first_name":"Matteo","last_name":"Mitrano","full_name":"Mitrano, Matteo"}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}]},{"date_created":"2023-08-13T22:01:11Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37536064"],"isi":["001053616200001"]},"_id":"14036","issue":"10","scopus_import":"1","month":"10","quality_controlled":"1","abstract":[{"lang":"eng","text":"Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies."}],"pmid":1,"type":"journal_article","citation":{"short":"F. Napoli, L.M. Becker, P. Schanda, Current Opinion in Structural Biology 82 (2023).","ista":"Napoli F, Becker LM, Schanda P. 2023. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 82(10), 102660.","chicago":"Napoli, Federico, Lea Marie Becker, and Paul Schanda. “Protein Dynamics Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.sbi.2023.102660\">https://doi.org/10.1016/j.sbi.2023.102660</a>.","mla":"Napoli, Federico, et al. “Protein Dynamics Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” <i>Current Opinion in Structural Biology</i>, vol. 82, no. 10, 102660, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.sbi.2023.102660\">10.1016/j.sbi.2023.102660</a>.","ieee":"F. Napoli, L. M. Becker, and P. Schanda, “Protein dynamics detected by magic-angle spinning relaxation dispersion NMR,” <i>Current Opinion in Structural Biology</i>, vol. 82, no. 10. Elsevier, 2023.","apa":"Napoli, F., Becker, L. M., &#38; Schanda, P. (2023). Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2023.102660\">https://doi.org/10.1016/j.sbi.2023.102660</a>","ama":"Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. <i>Current Opinion in Structural Biology</i>. 2023;82(10). doi:<a href=\"https://doi.org/10.1016/j.sbi.2023.102660\">10.1016/j.sbi.2023.102660</a>"},"department":[{"_id":"PaSc"}],"volume":82,"publisher":"Elsevier","corr_author":"1","oa_version":"Published Version","date_updated":"2025-04-14T09:10:17Z","author":[{"first_name":"Federico","orcid":"0000-0002-9043-136X","last_name":"Napoli","full_name":"Napoli, Federico","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b"},{"first_name":"Lea Marie","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"}],"title":"Protein dynamics detected by magic-angle spinning relaxation dispersion NMR","file_date_updated":"2024-01-30T12:36:39Z","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"status":"public","intvolume":"        82","date_published":"2023-10-01T00:00:00Z","day":"01","doi":"10.1016/j.sbi.2023.102660","file":[{"access_level":"open_access","success":1,"file_name":"2023_CurrentOpinionStrucBio_Napoli.pdf","date_created":"2024-01-30T12:36:39Z","creator":"dernst","file_size":1231998,"checksum":"c850f7ac8a4234319755b672c1df69ae","content_type":"application/pdf","relation":"main_file","date_updated":"2024-01-30T12:36:39Z","file_id":"14907"}],"oa":1,"publication_identifier":{"eissn":["1879-033X"],"issn":["0959-440X"]},"article_type":"original","year":"2023","acknowledgement":"We thank Petra Rovó for critical reading of this manuscript. We acknowledge the Austrian Science Foundation FWF (project AlloSpace, number I5812–B) and funding by the Institute of Science and Technology Austria.","article_number":"102660","publication":"Current Opinion in Structural Biology","isi":1,"ddc":["570"],"project":[{"name":"AlloSpace. The emergence and mechanisms of allostery","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","grant_number":"I05812"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"scopus_import":"1","issue":"32","month":"07","_id":"14037","external_id":{"isi":["001121663600001"],"pmid":["37523549"]},"date_created":"2023-08-13T22:01:12Z","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"National Academy of Sciences","department":[{"_id":"MiLe"}],"volume":120,"quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Traditionally, nuclear spin is not considered to affect biological processes. Recently, this has changed as isotopic fractionation that deviates from classical mass dependence was reported both in vitro and in vivo. In these cases, the isotopic effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial dioxygen production system and biological aquaporin channels in cells. We observe that oxygen dynamics in chiral environments (in particular its transport) depend on nuclear spin, suggesting future applications for controlled isotope separation to be used, for instance, in NMR. To demonstrate the mechanism behind our findings, we formulate theoretical models based on a nuclear-spin-enhanced switch between electronic spin states. Accounting for the role of nuclear spin in biology can provide insights into the role of quantum effects in living systems and help inspire the development of future biotechnology solutions."}],"pmid":1,"citation":{"ama":"Vardi O, Maroudas-Sklare N, Kolodny Y, et al. Nuclear spin effects in biological processes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(32). doi:<a href=\"https://doi.org/10.1073/pnas.2300828120\">10.1073/pnas.2300828120</a>","ieee":"O. Vardi <i>et al.</i>, “Nuclear spin effects in biological processes,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 32. National Academy of Sciences, 2023.","apa":"Vardi, O., Maroudas-Sklare, N., Kolodny, Y., Volosniev, A., Saragovi, A., Galili, N., … Paltiel, Y. (2023). Nuclear spin effects in biological processes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2300828120\">https://doi.org/10.1073/pnas.2300828120</a>","ista":"Vardi O, Maroudas-Sklare N, Kolodny Y, Volosniev A, Saragovi A, Galili N, Ferrera S, Ghazaryan A, Yuran N, Affek HP, Luz B, Goldsmith Y, Keren N, Yochelis S, Halevy I, Lemeshko M, Paltiel Y. 2023. Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. 120(32), e2300828120.","chicago":"Vardi, Ofek, Naama Maroudas-Sklare, Yuval Kolodny, Artem Volosniev, Amijai Saragovi, Nir Galili, Stav Ferrera, et al. “Nuclear Spin Effects in Biological Processes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2300828120\">https://doi.org/10.1073/pnas.2300828120</a>.","mla":"Vardi, Ofek, et al. “Nuclear Spin Effects in Biological Processes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 32, e2300828120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2300828120\">10.1073/pnas.2300828120</a>.","short":"O. Vardi, N. Maroudas-Sklare, Y. Kolodny, A. Volosniev, A. Saragovi, N. Galili, S. Ferrera, A. Ghazaryan, N. Yuran, H.P. Affek, B. Luz, Y. Goldsmith, N. Keren, S. Yochelis, I. Halevy, M. Lemeshko, Y. Paltiel, Proceedings of the National Academy of Sciences of the United States of America 120 (2023)."},"file_date_updated":"2023-08-14T07:43:45Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-09-09T12:47:53Z","title":"Nuclear spin effects in biological processes","author":[{"last_name":"Vardi","full_name":"Vardi, Ofek","first_name":"Ofek"},{"first_name":"Naama","full_name":"Maroudas-Sklare, Naama","last_name":"Maroudas-Sklare"},{"first_name":"Yuval","full_name":"Kolodny, Yuval","last_name":"Kolodny"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","first_name":"Artem"},{"first_name":"Amijai","full_name":"Saragovi, Amijai","last_name":"Saragovi"},{"last_name":"Galili","full_name":"Galili, Nir","first_name":"Nir"},{"last_name":"Ferrera","full_name":"Ferrera, Stav","first_name":"Stav"},{"orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"first_name":"Nir","full_name":"Yuran, Nir","last_name":"Yuran"},{"first_name":"Hagit P.","full_name":"Affek, Hagit P.","last_name":"Affek"},{"first_name":"Boaz","last_name":"Luz","full_name":"Luz, Boaz"},{"full_name":"Goldsmith, Yonaton","last_name":"Goldsmith","first_name":"Yonaton"},{"first_name":"Nir","last_name":"Keren","full_name":"Keren, Nir"},{"last_name":"Yochelis","full_name":"Yochelis, Shira","first_name":"Shira"},{"last_name":"Halevy","full_name":"Halevy, Itay","first_name":"Itay"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"last_name":"Paltiel","full_name":"Paltiel, Yossi","first_name":"Yossi"}],"oa_version":"Published Version","ddc":["530"],"project":[{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"ec_funded":1,"article_type":"original","year":"2023","acknowledgement":"N.M.-S. acknowledges the support of the Ministry of Energy, Israel, as part of the scholarship program for graduate students in the fields of energy. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. acknowledges the support of the Ministry of Innovation, Science and Technology, Israel Grant No. 1001593872. Y.P acknowledges the support of the BSF-NSF 094 Grant No. 2022503.","publication_identifier":{"eissn":["1091-6490"]},"article_number":"e2300828120","intvolume":"       120","date_published":"2023-07-31T00:00:00Z","doi":"10.1073/pnas.2300828120","day":"31","oa":1,"file":[{"checksum":"a5ed64788a5acef9b9a300a26fa5a177","content_type":"application/pdf","relation":"main_file","date_updated":"2023-08-14T07:43:45Z","file_id":"14047","access_level":"open_access","creator":"dernst","file_size":1003092,"file_name":"2023_PNAS_Vardi.pdf","date_created":"2023-08-14T07:43:45Z","success":1}]},{"quality_controlled":"1","abstract":[{"text":"Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them.","lang":"eng"}],"pmid":1,"type":"journal_article","citation":{"ama":"Leonard TA, Loose M, Martens S. The membrane surface as a platform that organizes cellular and biochemical processes. <i>Developmental Cell</i>. 2023;58(15):1315-1332. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.001\">10.1016/j.devcel.2023.06.001</a>","ieee":"T. A. Leonard, M. Loose, and S. Martens, “The membrane surface as a platform that organizes cellular and biochemical processes,” <i>Developmental Cell</i>, vol. 58, no. 15. Elsevier, pp. 1315–1332, 2023.","apa":"Leonard, T. A., Loose, M., &#38; Martens, S. (2023). The membrane surface as a platform that organizes cellular and biochemical processes. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.001\">https://doi.org/10.1016/j.devcel.2023.06.001</a>","chicago":"Leonard, Thomas A., Martin Loose, and Sascha Martens. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.001\">https://doi.org/10.1016/j.devcel.2023.06.001</a>.","ista":"Leonard TA, Loose M, Martens S. 2023. The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. 58(15), 1315–1332.","mla":"Leonard, Thomas A., et al. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” <i>Developmental Cell</i>, vol. 58, no. 15, Elsevier, 2023, pp. 1315–32, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.001\">10.1016/j.devcel.2023.06.001</a>.","short":"T.A. Leonard, M. Loose, S. Martens, Developmental Cell 58 (2023) 1315–1332."},"department":[{"_id":"MaLo"}],"volume":58,"publisher":"Elsevier","corr_author":"1","date_created":"2023-08-13T22:01:12Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37419118"],"isi":["001059110400001"]},"_id":"14039","issue":"15","scopus_import":"1","month":"08","intvolume":"        58","date_published":"2023-08-07T00:00:00Z","doi":"10.1016/j.devcel.2023.06.001","day":"07","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"d8c5dc97cd40c26da2ec98ae723ab368","file_id":"14049","date_updated":"2023-08-14T07:57:55Z","access_level":"open_access","date_created":"2023-08-14T07:57:55Z","success":1,"file_name":"2023_DevelopmentalCell_Leonard.pdf","file_size":3184217,"creator":"dernst"}],"oa":1,"article_type":"original","year":"2023","acknowledgement":"We acknowledge funding from the Austrian Science Fund (FWF F79, P32814-B, and P35061-B to S.M.; P34607-B to M.L.; and P30584-B and P33066-B to T.A.L.) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 101045340 to M.L.). We are grateful for comments on the manuscript by Justyna Sawa-Makarska, Verena Baumann, Marko Kojic, Philipp Radler, Ronja Reinhardt, and Sumire Antonioli.","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"publication":"Developmental Cell","isi":1,"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Synthetic and structural biology of Rab GTPase networks","_id":"bd6ae2ca-d553-11ed-ba76-a4aa239da5ee","grant_number":"101045340"}],"oa_version":"Published Version","page":"1315-1332","date_updated":"2024-10-22T11:40:18Z","author":[{"first_name":"Thomas A.","last_name":"Leonard","full_name":"Leonard, Thomas A."},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","first_name":"Martin"},{"first_name":"Sascha","last_name":"Martens","full_name":"Martens, Sascha"}],"title":"The membrane surface as a platform that organizes cellular and biochemical processes","file_date_updated":"2023-08-14T07:57:55Z","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public"},{"_id":"14040","month":"08","scopus_import":"1","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2023-08-13T22:01:13Z","external_id":{"isi":["001042606700004"],"pmid":["37542031"]},"volume":14,"department":[{"_id":"LeSa"}],"corr_author":"1","publisher":"Springer Nature","abstract":[{"text":"Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.","lang":"eng"}],"pmid":1,"type":"journal_article","citation":{"ama":"Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-40388-6\">10.1038/s41467-023-40388-6</a>","apa":"Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-40388-6\">https://doi.org/10.1038/s41467-023-40388-6</a>","ieee":"Z. Zhao <i>et al.</i>, “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-40388-6\">https://doi.org/10.1038/s41467-023-40388-6</a>.","ista":"Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 14, 4681.","mla":"Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” <i>Nature Communications</i>, vol. 14, 4681, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-40388-6\">10.1038/s41467-023-40388-6</a>.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023)."},"quality_controlled":"1","title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","author":[{"full_name":"Zhao, Ziyu","last_name":"Zhao","first_name":"Ziyu"},{"orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene"},{"first_name":"Jana","last_name":"Knoppová","full_name":"Knoppová, Jana"},{"first_name":"Roman","full_name":"Sobotka, Roman","last_name":"Sobotka"},{"last_name":"Murray","full_name":"Murray, James W.","first_name":"James W."},{"full_name":"Nixon, Peter J.","last_name":"Nixon","first_name":"Peter J."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A"},{"first_name":"Josef","full_name":"Komenda, Josef","last_name":"Komenda"}],"date_updated":"2025-04-23T13:05:33Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2023-08-14T07:01:12Z","has_accepted_license":"1","article_processing_charge":"Yes","oa_version":"Published Version","publication":"Nature Communications","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"doi":"10.1038/s41467-023-40388-6","day":"04","file":[{"date_created":"2023-08-14T07:01:12Z","success":1,"file_name":"2023_NatureComm_Zhao.pdf","file_size":2315325,"creator":"dernst","access_level":"open_access","file_id":"14044","date_updated":"2023-08-14T07:01:12Z","relation":"main_file","content_type":"application/pdf","checksum":"3b9043df3d51c300f9be95eac3ff9d0b"}],"oa":1,"intvolume":"        14","date_published":"2023-08-04T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"article_number":"4681","acknowledgement":"P.J.N. and J.W.M. are grateful for the support of the Biotechnology & Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J. Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project 19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster.","year":"2023","article_type":"original","publication_identifier":{"eissn":["2041-1723"]}},{"language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2023-08-14T07:17:36Z","title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","author":[{"last_name":"Méhes","full_name":"Méhes, Elod","first_name":"Elod"},{"last_name":"Mones","full_name":"Mones, Enys","first_name":"Enys"},{"first_name":"Máté","last_name":"Varga","full_name":"Varga, Máté"},{"first_name":"Áron","last_name":"Zsigmond","full_name":"Zsigmond, Áron"},{"full_name":"Biri-Kovács, Beáta","last_name":"Biri-Kovács","first_name":"Beáta"},{"first_name":"László","last_name":"Nyitray","full_name":"Nyitray, László"},{"orcid":"0000-0003-2676-3367","last_name":"Barone","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"first_name":"Gabriel","last_name":"Krens","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"full_name":"Vicsek, Tamás","last_name":"Vicsek","first_name":"Tamás"}],"date_updated":"2023-12-13T12:07:33Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"isi":1,"publication":"Communications Biology","article_number":"817","year":"2023","publication_identifier":{"eissn":["2399-3642"]},"acknowledgement":"We thank Marton Gulyas (ELTE Eötvös University) for development of videomicroscopy experiment manager and image analysis software. Authors are grateful to Gabor Forgacs (University of Missouri) for critical reading of earlier versions of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University) for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project No 227878 to TV, the National Research Development and Innovation Fund of Hungary, K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access funding provided by Eötvös Loránd University.","article_type":"original","file":[{"creator":"dernst","file_size":10181997,"date_created":"2023-08-14T07:17:36Z","file_name":"2023_CommBiology_Mehes.pdf","success":1,"access_level":"open_access","date_updated":"2023-08-14T07:17:36Z","file_id":"14045","checksum":"1f9324f736bdbb76426b07736651c4cd","content_type":"application/pdf","relation":"main_file"}],"oa":1,"day":"04","doi":"10.1038/s42003-023-05181-7","date_published":"2023-08-04T00:00:00Z","intvolume":"         6","month":"08","scopus_import":"1","_id":"14041","external_id":{"pmid":["37542157"],"isi":["001042544100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2023-08-13T22:01:13Z","publisher":"Springer Nature","volume":6,"department":[{"_id":"CaHe"},{"_id":"Bio"}],"citation":{"apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>","ieee":"E. Méhes <i>et al.</i>, “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” <i>Communications Biology</i>, vol. 6. Springer Nature, 2023.","ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>","ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817.","chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>.","mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>, vol. 6, 817, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>.","short":"E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023)."},"type":"journal_article","abstract":[{"text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering.","lang":"eng"}],"pmid":1,"quality_controlled":"1"},{"date_updated":"2023-12-13T12:08:08Z","title":"On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary","author":[{"full_name":"Bulíček, Miroslav","last_name":"Bulíček","first_name":"Miroslav"},{"last_name":"Málek","full_name":"Málek, Josef","first_name":"Josef"},{"first_name":"Erika","full_name":"Maringová, Erika","last_name":"Maringová","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2023-08-14T07:24:17Z","status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version","isi":1,"arxiv":1,"publication":"Journal of Mathematical Fluid Mechanics","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-08-01T00:00:00Z","intvolume":"        25","oa":1,"file":[{"relation":"main_file","checksum":"c549cd8f0dd02ed60477a05ca045f481","content_type":"application/pdf","file_id":"14046","date_updated":"2023-08-14T07:24:17Z","access_level":"open_access","file_name":"2023_JourMathFluidMech_Bulicek.pdf","date_created":"2023-08-14T07:24:17Z","success":1,"file_size":845748,"creator":"dernst"}],"doi":"10.1007/s00021-023-00803-w","day":"01","article_type":"original","publication_identifier":{"eissn":["1422-6952"],"issn":["1422-6928"]},"acknowledgement":"M. Bulíček and J. Málek acknowledge the support of the project No. 20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing supported by the National Technical Library in Prague.","year":"2023","article_number":"72","_id":"14042","scopus_import":"1","issue":"3","month":"08","date_created":"2023-08-13T22:01:13Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"arxiv":["2301.12834"],"isi":["001040354900001"]},"department":[{"_id":"JuFi"}],"volume":25,"publisher":"Springer Nature","quality_controlled":"1","citation":{"chicago":"Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” <i>Journal of Mathematical Fluid Mechanics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00021-023-00803-w\">https://doi.org/10.1007/s00021-023-00803-w</a>.","ista":"Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72.","mla":"Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” <i>Journal of Mathematical Fluid Mechanics</i>, vol. 25, no. 3, 72, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00021-023-00803-w\">10.1007/s00021-023-00803-w</a>.","apa":"Bulíček, M., Málek, J., &#38; Maringová, E. (2023). On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. <i>Journal of Mathematical Fluid Mechanics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00021-023-00803-w\">https://doi.org/10.1007/s00021-023-00803-w</a>","ieee":"M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary,” <i>Journal of Mathematical Fluid Mechanics</i>, vol. 25, no. 3. Springer Nature, 2023.","ama":"Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. <i>Journal of Mathematical Fluid Mechanics</i>. 2023;25(3). doi:<a href=\"https://doi.org/10.1007/s00021-023-00803-w\">10.1007/s00021-023-00803-w</a>","short":"M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics 25 (2023)."},"type":"journal_article","abstract":[{"text":"Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions.","lang":"eng"}]},{"external_id":{"isi":["001041254900002"],"arxiv":["2010.16316"]},"publication_status":"published","date_created":"2023-08-13T22:01:13Z","month":"12","scopus_import":"1","_id":"14043","abstract":[{"lang":"eng","text":"Over the last two decades, a significant line of work in theoretical algorithms has made progress in solving linear systems of the form Lx=b, where L is the Laplacian matrix of a weighted graph with weights w(i,j)>0 on the edges. The solution x of the linear system can be interpreted as the potentials of an electrical flow in which the resistance on edge (i, j) is 1/w(i, j). Kelner et al. (in: Proceedings of the 45th Annual ACM Symposium on the Theory of Computing, pp 911–920, 2013. https://doi.org/10.1145/2488608.2488724) give a combinatorial, near-linear time algorithm that maintains the Kirchoff Current Law, and gradually enforces the Kirchoff Potential Law by updating flows around cycles (cycle toggling). In this paper, we consider a dual version of the algorithm that maintains the Kirchoff Potential Law, and gradually enforces the Kirchoff Current Law by cut toggling: each iteration updates all potentials on one side of a fundamental cut of a spanning tree by the same amount. We prove that this dual algorithm also runs in a near-linear number of iterations. We show, however, that if we abstract cut toggling as a natural data structure problem, this problem can be reduced to the online vector–matrix-vector problem, which has been conjectured to be difficult for dynamic algorithms (Henzinger et al., in: Proceedings of the 47th Annual ACM Symposium on the Theory of Computing, pp 21–30, 2015. https://doi.org/10.1145/2746539.2746609). The conjecture implies that the data structure does not have an O(n1−ϵ) time algorithm for any ϵ>0, and thus a straightforward implementation of the cut-toggling algorithm requires essentially linear time per iteration. To circumvent the lower bound, we batch update steps, and perform them simultaneously instead of sequentially. An appropriate choice of batching leads to an O˜(m1.5) time cut-toggling algorithm for solving Laplacian systems. Furthermore, we show that if we sparsify the graph and call our algorithm recursively on the Laplacian system implied by batching and sparsifying, we can reduce the running time to O(m1+ϵ) for any ϵ>0. Thus, the dual cut-toggling algorithm can achieve (almost) the same running time as its primal cycle-toggling counterpart."}],"type":"journal_article","citation":{"chicago":"Henzinger, Monika, Billy Jin, Richard Peng, and David P. Williamson. “A Combinatorial Cut-Toggling Algorithm for Solving Laplacian Linear Systems.” <i>Algorithmica</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00453-023-01154-8\">https://doi.org/10.1007/s00453-023-01154-8</a>.","ista":"Henzinger M, Jin B, Peng R, Williamson DP. 2023. A combinatorial cut-toggling algorithm for solving Laplacian linear systems. Algorithmica. 85, 2680–3716.","mla":"Henzinger, Monika, et al. “A Combinatorial Cut-Toggling Algorithm for Solving Laplacian Linear Systems.” <i>Algorithmica</i>, vol. 85, Springer Nature, 2023, pp. 2680–3716, doi:<a href=\"https://doi.org/10.1007/s00453-023-01154-8\">10.1007/s00453-023-01154-8</a>.","ama":"Henzinger M, Jin B, Peng R, Williamson DP. A combinatorial cut-toggling algorithm for solving Laplacian linear systems. <i>Algorithmica</i>. 2023;85:2680-3716. doi:<a href=\"https://doi.org/10.1007/s00453-023-01154-8\">10.1007/s00453-023-01154-8</a>","ieee":"M. Henzinger, B. Jin, R. Peng, and D. P. Williamson, “A combinatorial cut-toggling algorithm for solving Laplacian linear systems,” <i>Algorithmica</i>, vol. 85. Springer Nature, pp. 2680–3716, 2023.","apa":"Henzinger, M., Jin, B., Peng, R., &#38; Williamson, D. P. (2023). A combinatorial cut-toggling algorithm for solving Laplacian linear systems. <i>Algorithmica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00453-023-01154-8\">https://doi.org/10.1007/s00453-023-01154-8</a>","short":"M. Henzinger, B. Jin, R. Peng, D.P. Williamson, Algorithmica 85 (2023) 2680–3716."},"quality_controlled":"1","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2010.16316","open_access":"1"}],"volume":85,"department":[{"_id":"MoHe"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","title":"A combinatorial cut-toggling algorithm for solving Laplacian linear systems","author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Billy","full_name":"Jin, Billy","last_name":"Jin"},{"last_name":"Peng","full_name":"Peng, Richard","first_name":"Richard"},{"first_name":"David P.","full_name":"Williamson, David P.","last_name":"Williamson"}],"page":"2680-3716","date_updated":"2025-04-15T06:24:05Z","ec_funded":1,"publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"acknowledgement":"Monika Henzinger was supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Billy Jin was Supported in part by NSERC fellowship PGSD3-532673-2019 and NSF grant CCF-2007009. Richard Peng was supported in part by an NSERC Discovery Grant and NSF grant CCF-1846218. David P. Williamson was supported in part by NSF grant CCF-2007009.","year":"2023","article_type":"original","doi":"10.1007/s00453-023-01154-8","day":"01","oa":1,"intvolume":"        85","date_published":"2023-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"}],"arxiv":1,"publication":"Algorithmica","isi":1},{"publication":"23nd International Conference on Runtime Verification","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020"}],"date_published":"2023-10-01T00:00:00Z","intvolume":"     14245","file":[{"relation":"main_file","checksum":"ee33bd6f1a26f4dae7a8192584869fd8","content_type":"application/pdf","file_id":"14430","date_updated":"2023-10-16T07:15:11Z","access_level":"open_access","file_size":867256,"creator":"dernst","file_name":"2023_LNCS_RV_Chalupa.pdf","date_created":"2023-10-16T07:15:11Z","success":1}],"oa":1,"doi":"10.1007/978-3-031-44267-4_9","day":"01","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank Ana Oliveira da Costa for commenting on a draft of the paper.","publication_identifier":{"eisbn":["978-3-031-44267-4"],"isbn":["978-3-031-44266-7"]},"ec_funded":1,"date_updated":"2025-04-14T09:42:55Z","page":"168-190","related_material":{"record":[{"status":"public","id":"15035","relation":"research_data"}]},"author":[{"first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"title":"Monitoring hyperproperties with prefix transducers","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2023-10-16T07:15:11Z","status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version","department":[{"_id":"ToHe"}],"volume":14245,"publisher":"Springer Nature","corr_author":"1","quality_controlled":"1","citation":{"ama":"Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers. In: <i>23nd International Conference on Runtime Verification</i>. Vol 14245. Springer Nature; 2023:168-190. doi:<a href=\"https://doi.org/10.1007/978-3-031-44267-4_9\">10.1007/978-3-031-44267-4_9</a>","apa":"Chalupa, M., &#38; Henzinger, T. A. (2023). Monitoring hyperproperties with prefix transducers. In <i>23nd International Conference on Runtime Verification</i> (Vol. 14245, pp. 168–190). Thessaloniki, Greek: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-44267-4_9\">https://doi.org/10.1007/978-3-031-44267-4_9</a>","ieee":"M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers,” in <i>23nd International Conference on Runtime Verification</i>, Thessaloniki, Greek, 2023, vol. 14245, pp. 168–190.","ista":"Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers. 23nd International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 14245, 168–190.","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” In <i>23nd International Conference on Runtime Verification</i>, 14245:168–90. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-44267-4_9\">https://doi.org/10.1007/978-3-031-44267-4_9</a>.","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” <i>23nd International Conference on Runtime Verification</i>, vol. 14245, Springer Nature, 2023, pp. 168–90, doi:<a href=\"https://doi.org/10.1007/978-3-031-44267-4_9\">10.1007/978-3-031-44267-4_9</a>.","short":"M. Chalupa, T.A. Henzinger, in:, 23nd International Conference on Runtime Verification, Springer Nature, 2023, pp. 168–190."},"type":"conference","abstract":[{"lang":"eng","text":"Hyperproperties are properties that relate multiple execution traces. Previous work on monitoring hyperproperties focused on synchronous hyperproperties, usually specified in HyperLTL. When monitoring synchronous hyperproperties, all traces are assumed to proceed at the same speed. We introduce (multi-trace) prefix transducers and show how to use them for monitoring synchronous as well as, for the first time, asynchronous hyperproperties. Prefix transducers map multiple input traces into one or more output traces by incrementally matching prefixes of the input traces against expressions similar to regular expressions. The prefixes of different traces which are consumed by a single matching step of the monitor may have different lengths. The deterministic and executable nature of prefix transducers makes them more suitable as an intermediate formalism for runtime verification than logical specifications, which tend to be highly non-deterministic, especially in the case of asynchronous hyperproperties. We report on a set of experiments about monitoring asynchronous version of observational determinism."}],"_id":"14076","scopus_import":"1","month":"10","date_created":"2023-08-16T20:46:08Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","alternative_title":["LNCS"],"conference":{"location":"Thessaloniki, Greek","name":"RV: Conference on Runtime Verification","start_date":"2023-10-04","end_date":"2023-10-07"}},{"abstract":[{"lang":"eng","text":"Extracellular signal-regulated kinase (ERK) has been recognized as a critical regulator in various physiological and pathological processes. Extensive research has elucidated the signaling mechanisms governing ERK activation via biochemical regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs). However, recent advances have highlighted the role of mechanical forces in activating the RTK–ERK signaling pathways, thereby opening new avenues of research into mechanochemical interplay in multicellular tissues. Here, we review the force-induced ERK activation in cells and propose possible mechanosensing mechanisms underlying the mechanoresponsive ERK activation. We conclude that mechanical forces are not merely passive factors shaping cells and tissues but also active regulators of cellular signaling pathways controlling collective cell behaviors."}],"pmid":1,"type":"journal_article","citation":{"short":"T. Hirashima, N. Hino, K. Aoki, M. Matsuda, Current Opinion in Cell Biology 84 (2023).","chicago":"Hirashima, Tsuyoshi, Naoya Hino, Kazuhiro Aoki, and Michiyuki Matsuda. “Stretching the Limits of Extracellular Signal-Related Kinase (ERK) Signaling — Cell Mechanosensing to ERK Activation.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ceb.2023.102217\">https://doi.org/10.1016/j.ceb.2023.102217</a>.","ista":"Hirashima T, Hino N, Aoki K, Matsuda M. 2023. Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation. Current Opinion in Cell Biology. 84(10), 102217.","mla":"Hirashima, Tsuyoshi, et al. “Stretching the Limits of Extracellular Signal-Related Kinase (ERK) Signaling — Cell Mechanosensing to ERK Activation.” <i>Current Opinion in Cell Biology</i>, vol. 84, no. 10, 102217, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.ceb.2023.102217\">10.1016/j.ceb.2023.102217</a>.","ama":"Hirashima T, Hino N, Aoki K, Matsuda M. Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation. <i>Current Opinion in Cell Biology</i>. 2023;84(10). doi:<a href=\"https://doi.org/10.1016/j.ceb.2023.102217\">10.1016/j.ceb.2023.102217</a>","ieee":"T. Hirashima, N. Hino, K. Aoki, and M. Matsuda, “Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation,” <i>Current Opinion in Cell Biology</i>, vol. 84, no. 10. Elsevier, 2023.","apa":"Hirashima, T., Hino, N., Aoki, K., &#38; Matsuda, M. (2023). Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2023.102217\">https://doi.org/10.1016/j.ceb.2023.102217</a>"},"quality_controlled":"1","volume":84,"department":[{"_id":"CaHe"}],"publisher":"Elsevier","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2023-08-20T22:01:12Z","external_id":{"isi":["001054692200001"],"pmid":["37574635"]},"_id":"14080","month":"10","scopus_import":"1","issue":"10","doi":"10.1016/j.ceb.2023.102217","day":"01","file":[{"access_level":"open_access","creator":"dernst","file_size":1173762,"date_created":"2024-01-30T12:52:12Z","success":1,"file_name":"2023_CurrentOpinionCellBio_Hirashima.pdf","content_type":"application/pdf","checksum":"25923f8ae71344e8974530dd23c71bdc","relation":"main_file","date_updated":"2024-01-30T12:52:12Z","file_id":"14909"}],"oa":1,"intvolume":"        84","date_published":"2023-10-01T00:00:00Z","article_number":"102217","publication_identifier":{"eissn":["1879-0410"],"issn":["0955-0674"]},"year":"2023","acknowledgement":"TH was supported by JSPS KAKENHI Grant (no. 21H05290) and the Ministry of Education under the Research Centres of Excellence programme through the Mechanobiology Institute at National University of Singapore and by Department of Physiology at National University of Singapore. NH was supported by JSPS KAKENHI Grant (no. 20K22653). KA was supported by JSPS KAKENHI Grants (no. 19H05798 and no. 22H02625). MM was supported by JSPS KAKENHI Grants (no. 19H00993 and no. 20H05898) and JST Moonshot R&D Grant JPMJPS2022. We appreciate Virgile Viasnoff and the lab members for their valuable comments on the manuscript. We apologize to authors whose work could not be highlighted due to space limitations.","article_type":"review","publication":"Current Opinion in Cell Biology","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa_version":"Published Version","title":"Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation","author":[{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"first_name":"Naoya","full_name":"Hino, Naoya","last_name":"Hino","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307"},{"first_name":"Kazuhiro","last_name":"Aoki","full_name":"Aoki, Kazuhiro"},{"first_name":"Michiyuki","full_name":"Matsuda, Michiyuki","last_name":"Matsuda"}],"date_updated":"2024-01-30T12:52:42Z","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2024-01-30T12:52:12Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)"},{"citation":{"apa":"Higashi, T., Stephenson, R. E., Schwayer, C., Huljev, K., Higashi, A. Y., Heisenberg, C.-P. J., … Miller, A. L. (2023). ZnUMBA - a live imaging method to detect local barrier breaches. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.260668\">https://doi.org/10.1242/jcs.260668</a>","ieee":"T. Higashi <i>et al.</i>, “ZnUMBA - a live imaging method to detect local barrier breaches,” <i>Journal of Cell Science</i>, vol. 136, no. 15. The Company of Biologists, 2023.","ama":"Higashi T, Stephenson RE, Schwayer C, et al. ZnUMBA - a live imaging method to detect local barrier breaches. <i>Journal of Cell Science</i>. 2023;136(15). doi:<a href=\"https://doi.org/10.1242/jcs.260668\">10.1242/jcs.260668</a>","mla":"Higashi, Tomohito, et al. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” <i>Journal of Cell Science</i>, vol. 136, no. 15, jcs260668, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.260668\">10.1242/jcs.260668</a>.","chicago":"Higashi, Tomohito, Rachel E. Stephenson, Cornelia Schwayer, Karla Huljev, Atsuko Y. Higashi, Carl-Philipp J Heisenberg, Hideki Chiba, and Ann L. Miller. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.260668\">https://doi.org/10.1242/jcs.260668</a>.","ista":"Higashi T, Stephenson RE, Schwayer C, Huljev K, Higashi AY, Heisenberg C-PJ, Chiba H, Miller AL. 2023. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 136(15), jcs260668.","short":"T. Higashi, R.E. Stephenson, C. Schwayer, K. Huljev, A.Y. Higashi, C.-P.J. Heisenberg, H. Chiba, A.L. Miller, Journal of Cell Science 136 (2023)."},"pmid":1,"abstract":[{"text":"Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","volume":136,"department":[{"_id":"CaHe"},{"_id":"EvBe"}],"OA_type":"free access","publisher":"The Company of Biologists","main_file_link":[{"url":"https://doi.org/10.1242/jcs.260668","open_access":"1"}],"publication_status":"published","date_created":"2023-08-20T22:01:13Z","external_id":{"pmid":["37461809"],"isi":["001070149000001"]},"_id":"14082","month":"08","scopus_import":"1","issue":"15","oa":1,"day":"01","doi":"10.1242/jcs.260668","date_published":"2023-08-01T00:00:00Z","intvolume":"       136","article_number":"jcs260668","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"article_type":"original","year":"2023","acknowledgement":"The authors thank their respective lab members for feedback and helpful discussions. We thank the bioimaging and zebrafish facilities of IST Austria for their support.\r\nThis work was supported by the National Institutes of Health [R01GM112794 to A.L.M.], by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science [21K06156 to T.H.], by the Grant Program for Biomedical Engineering Research from the Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering [to T.H.] and by funding from the European Research Council [advanced grant 742573 to C.-P.H.]. ","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"ec_funded":1,"isi":1,"publication":"Journal of Cell Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"OA_place":"publisher","oa_version":"None","title":"ZnUMBA - a live imaging method to detect local barrier breaches","author":[{"first_name":"Tomohito","full_name":"Higashi, Tomohito","last_name":"Higashi"},{"first_name":"Rachel E.","full_name":"Stephenson, Rachel E.","last_name":"Stephenson"},{"orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","full_name":"Schwayer, Cornelia","first_name":"Cornelia"},{"last_name":"Huljev","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla"},{"full_name":"Higashi, Atsuko Y.","last_name":"Higashi","first_name":"Atsuko Y."},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"first_name":"Hideki","full_name":"Chiba, Hideki","last_name":"Chiba"},{"first_name":"Ann L.","full_name":"Miller, Ann L.","last_name":"Miller"}],"date_updated":"2025-06-25T06:28:45Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","corr_author":"1","department":[{"_id":"MaMo"}],"volume":261,"quality_controlled":"1","type":"conference","abstract":[{"lang":"eng","text":"In this work we consider the list-decodability and list-recoverability of arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable if every radius pn Hamming ball contains less than L codewords; (p,𝓁,L)_q-list-recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length 𝓁 and again stipulate that there be less than L codewords.\r\nOur main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate (p,𝓁,L)_q-list-recoverable codes, the quantity we call the zero-rate threshold. Denoting this value by p_*, we in fact show that codes correcting a p_*+ε fraction of errors must have size O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin bound.\" To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p_*-ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin bound boils down to demonstrating the Schur convexity of a certain function defined on the q-simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q-ary list-decoding; however, we point out that this earlier proof is flawed."}],"citation":{"short":"N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261.","apa":"Resch, N., Yuan, C., &#38; Zhang, Y. (2023). Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In <i>50th International Colloquium on Automata, Languages, and Programming</i> (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.99\">https://doi.org/10.4230/LIPIcs.ICALP.2023.99</a>","ama":"Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In: <i>50th International Colloquium on Automata, Languages, and Programming</i>. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.99\">10.4230/LIPIcs.ICALP.2023.99</a>","mla":"Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.99\">10.4230/LIPIcs.ICALP.2023.99</a>.","chicago":"Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” In <i>50th International Colloquium on Automata, Languages, and Programming</i>, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.99\">https://doi.org/10.4230/LIPIcs.ICALP.2023.99</a>.","ista":"Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. 50th International Colloquium on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 261, 99."},"scopus_import":"1","month":"07","_id":"14083","external_id":{"arxiv":["2210.07754"]},"alternative_title":["LIPIcs"],"conference":{"location":"Paderborn, Germany","name":"ICALP: Automata, Languages and Programming","start_date":"2023-07-10","end_date":"2023-07-14"},"date_created":"2023-08-20T22:01:13Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication":"50th International Colloquium on Automata, Languages, and Programming","acknowledgement":"Nicolas Resch: Research supported in part by ERC H2020 grant No.74079 (ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions.","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"year":"2023","article_number":"99","intvolume":"       261","date_published":"2023-07-01T00:00:00Z","day":"01","doi":"10.4230/LIPIcs.ICALP.2023.99","file":[{"relation":"main_file","checksum":"a449143fec3fbebb092cb8ef3b53c226","content_type":"application/pdf","file_id":"14091","date_updated":"2023-08-21T07:23:18Z","access_level":"open_access","date_created":"2023-08-21T07:23:18Z","success":1,"file_name":"2023_LIPIcsICALP_Resch.pdf","file_size":1141497,"creator":"dernst"}],"oa":1,"file_date_updated":"2023-08-21T07:23:18Z","has_accepted_license":"1","article_processing_charge":"Yes","status":"public","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","id":"17330","status":"public"}]},"date_updated":"2025-09-08T08:31:53Z","author":[{"first_name":"Nicolas","full_name":"Resch, Nicolas","last_name":"Resch"},{"full_name":"Yuan, Chen","last_name":"Yuan","first_name":"Chen"},{"full_name":"Zhang, Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","first_name":"Yihan"}],"title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","oa_version":"Published Version"},{"date_created":"2023-08-20T22:01:14Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"arxiv":["2007.10824"]},"alternative_title":["LIPIcs"],"conference":{"end_date":"2023-07-14","name":"ICALP: Automata, Languages and Programming","location":"Paderborn, Germany","start_date":"2023-07-10"},"_id":"14084","scopus_import":"1","month":"07","quality_controlled":"1","citation":{"short":"D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261.","apa":"Harris, D. G., &#38; Kolmogorov, V. (2023). Parameter estimation for Gibbs distributions. In <i>50th International Colloquium on Automata, Languages, and Programming</i> (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.72\">https://doi.org/10.4230/LIPIcs.ICALP.2023.72</a>","ama":"Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In: <i>50th International Colloquium on Automata, Languages, and Programming</i>. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.72\">10.4230/LIPIcs.ICALP.2023.72</a>","mla":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.72\">10.4230/LIPIcs.ICALP.2023.72</a>.","ista":"Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions. 50th International Colloquium on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 261, 72.","chicago":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” In <i>50th International Colloquium on Automata, Languages, and Programming</i>, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.72\">https://doi.org/10.4230/LIPIcs.ICALP.2023.72</a>."},"abstract":[{"lang":"eng","text":"A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We will consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²) samples for integer-valued distributions (ignoring some second-order terms and parameters), We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs and perfect matchings in a graph."}],"type":"conference","department":[{"_id":"VlKo"}],"volume":261,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","corr_author":"1","oa_version":"Published Version","related_material":{"record":[{"relation":"later_version","id":"18855","status":"public"}]},"date_updated":"2025-07-10T11:50:45Z","title":"Parameter estimation for Gibbs distributions","author":[{"first_name":"David G.","last_name":"Harris","full_name":"Harris, David G."},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir"}],"has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2023-08-21T06:45:16Z","status":"public","language":[{"iso":"eng"}],"date_published":"2023-07-01T00:00:00Z","intvolume":"       261","oa":1,"file":[{"file_id":"14088","date_updated":"2023-08-21T06:45:16Z","relation":"main_file","checksum":"6dee0684245bb1c524b9c955db1e933d","content_type":"application/pdf","file_size":917791,"creator":"dernst","date_created":"2023-08-21T06:45:16Z","success":1,"file_name":"2023_LIPIcsICALP_Harris.pdf","access_level":"open_access"}],"doi":"10.4230/LIPIcs.ICALP.2023.72","day":"01","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"year":"2023","acknowledgement":"We thank Heng Guo for helpful explanations of algorithms for sampling connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the Wang-Landau algorithm and its use in physics.","article_number":"72","arxiv":1,"publication":"50th International Colloquium on Automata, Languages, and Programming","ddc":["000","510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]