[{"scopus_import":"1","department":[{"_id":"BaPi"}],"volume":100,"citation":{"short":"A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses 100 (2023) 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>.","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.","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>","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>","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.","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>."},"doi":"10.15227/orgsyn.100.0271","_id":"13970","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15227/orgsyn.100.0271"}],"oa_version":"Published Version","quality_controlled":"1","publication_identifier":{"issn":["0078-6209"],"eissn":["2333-3553"]},"article_type":"original","day":"01","author":[{"full_name":"Madani, Amiera","first_name":"Amiera","last_name":"Madani"},{"first_name":"Eric T.","last_name":"Sletten","full_name":"Sletten, Eric T."},{"full_name":"Cavedon, Cristian","last_name":"Cavedon","first_name":"Cristian"},{"first_name":"Peter H.","last_name":"Seeberger","full_name":"Seeberger, Peter H."},{"first_name":"Bartholomäus","orcid":"0000-0001-8689-388X","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus"}],"date_updated":"2026-06-18T17:32:17Z","title":"Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose","date_created":"2023-08-06T22:01:11Z","publisher":"Organic Syntheses","language":[{"iso":"eng"}],"intvolume":"       100","status":"public","ddc":["540"],"corr_author":"1","month":"07","publication":"Organic Syntheses","page":"271-286","type":"journal_article","oa":1,"year":"2023","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-07-01T00:00:00Z"},{"_id":"13971","quality_controlled":"1","oa_version":"Published Version","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"},{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 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>.","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.","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>","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>.","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."},"doi":"10.1038/s41567-023-02136-x","scopus_import":"1","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"volume":19,"date_updated":"2025-04-14T07:43:56Z","title":"Unconventional colloidal aggregation in chiral bacterial baths","author":[{"first_name":"Daniel","last_name":"Grober","id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99","full_name":"Grober, Daniel"},{"full_name":"Palaia, Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan"},{"first_name":"Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A"}],"external_id":{"isi":["001037346400005"]},"file_date_updated":"2024-01-30T12:26:08Z","article_type":"original","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"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.","day":"01","ddc":["530"],"month":"11","corr_author":"1","status":"public","publication":"Nature Physics","language":[{"iso":"eng"}],"intvolume":"        19","has_accepted_license":"1","date_created":"2023-08-06T22:01:11Z","abstract":[{"lang":"eng","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."}],"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-11-01T00:00:00Z","year":"2023","article_processing_charge":"Yes","publication_status":"published","file":[{"file_id":"14906","success":1,"date_updated":"2024-01-30T12:26:08Z","relation":"main_file","date_created":"2024-01-30T12:26:08Z","checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","creator":"dernst","file_name":"2023_NaturePhysics_Grober.pdf","file_size":6365607,"content_type":"application/pdf","access_level":"open_access"}],"ec_funded":1,"type":"journal_article","isi":1,"oa":1,"page":"1680-1688"},{"type":"journal_article","isi":1,"oa":1,"publication_status":"published","year":"2023","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-09-08T00:00:00Z","article_number":"e202300683","abstract":[{"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.","lang":"eng"}],"date_created":"2023-08-06T22:01:12Z","publisher":"Wiley","language":[{"iso":"eng"}],"intvolume":"        15","issue":"17","corr_author":"1","status":"public","ddc":["540"],"month":"09","publication":"ChemCatChem","day":"08","article_type":"letter_note","publication_identifier":{"issn":["1867-3880"],"eissn":["1867-3899"]},"external_id":{"isi":["001037859900001"]},"author":[{"full_name":"Næsborg, Line","first_name":"Line","last_name":"Næsborg"},{"first_name":"Bartholomäus","last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"},{"last_name":"Wenger","first_name":"Oliver S.","full_name":"Wenger, Oliver S."}],"title":"Special Collection: Photocatalytic synthesis","date_updated":"2026-06-18T17:32:51Z","scopus_import":"1","department":[{"_id":"BaPi"}],"volume":15,"citation":{"short":"L. Næsborg, B. Pieber, O.S. Wenger, ChemCatChem 15 (2023).","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>.","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>","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>","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.","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>."},"doi":"10.1002/cctc.202300683","_id":"13972","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/cctc.202300683"}]},{"publication_status":"published","article_processing_charge":"Yes","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-07-27T00:00:00Z","article_number":"giad045","type":"journal_article","isi":1,"oa":1,"publication":"GigaScience","status":"public","ddc":["000"],"month":"07","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"}],"date_created":"2023-08-06T22:01:13Z","pmid":1,"publisher":"Oxford University Press","language":[{"iso":"eng"}],"intvolume":"        12","author":[{"first_name":"Walter","last_name":"Wolfsberger","full_name":"Wolfsberger, Walter"},{"first_name":"Karishma","last_name":"Chhugani","full_name":"Chhugani, Karishma"},{"first_name":"Khrystyna","last_name":"Shchubelka","full_name":"Shchubelka, Khrystyna"},{"first_name":"Alina","last_name":"Frolova","full_name":"Frolova, Alina"},{"last_name":"Salyha","first_name":"Yuriy","full_name":"Salyha, Yuriy"},{"full_name":"Zlenko, Oksana","last_name":"Zlenko","first_name":"Oksana"},{"first_name":"Mykhailo","last_name":"Arych","full_name":"Arych, Mykhailo"},{"first_name":"Dmytro","last_name":"Dziuba","full_name":"Dziuba, Dmytro"},{"last_name":"Parkhomenko","first_name":"Andrii","full_name":"Parkhomenko, Andrii"},{"last_name":"Smolanka","first_name":"Volodymyr","full_name":"Smolanka, Volodymyr"},{"full_name":"Gümüş, Zeynep H.","first_name":"Zeynep H.","last_name":"Gümüş"},{"full_name":"Sezgin, Efe","first_name":"Efe","last_name":"Sezgin"},{"last_name":"Diaz-Lameiro","first_name":"Alondra","full_name":"Diaz-Lameiro, Alondra"},{"full_name":"Toth, Viktor R.","first_name":"Viktor R.","last_name":"Toth"},{"first_name":"Megi","last_name":"Maci","full_name":"Maci, Megi"},{"last_name":"Bortz","first_name":"Eric","full_name":"Bortz, Eric"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"full_name":"Morton, Patricia M.","last_name":"Morton","first_name":"Patricia M."},{"full_name":"Łabaj, Paweł P.","first_name":"Paweł P.","last_name":"Łabaj"},{"first_name":"Veronika","last_name":"Romero","full_name":"Romero, Veronika"},{"full_name":"Hlávka, Jakub","last_name":"Hlávka","first_name":"Jakub"},{"full_name":"Mangul, Serghei","first_name":"Serghei","last_name":"Mangul"},{"first_name":"Taras K.","last_name":"Oleksyk","full_name":"Oleksyk, Taras K."}],"title":"Scientists without borders: Lessons from Ukraine","date_updated":"2026-06-18T17:33:34Z","day":"27","article_type":"review","publication_identifier":{"eissn":["2047-217X"]},"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.","related_material":{"link":[{"url":"https://doi.org/10.1093/gigascience/giad066","relation":"erratum"}]},"external_id":{"isi":["001081086100001"],"pmid":["37496156"]},"_id":"13976","quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1093/gigascience/giad045","open_access":"1"}],"department":[{"_id":"FyKo"}],"scopus_import":"1","volume":12,"citation":{"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).","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>.","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>","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.","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>","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."},"doi":"10.1093/gigascience/giad045"},{"scopus_import":"1","volume":14,"doi":"10.1038/s41467-023-38540-3","citation":{"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.","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>","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>","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>.","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.","short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023).","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>."},"_id":"13989","extern":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41467-023-38540-3","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","day":"14","arxiv":1,"external_id":{"arxiv":["2209.02283"],"pmid":["37316515"]},"author":[{"first_name":"Jordyn","last_name":"Hales","full_name":"Hales, Jordyn"},{"full_name":"Bajpai, Utkarsh","last_name":"Bajpai","first_name":"Utkarsh"},{"first_name":"Tongtong","last_name":"Liu","full_name":"Liu, 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","last_name":"Mitrano","full_name":"Mitrano, Matteo"},{"full_name":"Wang, Yao","first_name":"Yao","last_name":"Wang"}],"date_updated":"2023-08-22T06:50:04Z","title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","pmid":1,"date_created":"2023-08-09T13:06:59Z","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"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"        14","publication":"Nature Communications","month":"06","status":"public","type":"journal_article","oa":1,"article_processing_charge":"No","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"year":"2023","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-06-14T00:00:00Z","article_number":"3512"},{"month":"03","publication":"Physical Review Letters","status":"public","issue":"10","language":[{"iso":"eng"}],"intvolume":"       130","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."}],"pmid":1,"date_created":"2023-08-09T13:07:24Z","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-03-10T00:00:00Z","article_number":"106902","keyword":["General Physics and Astronomy"],"article_processing_charge":"No","year":"2023","publication_status":"published","type":"journal_article","oa":1,"extern":"1","_id":"13990","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2209.02081"}],"oa_version":"Preprint","quality_controlled":"1","doi":"10.1103/physrevlett.130.106902","citation":{"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>.","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.","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.","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>","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>","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>.","short":"D.R. Baykusheva, M.H. Kalthoff, D. Hofmann, M. Claassen, D.M. Kennes, M.A. Sentef, M. Mitrano, Physical Review Letters 130 (2023)."},"scopus_import":"1","volume":130,"date_updated":"2024-10-14T12:23:16Z","title":"Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain","author":[{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"last_name":"Kalthoff","first_name":"Mona H.","full_name":"Kalthoff, Mona H."},{"full_name":"Hofmann, Damian","last_name":"Hofmann","first_name":"Damian"},{"last_name":"Claassen","first_name":"Martin","full_name":"Claassen, Martin"},{"last_name":"Kennes","first_name":"Dante M.","full_name":"Kennes, Dante M."},{"full_name":"Sentef, Michael A.","last_name":"Sentef","first_name":"Michael A."},{"full_name":"Mitrano, Matteo","last_name":"Mitrano","first_name":"Matteo"}],"external_id":{"arxiv":["2209.02081"],"pmid":["36962013"]},"article_type":"original","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"day":"10","arxiv":1},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2023-07-31T00:00:00Z","article_number":"e2300828120","year":"2023","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","file":[{"file_id":"14047","success":1,"date_updated":"2023-08-14T07:43:45Z","date_created":"2023-08-14T07:43:45Z","relation":"main_file","creator":"dernst","checksum":"a5ed64788a5acef9b9a300a26fa5a177","file_name":"2023_PNAS_Vardi.pdf","file_size":1003092,"access_level":"open_access","content_type":"application/pdf"}],"type":"journal_article","ec_funded":1,"isi":1,"oa":1,"status":"public","ddc":["530"],"month":"07","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"32","language":[{"iso":"eng"}],"intvolume":"       120","date_created":"2023-08-13T22:01:12Z","has_accepted_license":"1","pmid":1,"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."}],"publisher":"National Academy of Sciences","date_updated":"2025-09-09T12:47:53Z","title":"Nuclear spin effects in biological processes","author":[{"first_name":"Ofek","last_name":"Vardi","full_name":"Vardi, Ofek"},{"first_name":"Naama","last_name":"Maroudas-Sklare","full_name":"Maroudas-Sklare, Naama"},{"full_name":"Kolodny, Yuval","last_name":"Kolodny","first_name":"Yuval"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amijai","last_name":"Saragovi","full_name":"Saragovi, Amijai"},{"full_name":"Galili, Nir","first_name":"Nir","last_name":"Galili"},{"full_name":"Ferrera, Stav","last_name":"Ferrera","first_name":"Stav"},{"first_name":"Areg","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nir","last_name":"Yuran","full_name":"Yuran, Nir"},{"first_name":"Hagit P.","last_name":"Affek","full_name":"Affek, Hagit P."},{"first_name":"Boaz","last_name":"Luz","full_name":"Luz, Boaz"},{"full_name":"Goldsmith, Yonaton","first_name":"Yonaton","last_name":"Goldsmith"},{"full_name":"Keren, Nir","last_name":"Keren","first_name":"Nir"},{"first_name":"Shira","last_name":"Yochelis","full_name":"Yochelis, Shira"},{"full_name":"Halevy, Itay","first_name":"Itay","last_name":"Halevy"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"last_name":"Paltiel","first_name":"Yossi","full_name":"Paltiel, Yossi"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"pmid":["37523549"],"isi":["001121663600001"]},"file_date_updated":"2023-08-14T07:43:45Z","article_type":"original","publication_identifier":{"eissn":["1091-6490"]},"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.","day":"31","_id":"14037","quality_controlled":"1","oa_version":"Published Version","project":[{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.1073/pnas.2300828120","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"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.","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>","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>","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.","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).","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>."},"scopus_import":"1","department":[{"_id":"MiLe"}],"volume":120},{"language":[{"iso":"eng"}],"intvolume":"        58","date_created":"2023-08-13T22:01:12Z","pmid":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"}],"has_accepted_license":"1","publisher":"Elsevier","publication":"Developmental Cell","corr_author":"1","month":"08","status":"public","ddc":["570"],"issue":"15","isi":1,"type":"journal_article","oa":1,"page":"1315-1332","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-08-07T00:00:00Z","publication_status":"published","year":"2023","article_processing_charge":"Yes (via OA deal)","file":[{"success":1,"file_id":"14049","date_updated":"2023-08-14T07:57:55Z","checksum":"d8c5dc97cd40c26da2ec98ae723ab368","file_name":"2023_DevelopmentalCell_Leonard.pdf","creator":"dernst","date_created":"2023-08-14T07:57:55Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":3184217}],"project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607"},{"_id":"bd6ae2ca-d553-11ed-ba76-a4aa239da5ee","name":"Synthetic and structural biology of Rab GTPase networks","grant_number":"101045340"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.devcel.2023.06.001","citation":{"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.","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>.","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.","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>","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>.","short":"T.A. Leonard, M. Loose, S. Martens, Developmental Cell 58 (2023) 1315–1332."},"scopus_import":"1","department":[{"_id":"MaLo"}],"volume":58,"_id":"14039","quality_controlled":"1","oa_version":"Published Version","external_id":{"pmid":["37419118"],"isi":["001059110400001"]},"day":"07","article_type":"original","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.","file_date_updated":"2023-08-14T07:57:55Z","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"title":"The membrane surface as a platform that organizes cellular and biochemical processes","date_updated":"2024-10-22T11:40:18Z","author":[{"full_name":"Leonard, Thomas A.","last_name":"Leonard","first_name":"Thomas A."},{"first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"full_name":"Martens, Sascha","last_name":"Martens","first_name":"Sascha"}]},{"file":[{"date_updated":"2023-08-14T07:01:12Z","file_id":"14044","success":1,"file_size":2315325,"access_level":"open_access","content_type":"application/pdf","date_created":"2023-08-14T07:01:12Z","relation":"main_file","file_name":"2023_NatureComm_Zhao.pdf","checksum":"3b9043df3d51c300f9be95eac3ff9d0b","creator":"dernst"}],"publication_status":"published","article_processing_charge":"Yes","year":"2023","article_number":"4681","date_published":"2023-08-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"isi":1,"type":"journal_article","publication":"Nature Communications","status":"public","corr_author":"1","ddc":["570"],"month":"08","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"publisher":"Springer Nature","abstract":[{"lang":"eng","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."}],"date_created":"2023-08-13T22:01:13Z","pmid":1,"has_accepted_license":"1","intvolume":"        14","language":[{"iso":"eng"}],"author":[{"full_name":"Zhao, Ziyu","first_name":"Ziyu","last_name":"Zhao"},{"full_name":"Vercellino, Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","last_name":"Vercellino","orcid":"0000-0001-5618-3449","first_name":"Irene"},{"last_name":"Knoppová","first_name":"Jana","full_name":"Knoppová, Jana"},{"last_name":"Sobotka","first_name":"Roman","full_name":"Sobotka, Roman"},{"last_name":"Murray","first_name":"James W.","full_name":"Murray, James W."},{"full_name":"Nixon, Peter J.","first_name":"Peter J.","last_name":"Nixon"},{"first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Komenda, Josef","last_name":"Komenda","first_name":"Josef"}],"title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","date_updated":"2025-04-23T13:05:33Z","day":"04","publication_identifier":{"eissn":["2041-1723"]},"file_date_updated":"2023-08-14T07:01:12Z","article_type":"original","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.","external_id":{"isi":["001042606700004"],"pmid":["37542031"]},"oa_version":"Published Version","quality_controlled":"1","_id":"14040","volume":14,"scopus_import":"1","department":[{"_id":"LeSa"}],"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>","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>.","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.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (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>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-023-40388-6"},{"type":"journal_article","isi":1,"oa":1,"publication_status":"published","year":"2023","article_processing_charge":"Yes","file":[{"file_size":10181997,"access_level":"open_access","content_type":"application/pdf","date_created":"2023-08-14T07:17:36Z","relation":"main_file","creator":"dernst","checksum":"1f9324f736bdbb76426b07736651c4cd","file_name":"2023_CommBiology_Mehes.pdf","date_updated":"2023-08-14T07:17:36Z","file_id":"14045","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"817","date_published":"2023-08-04T00:00:00Z","abstract":[{"lang":"eng","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."}],"date_created":"2023-08-13T22:01:13Z","has_accepted_license":"1","pmid":1,"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"         6","ddc":["570"],"publication":"Communications Biology","status":"public","month":"08","day":"04","article_type":"original","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.","file_date_updated":"2023-08-14T07:17:36Z","publication_identifier":{"eissn":["2399-3642"]},"external_id":{"pmid":["37542157"],"isi":["001042544100001"]},"author":[{"first_name":"Elod","last_name":"Méhes","full_name":"Méhes, Elod"},{"full_name":"Mones, Enys","first_name":"Enys","last_name":"Mones"},{"full_name":"Varga, Máté","first_name":"Máté","last_name":"Varga"},{"last_name":"Zsigmond","first_name":"Áron","full_name":"Zsigmond, Áron"},{"first_name":"Beáta","last_name":"Biri-Kovács","full_name":"Biri-Kovács, Beáta"},{"full_name":"Nyitray, László","last_name":"Nyitray","first_name":"László"},{"first_name":"Vanessa","last_name":"Barone","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","orcid":"0000-0003-4761-5996","first_name":"Gabriel"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Vicsek, Tamás","first_name":"Tamás","last_name":"Vicsek"}],"title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","date_updated":"2023-12-13T12:07:33Z","scopus_import":"1","department":[{"_id":"CaHe"},{"_id":"Bio"}],"volume":6,"citation":{"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>.","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>","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>","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>.","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)."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s42003-023-05181-7","_id":"14041","quality_controlled":"1","oa_version":"Published Version"},{"date_published":"2023-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","year":"2023","publication_status":"published","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","page":"2680-3716","status":"public","month":"12","publication":"Algorithmica","intvolume":"        85","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_created":"2023-08-13T22:01:13Z","abstract":[{"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.","lang":"eng"}],"date_updated":"2025-04-15T06:24:05Z","title":"A combinatorial cut-toggling algorithm for solving Laplacian linear systems","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Jin, Billy","last_name":"Jin","first_name":"Billy"},{"full_name":"Peng, Richard","last_name":"Peng","first_name":"Richard"},{"first_name":"David P.","last_name":"Williamson","full_name":"Williamson, David P."}],"external_id":{"arxiv":["2010.16316"],"isi":["001041254900002"]},"arxiv":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.","article_type":"original","day":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2010.16316","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","_id":"14043","doi":"10.1007/s00453-023-01154-8","citation":{"short":"M. Henzinger, B. Jin, R. Peng, D.P. Williamson, Algorithmica 85 (2023) 2680–3716.","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>.","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>","ista":"Henzinger M, Jin B, Peng R, Williamson DP. 2023. A combinatorial cut-toggling algorithm for solving Laplacian linear systems. Algorithmica. 85, 2680–3716.","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>","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>.","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."},"project":[{"grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer"}],"volume":85,"scopus_import":"1","department":[{"_id":"MoHe"}]},{"_id":"14058","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/at:ista:14058","citation":{"short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>.","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>","apa":"Puixeu Sala, G. (2023). <i>The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","mla":"Puixeu Sala, Gemma. <i>The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>."},"author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","first_name":"Gemma"}],"date_updated":"2026-04-07T13:25:34Z","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","file_date_updated":"2023-08-18T10:47:55Z","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"9803"},{"relation":"research_data","id":"12933","status":"public"},{"status":"public","id":"6831","relation":"part_of_dissertation"},{"id":"14077","relation":"part_of_dissertation","status":"public"}]},"day":"15","OA_place":"publisher","degree_awarded":"PhD","status":"public","month":"08","ddc":["576"],"corr_author":"1","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution."}],"date_created":"2023-08-15T10:20:40Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2023","publication_status":"published","file":[{"file_id":"14075","date_updated":"2023-08-17T06:55:24Z","date_created":"2023-08-16T18:15:17Z","relation":"source_file","file_name":"Thesis_latex_forpdfa.zip","creator":"gpuixeus","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_size":10891454,"access_level":"closed","content_type":"application/zip"},{"date_updated":"2023-08-18T10:47:55Z","success":1,"file_id":"14079","file_size":19856686,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-08-18T10:47:55Z","creator":"gpuixeus","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","file_name":"PhDThesis_PuixeuG.pdf"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2023-08-15T00:00:00Z","page":"230","ec_funded":1,"type":"dissertation","oa":1},{"date_updated":"2025-04-14T09:42:55Z","title":"Monitoring hyperproperties with prefix transducers","author":[{"full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","last_name":"Chalupa"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"conference":{"end_date":"2023-10-07","name":"RV: Conference on Runtime Verification","location":"Thessaloniki, Greek","start_date":"2023-10-04"},"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":{"isbn":["978-3-031-44266-7"],"eisbn":["978-3-031-44267-4"]},"file_date_updated":"2023-10-16T07:15:11Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"15035"}]},"day":"01","_id":"14076","oa_version":"Published Version","quality_controlled":"1","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"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>.","short":"M. Chalupa, T.A. Henzinger, in:, 23nd International Conference on Runtime Verification, Springer Nature, 2023, pp. 168–190.","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.","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>.","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>","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."},"doi":"10.1007/978-3-031-44267-4_9","department":[{"_id":"ToHe"}],"scopus_import":"1","volume":14245,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-10-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","year":"2023","publication_status":"published","file":[{"date_updated":"2023-10-16T07:15:11Z","success":1,"file_id":"14430","file_size":867256,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-10-16T07:15:11Z","file_name":"2023_LNCS_RV_Chalupa.pdf","creator":"dernst","checksum":"ee33bd6f1a26f4dae7a8192584869fd8"}],"type":"conference","ec_funded":1,"oa":1,"page":"168-190","publication":"23nd International Conference on Runtime Verification","status":"public","ddc":["000"],"corr_author":"1","month":"10","language":[{"iso":"eng"}],"intvolume":"     14245","alternative_title":["LNCS"],"date_created":"2023-08-16T20:46:08Z","has_accepted_license":"1","abstract":[{"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.","lang":"eng"}],"publisher":"Springer Nature"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/g3journal/jkad121","citation":{"mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>.","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","apa":"Puixeu Sala, G., Macon, A., &#38; Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>","ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. 2023;13(8). doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023)."},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"volume":13,"scopus_import":"1","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"quality_controlled":"1","oa_version":"Published Version","_id":"14077","external_id":{"pmid":["37259621"],"isi":["001002997200001"]},"publication_identifier":{"issn":["2160-1836"]},"file_date_updated":"2023-11-07T09:00:19Z","related_material":{"record":[{"relation":"research_data","id":"12933","status":"public"},{"status":"public","id":"14058","relation":"dissertation_contains"}]},"article_type":"original","acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","day":"01","date_updated":"2026-04-07T13:25:34Z","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","author":[{"full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","first_name":"Gemma"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","first_name":"Ariana","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"intvolume":"        13","language":[{"iso":"eng"}],"publisher":"Oxford University Press","has_accepted_license":"1","abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}],"date_created":"2023-08-18T06:52:14Z","pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"publication":"G3: Genes, Genomes, Genetics","ddc":["570"],"status":"public","corr_author":"1","month":"08","issue":"8","oa":1,"type":"journal_article","isi":1,"ec_funded":1,"date_published":"2023-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"success":1,"file_id":"14498","date_updated":"2023-11-07T09:00:19Z","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","creator":"dernst","file_name":"2023_G3_Puixeu.pdf","relation":"main_file","date_created":"2023-11-07T09:00:19Z","content_type":"application/pdf","access_level":"open_access","file_size":845642}],"year":"2023","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"article_processing_charge":"Yes","publication_status":"published"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.ceb.2023.102217","citation":{"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>","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>","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.","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.","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>.","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>."},"department":[{"_id":"CaHe"}],"scopus_import":"1","volume":84,"_id":"14080","quality_controlled":"1","oa_version":"Published Version","external_id":{"isi":["001054692200001"],"pmid":["37574635"]},"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.","publication_identifier":{"issn":["0955-0674"],"eissn":["1879-0410"]},"article_type":"review","file_date_updated":"2024-01-30T12:52:12Z","day":"01","date_updated":"2024-01-30T12:52:42Z","title":"Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation","author":[{"last_name":"Hirashima","first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi"},{"id":"5299a9ce-7679-11eb-a7bc-d1e62b936307","full_name":"Hino, Naoya","last_name":"Hino","first_name":"Naoya"},{"full_name":"Aoki, Kazuhiro","last_name":"Aoki","first_name":"Kazuhiro"},{"first_name":"Michiyuki","last_name":"Matsuda","full_name":"Matsuda, Michiyuki"}],"language":[{"iso":"eng"}],"intvolume":"        84","pmid":1,"date_created":"2023-08-20T22:01:12Z","has_accepted_license":"1","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."}],"publisher":"Elsevier","publication":"Current Opinion in Cell Biology","month":"10","ddc":["570"],"status":"public","issue":"10","isi":1,"type":"journal_article","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"102217","date_published":"2023-10-01T00:00:00Z","year":"2023","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","file":[{"creator":"dernst","file_name":"2023_CurrentOpinionCellBio_Hirashima.pdf","checksum":"25923f8ae71344e8974530dd23c71bdc","date_created":"2024-01-30T12:52:12Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":1173762,"file_id":"14909","success":1,"date_updated":"2024-01-30T12:52:12Z"}]},{"year":"2023","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"jcs260668","date_published":"2023-08-01T00:00:00Z","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"issue":"15","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"status":"public","month":"08","ddc":["570"],"publication":"Journal of Cell Science","abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","date_created":"2023-08-20T22:01:13Z","pmid":1,"publisher":"The Company of Biologists","OA_type":"free access","language":[{"iso":"eng"}],"intvolume":"       136","author":[{"first_name":"Tomohito","last_name":"Higashi","full_name":"Higashi, Tomohito"},{"full_name":"Stephenson, Rachel E.","last_name":"Stephenson","first_name":"Rachel E."},{"full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","orcid":"0000-0001-5130-2226","first_name":"Cornelia"},{"last_name":"Huljev","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla"},{"first_name":"Atsuko Y.","last_name":"Higashi","full_name":"Higashi, Atsuko Y."},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"},{"first_name":"Hideki","last_name":"Chiba","full_name":"Chiba, Hideki"},{"full_name":"Miller, Ann L.","last_name":"Miller","first_name":"Ann L."}],"date_updated":"2025-06-25T06:28:45Z","title":"ZnUMBA - a live imaging method to detect local barrier breaches","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"]},"article_type":"original","day":"01","OA_place":"publisher","external_id":{"pmid":["37461809"],"isi":["001070149000001"]},"_id":"14082","main_file_link":[{"url":"https://doi.org/10.1242/jcs.260668","open_access":"1"}],"oa_version":"None","quality_controlled":"1","department":[{"_id":"CaHe"},{"_id":"EvBe"}],"scopus_import":"1","volume":136,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"doi":"10.1242/jcs.260668","citation":{"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.","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>.","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.","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>","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>","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>.","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)."}},{"author":[{"full_name":"Resch, Nicolas","last_name":"Resch","first_name":"Nicolas"},{"full_name":"Yuan, Chen","last_name":"Yuan","first_name":"Chen"},{"orcid":"0000-0002-6465-6258","last_name":"Zhang","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan"}],"date_updated":"2025-09-08T08:31:53Z","title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","arxiv":1,"related_material":{"record":[{"id":"17330","relation":"later_version","status":"public"}]},"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"]},"file_date_updated":"2023-08-21T07:23:18Z","day":"01","external_id":{"arxiv":["2210.07754"]},"conference":{"end_date":"2023-07-14","start_date":"2023-07-10","location":"Paderborn, Germany","name":"ICALP: Automata, Languages and Programming"},"oa_version":"Published Version","quality_controlled":"1","_id":"14083","volume":261,"department":[{"_id":"MaMo"}],"scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"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>.","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.","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.","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>","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>","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>.","short":"N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023."},"doi":"10.4230/LIPIcs.ICALP.2023.99","file":[{"creator":"dernst","file_name":"2023_LIPIcsICALP_Resch.pdf","checksum":"a449143fec3fbebb092cb8ef3b53c226","date_created":"2023-08-21T07:23:18Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":1141497,"success":1,"file_id":"14091","date_updated":"2023-08-21T07:23:18Z"}],"article_processing_charge":"Yes","year":"2023","publication_status":"published","date_published":"2023-07-01T00:00:00Z","article_number":"99","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"conference","publication":"50th International Colloquium on Automata, Languages, and Programming","month":"07","corr_author":"1","ddc":["000"],"status":"public","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"date_created":"2023-08-20T22:01:13Z","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."}],"has_accepted_license":"1","intvolume":"       261","language":[{"iso":"eng"}]},{"intvolume":"       261","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","has_accepted_license":"1","abstract":[{"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.","lang":"eng"}],"date_created":"2023-08-20T22:01:14Z","alternative_title":["LIPIcs"],"publication":"50th International Colloquium on Automata, Languages, and Programming","status":"public","ddc":["000","510"],"month":"07","corr_author":"1","oa":1,"type":"conference","date_published":"2023-07-01T00:00:00Z","article_number":"72","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":917791,"checksum":"6dee0684245bb1c524b9c955db1e933d","file_name":"2023_LIPIcsICALP_Harris.pdf","creator":"dernst","date_created":"2023-08-21T06:45:16Z","relation":"main_file","date_updated":"2023-08-21T06:45:16Z","success":1,"file_id":"14088"}],"publication_status":"published","article_processing_charge":"Yes","year":"2023","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"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.","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.","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>","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>","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>.","short":"D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023."},"doi":"10.4230/LIPIcs.ICALP.2023.72","volume":261,"department":[{"_id":"VlKo"}],"scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","_id":"14084","external_id":{"arxiv":["2007.10824"]},"conference":{"start_date":"2023-07-10","name":"ICALP: Automata, Languages and Programming","location":"Paderborn, Germany","end_date":"2023-07-14"},"arxiv":1,"day":"01","related_material":{"record":[{"status":"public","relation":"later_version","id":"18855"}]},"file_date_updated":"2023-08-21T06:45:16Z","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.","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"title":"Parameter estimation for Gibbs distributions","date_updated":"2025-07-10T11:50:45Z","author":[{"first_name":"David G.","last_name":"Harris","full_name":"Harris, David G."},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}]},{"citation":{"short":"G. Goranci, M. Henzinger, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Goranci, Gramoz, and Monika Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” 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.2023.69\">https://doi.org/10.4230/LIPIcs.ICALP.2023.69</a>.","apa":"Goranci, G., &#38; Henzinger, M. (2023). Efficient data structures for incremental exact and approximate maximum flow. 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.2023.69\">https://doi.org/10.4230/LIPIcs.ICALP.2023.69</a>","ama":"Goranci G, Henzinger M. Efficient data structures for incremental exact and approximate maximum flow. 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.2023.69\">10.4230/LIPIcs.ICALP.2023.69</a>","ista":"Goranci G, Henzinger M. 2023. Efficient data structures for incremental exact and approximate maximum flow. 50th International Colloquium on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 261, 69.","mla":"Goranci, Gramoz, and Monika Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.69\">10.4230/LIPIcs.ICALP.2023.69</a>.","ieee":"G. Goranci and M. Henzinger, “Efficient data structures for incremental exact and approximate maximum flow,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.4230/LIPIcs.ICALP.2023.69","project":[{"call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer"}],"volume":261,"scopus_import":"1","department":[{"_id":"MoHe"}],"oa_version":"Published Version","quality_controlled":"1","_id":"14085","external_id":{"arxiv":["2211.09606"]},"conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","name":"ICALP: Automata, Languages and Programming","start_date":"2023-07-10"},"arxiv":1,"file_date_updated":"2023-08-21T06:59:05Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There, he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their insightful comments.","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"day":"01","date_updated":"2025-06-04T07:19:37Z","title":"Efficient data structures for incremental exact and approximate maximum flow","author":[{"first_name":"Gramoz","last_name":"Goranci","full_name":"Goranci, Gramoz"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H"}],"intvolume":"       261","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"abstract":[{"text":"We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed, unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm in general sparse graphs with arbitrarily good approximation guarantee.","lang":"eng"}],"date_created":"2023-08-20T22:01:14Z","has_accepted_license":"1","publication":"50th International Colloquium on Automata, Languages, and Programming","month":"07","ddc":["000"],"corr_author":"1","status":"public","oa":1,"type":"conference","ec_funded":1,"date_published":"2023-07-01T00:00:00Z","article_number":"69","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-08-21T06:59:05Z","success":1,"file_id":"14089","file_size":875910,"access_level":"open_access","content_type":"application/pdf","date_created":"2023-08-21T06:59:05Z","relation":"main_file","file_name":"2023_LIPIcsICALP_Goranci.pdf","creator":"dernst","checksum":"074177e815a1656de5d4071c7a3dffa6"}],"article_processing_charge":"Yes","year":"2023","publication_status":"published"},{"author":[{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530"},{"full_name":"Liu, Paul","last_name":"Liu","first_name":"Paul"},{"full_name":"Vondrák, Jan","first_name":"Jan","last_name":"Vondrák"},{"first_name":"Da Wei","last_name":"Zheng","full_name":"Zheng, Da Wei"}],"date_updated":"2025-07-10T11:50:45Z","title":"Faster submodular maximization for several classes of matroids","arxiv":1,"file_date_updated":"2023-08-21T07:04:36Z","acknowledgement":" Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by NSF Award 2127781.","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"day":"01","external_id":{"arxiv":["2305.00122"]},"conference":{"name":"ICALP: Automata, Languages and Programming","location":"Paderborn, Germany","start_date":"2023-07-10","end_date":"2023-07-14"},"quality_controlled":"1","oa_version":"Published Version","_id":"14086","volume":261,"scopus_import":"1","department":[{"_id":"MoHe"}],"citation":{"ista":"Henzinger M, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization for several classes of matroids. 50th International Colloquium on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 261, 74.","ama":"Henzinger M, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for several classes of matroids. 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.2023.74\">10.4230/LIPIcs.ICALP.2023.74</a>","apa":"Henzinger, M., Liu, P., Vondrák, J., &#38; Zheng, D. W. (2023). Faster submodular maximization for several classes of matroids. 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.2023.74\">https://doi.org/10.4230/LIPIcs.ICALP.2023.74</a>","mla":"Henzinger, Monika, et al. “Faster Submodular Maximization for Several Classes of Matroids.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.74\">10.4230/LIPIcs.ICALP.2023.74</a>.","ieee":"M. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization for several classes of matroids,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261.","short":"M. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Henzinger, Monika, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular Maximization for Several Classes of Matroids.” 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.2023.74\">https://doi.org/10.4230/LIPIcs.ICALP.2023.74</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.4230/LIPIcs.ICALP.2023.74","project":[{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer"}],"file":[{"content_type":"application/pdf","access_level":"open_access","file_size":930943,"creator":"dernst","file_name":"2023_LIPIcsICALP_HenzingerM.pdf","checksum":"a5eef225014e003efbfbe4830fdd23cb","relation":"main_file","date_created":"2023-08-21T07:04:36Z","date_updated":"2023-08-21T07:04:36Z","file_id":"14090","success":1}],"year":"2023","article_processing_charge":"Yes","publication_status":"published","date_published":"2023-07-01T00:00:00Z","article_number":"74","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ec_funded":1,"type":"conference","status":"public","publication":"50th International Colloquium on Automata, Languages, and Programming","corr_author":"1","ddc":["000"],"month":"07","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"date_created":"2023-08-20T22:01:14Z","abstract":[{"lang":"eng","text":"The maximization of submodular functions have found widespread application in areas such as machine learning, combinatorial optimization, and economics, where practitioners often wish to enforce various constraints; the matroid constraint has been investigated extensively due to its algorithmic properties and expressive power. Though tight approximation algorithms for general matroid constraints exist in theory, the running times of such algorithms typically scale quadratically, and are not practical for truly large scale settings. Recent progress has focused on fast algorithms for important classes of matroids given in explicit form. Currently, nearly-linear time algorithms only exist for graphic and partition matroids [Alina Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone submodular maximization constrained by graphic, transversal matroids, or laminar matroids in time near-linear in the size of their representation. Our algorithms achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the running time of our algorithm cannot be improved within the fast continuous greedy framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák, 2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures that maintain bases with approximate maximum cardinality and weight under certain element updates. These data structures need to support a weight decrease operation and a novel Freeze operation that allows the algorithm to freeze elements (i.e. force to be contained) in its basis regardless of future data structure operations. For the laminar matroid, we present a new dynamic data structure using the top tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et al., 2005] that maintains the maximum weight basis under insertions and deletions of elements in O(log n) time. This data structure needs to support certain subtree query and path update operations that are performed every insertion and deletion that are non-trivial to handle in conjunction. For the transversal matroid the Freeze operation corresponds to requiring the data structure to keep a certain set S of vertices matched, a property that we call S-stability. While there is a large body of work on dynamic matching algorithms, none are S-stable and maintain an approximate maximum weight matching under vertex updates. We give the first such algorithm for bipartite graphs with total running time linear (up to log factors) in the number of edges."}],"has_accepted_license":"1","intvolume":"       261","language":[{"iso":"eng"}]}]