[{"page":"1343-1348","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"6340","doi":"10.1109/Cybermatics_2018.2018.00231","external_id":{"arxiv":["1805.09104"],"isi":["000481634500196"]},"department":[{"_id":"KrCh"}],"quality_controlled":"1","isi":1,"article_processing_charge":"No","citation":{"chicago":"Goharshady, Amir Kafshdar, Ali Behrouz, and Krishnendu Chatterjee. “Secure Credit Reporting on the Blockchain.” In <i>Proceedings of the IEEE International Conference on Blockchain</i>, 1343–48. IEEE, 2018. <a href=\"https://doi.org/10.1109/Cybermatics_2018.2018.00231\">https://doi.org/10.1109/Cybermatics_2018.2018.00231</a>.","ama":"Goharshady AK, Behrouz A, Chatterjee K. Secure Credit Reporting on the Blockchain. In: <i>Proceedings of the IEEE International Conference on Blockchain</i>. IEEE; 2018:1343-1348. doi:<a href=\"https://doi.org/10.1109/Cybermatics_2018.2018.00231\">10.1109/Cybermatics_2018.2018.00231</a>","short":"A.K. Goharshady, A. Behrouz, K. Chatterjee, in:, Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–1348.","apa":"Goharshady, A. K., Behrouz, A., &#38; Chatterjee, K. (2018). Secure Credit Reporting on the Blockchain. In <i>Proceedings of the IEEE International Conference on Blockchain</i> (pp. 1343–1348). Halifax, Canada: IEEE. <a href=\"https://doi.org/10.1109/Cybermatics_2018.2018.00231\">https://doi.org/10.1109/Cybermatics_2018.2018.00231</a>","mla":"Goharshady, Amir Kafshdar, et al. “Secure Credit Reporting on the Blockchain.” <i>Proceedings of the IEEE International Conference on Blockchain</i>, IEEE, 2018, pp. 1343–48, doi:<a href=\"https://doi.org/10.1109/Cybermatics_2018.2018.00231\">10.1109/Cybermatics_2018.2018.00231</a>.","ieee":"A. K. Goharshady, A. Behrouz, and K. Chatterjee, “Secure Credit Reporting on the Blockchain,” in <i>Proceedings of the IEEE International Conference on Blockchain</i>, Halifax, Canada, 2018, pp. 1343–1348.","ista":"Goharshady AK, Behrouz A, Chatterjee K. 2018. Secure Credit Reporting on the Blockchain. Proceedings of the IEEE International Conference on Blockchain. IEEE International Conference on Blockchain, 1343–1348."},"status":"public","type":"conference","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Secure Credit Reporting on the Blockchain","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"oa_version":"Submitted Version","month":"09","date_updated":"2025-06-02T08:53:45Z","ddc":["000"],"publication_identifier":{"isbn":["978-1-5386-7975-3 "]},"publication_status":"published","oa":1,"conference":{"location":"Halifax, Canada","end_date":"2018-08-03","name":"IEEE International Conference on Blockchain","start_date":"2018-07-30"},"arxiv":1,"has_accepted_license":"1","date_created":"2019-04-18T10:37:35Z","project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"publisher":"IEEE","file":[{"file_size":624338,"access_level":"open_access","file_name":"blockchain2018.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:27Z","checksum":"b25c9bb7cf6e7e6634e692d26d41ead8","relation":"main_file","date_created":"2019-04-18T10:36:39Z","creator":"akafshda","file_id":"6341"}],"scopus_import":"1","day":"01","year":"2018","language":[{"iso":"eng"}],"publication":"Proceedings of the IEEE International Conference on Blockchain","ec_funded":1,"file_date_updated":"2020-07-14T12:47:27Z","abstract":[{"lang":"eng","text":"We  present  a  secure  approach  for  maintaining  andreporting  credit  history  records  on  the  Blockchain.  Our  ap-proach  removes  third-parties  such  as  credit  reporting  agen-cies  from  the  lending  process  and  replaces  them  with  smartcontracts.  This  allows  customers  to  interact  directly  with  thelenders  or  banks  while  ensuring  the  integrity,  unmalleabilityand  privacy  of  their  credit  data.  Additionally,  each  customerhas  full  control  over  complete  or  selective  disclosure  of  hercredit records, eliminating the risk of privacy violations or databreaches. Moreover, our approach provides strong guaranteesfor the lenders as well. A lender can check both correctness andcompleteness of the credit data disclosed to her. This is the firstapproach  that  can  perform  all  credit  reporting  tasks  withouta  central  authority  or  changing  the  financial  mechanisms*."}],"date_published":"2018-09-01T00:00:00Z","author":[{"orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ali","last_name":"Behrouz","full_name":"Behrouz, Ali"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"}]},{"file":[{"date_created":"2019-04-30T08:04:33Z","creator":"dernst","checksum":"d4588377e789da7f360b553ae02c5119","relation":"main_file","file_id":"6360","file_name":"2018_BioProtocol_Fan.pdf","file_size":2928337,"access_level":"open_access","date_updated":"2020-07-14T12:47:28Z","content_type":"application/pdf"}],"publisher":"Bio-Protocol","project":[{"call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"date_created":"2019-04-29T09:40:33Z","issue":"18","file_date_updated":"2020-07-14T12:47:28Z","date_published":"2018-09-20T00:00:00Z","abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.","lang":"eng"}],"volume":8,"author":[{"full_name":"Fan, Shuxia","first_name":"Shuxia","last_name":"Fan"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"},{"first_name":"Florian R","last_name":"Gärtner","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R"}],"year":"2018","language":[{"iso":"eng"}],"day":"20","publication":"Bio-Protocol","ec_funded":1,"keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"citation":{"short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. <i>Bio-Protocol</i>. 2018;8(18). doi:<a href=\"https://doi.org/10.21769/bioprotoc.3018\">10.21769/bioprotoc.3018</a>","chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” <i>Bio-Protocol</i>. Bio-Protocol, 2018. <a href=\"https://doi.org/10.21769/bioprotoc.3018\">https://doi.org/10.21769/bioprotoc.3018</a>.","apa":"Fan, S., Lorenz, M., Massberg, S., &#38; Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. <i>Bio-Protocol</i>. Bio-Protocol. <a href=\"https://doi.org/10.21769/bioprotoc.3018\">https://doi.org/10.21769/bioprotoc.3018</a>","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” <i>Bio-Protocol</i>, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:<a href=\"https://doi.org/10.21769/bioprotoc.3018\">10.21769/bioprotoc.3018</a>.","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” <i>Bio-Protocol</i>, vol. 8, no. 18. Bio-Protocol, 2018."},"status":"public","type":"journal_article","title":"Platelet migration and bacterial trapping assay under flow","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"         8","_id":"6354","license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.21769/bioprotoc.3018","department":[{"_id":"MiSi"}],"quality_controlled":"1","acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)","has_accepted_license":"1","article_number":"e3018","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"09","publication_identifier":{"issn":["2331-8325"]},"date_updated":"2021-01-12T08:07:12Z","ddc":["570"],"oa":1,"publication_status":"published"},{"article_number":"e7","has_accepted_license":"1","arxiv":1,"publication_status":"published","oa":1,"publication_identifier":{"issn":["2050-5094"]},"ddc":["510"],"date_updated":"2023-09-19T14:50:12Z","oa_version":"Published Version","month":"05","related_material":{"record":[{"id":"8156","relation":"dissertation_contains","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Any cyclic quadrilateral can be inscribed in any closed convex smooth curve","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","status":"public","article_processing_charge":"No","citation":{"ieee":"A. Akopyan and S. Avvakumov, “Any cyclic quadrilateral can be inscribed in any closed convex smooth curve,” <i>Forum of Mathematics, Sigma</i>, vol. 6. Cambridge University Press, 2018.","ista":"Akopyan A, Avvakumov S. 2018. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 6, e7.","apa":"Akopyan, A., &#38; Avvakumov, S. (2018). Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2018.7\">https://doi.org/10.1017/fms.2018.7</a>","mla":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” <i>Forum of Mathematics, Sigma</i>, vol. 6, e7, Cambridge University Press, 2018, doi:<a href=\"https://doi.org/10.1017/fms.2018.7\">10.1017/fms.2018.7</a>.","short":"A. Akopyan, S. Avvakumov, Forum of Mathematics, Sigma 6 (2018).","ama":"Akopyan A, Avvakumov S. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. <i>Forum of Mathematics, Sigma</i>. 2018;6. doi:<a href=\"https://doi.org/10.1017/fms.2018.7\">10.1017/fms.2018.7</a>","chicago":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2018. <a href=\"https://doi.org/10.1017/fms.2018.7\">https://doi.org/10.1017/fms.2018.7</a>."},"isi":1,"quality_controlled":"1","department":[{"_id":"UlWa"},{"_id":"HeEd"},{"_id":"JaMa"}],"external_id":{"arxiv":["1712.10205"],"isi":["000433915500001"]},"doi":"10.1017/fms.2018.7","intvolume":"         6","_id":"6355","author":[{"last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey","first_name":"Sergey","last_name":"Avvakumov"}],"date_published":"2018-05-31T00:00:00Z","abstract":[{"text":"We  prove  that  any  cyclic  quadrilateral  can  be  inscribed  in  any  closed  convex C1-curve.  The smoothness condition is not required if the quadrilateral is a rectangle.","lang":"eng"}],"volume":6,"file_date_updated":"2020-07-14T12:47:28Z","ec_funded":1,"publication":"Forum of Mathematics, Sigma","language":[{"iso":"eng"}],"year":"2018","day":"31","file":[{"file_name":"2018_ForumMahtematics_Akopyan.pdf","file_size":249246,"access_level":"open_access","date_updated":"2020-07-14T12:47:28Z","content_type":"application/pdf","creator":"dernst","date_created":"2019-04-30T06:14:58Z","relation":"main_file","checksum":"5a71b24ba712a3eb2e46165a38fbc30a","file_id":"6356"}],"publisher":"Cambridge University Press","project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020"}],"date_created":"2019-04-30T06:09:57Z"},{"oa_version":"Preprint","month":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"publication_identifier":{"issn":["1745-2473","1745-2481"]},"date_updated":"2021-01-12T08:07:15Z","arxiv":1,"external_id":{"arxiv":["1712.06535"]},"doi":"10.1038/s41567-018-0210-0","intvolume":"        14","_id":"6368","page":"1038-1042","quality_controlled":"1","citation":{"apa":"Higginbotham, A. P., Burns, P. S., Urmey, M. D., Peterson, R. W., Kampel, N. S., Brubaker, B. M., … Regal, C. A. (2018). Harnessing electro-optic correlations in an efficient mechanical converter. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-018-0210-0\">https://doi.org/10.1038/s41567-018-0210-0</a>","mla":"Higginbotham, Andrew P., et al. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” <i>Nature Physics</i>, vol. 14, no. 10, Springer Nature, 2018, pp. 1038–42, doi:<a href=\"https://doi.org/10.1038/s41567-018-0210-0\">10.1038/s41567-018-0210-0</a>.","ama":"Higginbotham AP, Burns PS, Urmey MD, et al. Harnessing electro-optic correlations in an efficient mechanical converter. <i>Nature Physics</i>. 2018;14(10):1038-1042. doi:<a href=\"https://doi.org/10.1038/s41567-018-0210-0\">10.1038/s41567-018-0210-0</a>","short":"A.P. Higginbotham, P.S. Burns, M.D. Urmey, R.W. Peterson, N.S. Kampel, B.M. Brubaker, G. Smith, K.W. Lehnert, C.A. Regal, Nature Physics 14 (2018) 1038–1042.","chicago":"Higginbotham, Andrew P, P. S. Burns, M. D. Urmey, R. W. Peterson, N. S. Kampel, B. M. Brubaker, G. Smith, K. W. Lehnert, and C. A. Regal. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” <i>Nature Physics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41567-018-0210-0\">https://doi.org/10.1038/s41567-018-0210-0</a>.","ieee":"A. P. Higginbotham <i>et al.</i>, “Harnessing electro-optic correlations in an efficient mechanical converter,” <i>Nature Physics</i>, vol. 14, no. 10. Springer Nature, pp. 1038–1042, 2018.","ista":"Higginbotham AP, Burns PS, Urmey MD, Peterson RW, Kampel NS, Brubaker BM, Smith G, Lehnert KW, Regal CA. 2018. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 14(10), 1038–1042."},"extern":"1","title":"Harnessing electro-optic correlations in an efficient mechanical converter","status":"public","type":"journal_article","publication":"Nature Physics","year":"2018","language":[{"iso":"eng"}],"day":"01","issue":"10","author":[{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363"},{"full_name":"Burns, P. S.","first_name":"P. S.","last_name":"Burns"},{"full_name":"Urmey, M. D.","first_name":"M. D.","last_name":"Urmey"},{"full_name":"Peterson, R. W.","first_name":"R. W.","last_name":"Peterson"},{"full_name":"Kampel, N. S.","first_name":"N. S.","last_name":"Kampel"},{"first_name":"B. M.","last_name":"Brubaker","full_name":"Brubaker, B. M."},{"last_name":"Smith","first_name":"G.","full_name":"Smith, G."},{"full_name":"Lehnert, K. W.","first_name":"K. W.","last_name":"Lehnert"},{"full_name":"Regal, C. A.","first_name":"C. A.","last_name":"Regal"}],"date_published":"2018-10-01T00:00:00Z","abstract":[{"text":"An optical network of superconducting quantum bits (qubits) is an appealing platform for quantum communication and distributed quantum computing, but developing a quantum-compatible link between the microwave and optical domains remains an outstanding challenge. Operating at T < 100 mK temperatures, as required for quantum electrical circuits, we demonstrate a mechanically mediated microwave–optical converter with 47% conversion efficiency, and use a classical feed-forward protocol to reduce added noise to 38 photons. The feed-forward protocol harnesses our discovery that noise emitted from the two converter output ports is strongly correlated because both outputs record thermal motion of the same mechanical mode. We also discuss a quantum feed-forward protocol that, given high system efficiencies, would allow quantum information to be transferred even when thermal phonons enter the mechanical element faster than the electro-optic conversion rate.","lang":"eng"}],"volume":14,"date_created":"2019-05-03T09:17:20Z","main_file_link":[{"url":"https://arxiv.org/abs/1712.06535","open_access":"1"}],"publisher":"Springer Nature"},{"publication_identifier":{"issn":["2469-9950","2469-9969"]},"date_updated":"2021-01-12T08:07:16Z","oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"06","oa_version":"Preprint","article_number":"220301","arxiv":1,"quality_controlled":"1","intvolume":"        97","_id":"6369","external_id":{"arxiv":["1802.02243"]},"doi":"10.1103/physrevb.97.220301","status":"public","type":"journal_article","title":"Topological phase transition measured in a dissipative metamaterial","extern":"1","citation":{"ista":"Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. 2018. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 97(22), 220301.","ieee":"E. I. Rosenthal, N. K. Ehrlich, M. S. Rudner, A. P. Higginbotham, and K. W. Lehnert, “Topological phase transition measured in a dissipative metamaterial,” <i>Physical Review B</i>, vol. 97, no. 22. American Physical Society (APS), 2018.","apa":"Rosenthal, E. I., Ehrlich, N. K., Rudner, M. S., Higginbotham, A. P., &#38; Lehnert, K. W. (2018). Topological phase transition measured in a dissipative metamaterial. <i>Physical Review B</i>. American Physical Society (APS). <a href=\"https://doi.org/10.1103/physrevb.97.220301\">https://doi.org/10.1103/physrevb.97.220301</a>","mla":"Rosenthal, Eric I., et al. “Topological Phase Transition Measured in a Dissipative Metamaterial.” <i>Physical Review B</i>, vol. 97, no. 22, 220301, American Physical Society (APS), 2018, doi:<a href=\"https://doi.org/10.1103/physrevb.97.220301\">10.1103/physrevb.97.220301</a>.","chicago":"Rosenthal, Eric I., Nicole K. Ehrlich, Mark S. Rudner, Andrew P Higginbotham, and K. W. Lehnert. “Topological Phase Transition Measured in a Dissipative Metamaterial.” <i>Physical Review B</i>. American Physical Society (APS), 2018. <a href=\"https://doi.org/10.1103/physrevb.97.220301\">https://doi.org/10.1103/physrevb.97.220301</a>.","ama":"Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. Topological phase transition measured in a dissipative metamaterial. <i>Physical Review B</i>. 2018;97(22). doi:<a href=\"https://doi.org/10.1103/physrevb.97.220301\">10.1103/physrevb.97.220301</a>","short":"E.I. Rosenthal, N.K. Ehrlich, M.S. Rudner, A.P. Higginbotham, K.W. Lehnert, Physical Review B 97 (2018)."},"year":"2018","language":[{"iso":"eng"}],"day":"04","publication":"Physical Review B","date_published":"2018-06-04T00:00:00Z","abstract":[{"lang":"eng","text":"We construct a metamaterial from radio-frequency harmonic oscillators, and find two topologically distinct phases resulting from dissipation engineered into the system. These phases are distinguished by a quantized value of bulk energy transport. The impulse response of our circuit is measured and used to reconstruct the band structure and winding number of circuit eigenfunctions around a dark mode. Our results demonstrate that dissipative topological transport can occur in a wider class of physical systems than considered before."}],"volume":97,"author":[{"last_name":"Rosenthal","first_name":"Eric I.","full_name":"Rosenthal, Eric I."},{"first_name":"Nicole K.","last_name":"Ehrlich","full_name":"Ehrlich, Nicole K."},{"first_name":"Mark S.","last_name":"Rudner","full_name":"Rudner, Mark S."},{"first_name":"Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lehnert, K. W.","first_name":"K. W.","last_name":"Lehnert"}],"issue":"22","date_created":"2019-05-03T09:29:49Z","main_file_link":[{"url":"https://arxiv.org/abs/1802.02243","open_access":"1"}],"publisher":"American Physical Society (APS)"},{"date_created":"2018-12-11T11:44:26Z","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_type":"original","scopus_import":"1","publisher":"National Academy of Sciences","main_file_link":[{"url":"https://arxiv.org/abs/1806.09153","open_access":"1"}],"ec_funded":1,"publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","day":"28","year":"2018","language":[{"iso":"eng"}],"author":[{"last_name":"Kalinin","first_name":"Nikita","full_name":"Kalinin, Nikita"},{"last_name":"Guzmán Sáenz","first_name":"Aldo","full_name":"Guzmán Sáenz, Aldo"},{"last_name":"Prieto","first_name":"Y","full_name":"Prieto, Y"},{"orcid":"0000-0002-4310-178X","last_name":"Shkolnikov","first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","full_name":"Shkolnikov, Mikhail"},{"full_name":"Kalinina, V","last_name":"Kalinina","first_name":"V"},{"first_name":"Ernesto","last_name":"Lupercio","full_name":"Lupercio, Ernesto"}],"abstract":[{"text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation.","lang":"eng"}],"volume":115,"date_published":"2018-08-28T00:00:00Z","issue":"35","quality_controlled":"1","department":[{"_id":"TaHa"}],"doi":"10.1073/pnas.1805847115","external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"page":"E8135 - E8142","_id":"64","intvolume":"       115","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","type":"journal_article","status":"public","citation":{"ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” <i>PNAS: Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, PNAS: Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. <i>PNAS: Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(35):E8135-E8142. doi:<a href=\"https://doi.org/10.1073/pnas.1805847115\">10.1073/pnas.1805847115</a>","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” <i>PNAS: Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1805847115\">https://doi.org/10.1073/pnas.1805847115</a>.","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” <i>PNAS: Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:<a href=\"https://doi.org/10.1073/pnas.1805847115\">10.1073/pnas.1805847115</a>.","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., &#38; Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. <i>PNAS: 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.1805847115\">https://doi.org/10.1073/pnas.1805847115</a>"},"article_processing_charge":"No","isi":1,"publication_status":"published","oa":1,"date_updated":"2023-09-18T08:41:16Z","publication_identifier":{"issn":["00278424"]},"oa_version":"Preprint","month":"08","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7990","arxiv":1},{"type":"conference_poster","status":"public","title":"Open Access at IST Austria 2009-2017","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"6460","date_created":"2019-05-16T07:26:25Z","creator":"dernst","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","relation":"main_file","date_updated":"2020-07-14T12:47:30Z","content_type":"application/pdf","file_name":"Poster_Beitrag_125_Petritsch.pdf","file_size":1967778,"access_level":"open_access"}],"publisher":"IST Austria","citation":{"mla":"Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018, doi:<a href=\"https://doi.org/10.5281/zenodo.1410279\">10.5281/zenodo.1410279</a>.","apa":"Petritsch, B. (2018). <i>Open Access at IST Austria 2009-2017</i>. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. <a href=\"https://doi.org/10.5281/zenodo.1410279\">https://doi.org/10.5281/zenodo.1410279</a>","chicago":"Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018. <a href=\"https://doi.org/10.5281/zenodo.1410279\">https://doi.org/10.5281/zenodo.1410279</a>.","ama":"Petritsch B. <i>Open Access at IST Austria 2009-2017</i>. IST Austria; 2018. doi:<a href=\"https://doi.org/10.5281/zenodo.1410279\">10.5281/zenodo.1410279</a>","short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","ieee":"B. Petritsch, <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018."},"department":[{"_id":"E-Lib"}],"_id":"6459","doi":"10.5281/zenodo.1410279","date_created":"2019-05-16T07:27:14Z","date_published":"2018-09-24T00:00:00Z","author":[{"orcid":"0000-0003-2724-4614","last_name":"Petritsch","first_name":"Barbara","full_name":"Petritsch, Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:30Z","has_accepted_license":"1","keyword":["Open Access","Publication Analysis"],"date_updated":"2020-07-14T23:06:21Z","ddc":["020"],"oa":1,"publication_status":"published","conference":{"location":"Graz, Austria","start_date":"2018-09-24","end_date":"2018-09-26","name":"Open-Access-Tage"},"day":"24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","language":[{"iso":"eng"}],"month":"09","oa_version":"Published Version"},{"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"title":"The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"ama":"Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. <i>The Journal of Experimental Medicine</i>. 2018;2015(7):1869–1890. doi:<a href=\"https://doi.org/10.1084/jem.20170896\">10.1084/jem.20170896</a>","short":"F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R. Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga, M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal of Experimental Medicine 2015 (2018) 1869–1890.","chicago":"Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” <i>The Journal of Experimental Medicine</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1084/jem.20170896\">https://doi.org/10.1084/jem.20170896</a>.","mla":"Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” <i>The Journal of Experimental Medicine</i>, vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:<a href=\"https://doi.org/10.1084/jem.20170896\">10.1084/jem.20170896</a>.","apa":"Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I., … Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. <i>The Journal of Experimental Medicine</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1084/jem.20170896\">https://doi.org/10.1084/jem.20170896</a>","ista":"Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2015(7), 1869–1890.","ieee":"F. Moalli <i>et al.</i>, “The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells,” <i>The Journal of Experimental Medicine</i>, vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018."},"isi":1,"quality_controlled":"1","department":[{"_id":"MiSi"}],"external_id":{"isi":["000440822900011"]},"doi":"10.1084/jem.20170896","intvolume":"      2015","_id":"6497","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"1869–1890","has_accepted_license":"1","oa":1,"publication_status":"published","publication_identifier":{"eissn":["1540-9538"],"issn":["0022-1007"]},"date_updated":"2023-09-19T14:52:08Z","ddc":["570"],"oa_version":"Published Version","month":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","file":[{"file_id":"6498","creator":"kschuh","date_created":"2019-05-28T12:40:05Z","checksum":"86ae5331f9bfced9a6358a790a04bef4","relation":"main_file","date_updated":"2020-07-14T12:47:32Z","content_type":"application/pdf","file_name":"2018_rupress_Moalli.pdf","file_size":3841660,"access_level":"open_access"}],"publisher":"Rockefeller University Press","date_created":"2019-05-28T12:36:47Z","author":[{"full_name":"Moalli, Federica","first_name":"Federica","last_name":"Moalli"},{"last_name":"Ficht","first_name":"Xenia","full_name":"Ficht, Xenia"},{"last_name":"Germann","first_name":"Philipp","full_name":"Germann, Philipp"},{"first_name":"Mykhailo","last_name":"Vladymyrov","full_name":"Vladymyrov, Mykhailo"},{"full_name":"Stolp, Bettina","last_name":"Stolp","first_name":"Bettina"},{"first_name":"Ingrid","last_name":"de Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"de Vries, Ingrid"},{"first_name":"Ruth","last_name":"Lyck","full_name":"Lyck, Ruth"},{"last_name":"Balmer","first_name":"Jasmin","full_name":"Balmer, Jasmin"},{"full_name":"Fiocchi, Amleto","last_name":"Fiocchi","first_name":"Amleto"},{"full_name":"Kreutzfeldt, Mario","last_name":"Kreutzfeldt","first_name":"Mario"},{"full_name":"Merkler, Doron","last_name":"Merkler","first_name":"Doron"},{"last_name":"Iannacone","first_name":"Matteo","full_name":"Iannacone, Matteo"},{"first_name":"Akitaka","last_name":"Ariga","full_name":"Ariga, Akitaka"},{"first_name":"Michael H.","last_name":"Stoffel","full_name":"Stoffel, Michael H."},{"full_name":"Sharpe, James","last_name":"Sharpe","first_name":"James"},{"first_name":"Martin","last_name":"Bähler","full_name":"Bähler, Martin"},{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Diz-Muñoz","first_name":"Alba","full_name":"Diz-Muñoz, Alba"},{"first_name":"Jens V.","last_name":"Stein","full_name":"Stein, Jens V."}],"date_published":"2018-06-06T00:00:00Z","volume":2015,"abstract":[{"text":"T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:32Z","issue":"7","publication":"The Journal of Experimental Medicine","year":"2018","language":[{"iso":"eng"}],"day":"06"},{"language":[{"iso":"eng"}],"year":"2018","day":"01","publication":"EMBO reports","date_published":"2018-09-01T00:00:00Z","abstract":[{"lang":"eng","text":"Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge."}],"volume":19,"author":[{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M","first_name":"Sven M","last_name":"Truckenbrodt"},{"full_name":"Maidorn, Manuel","last_name":"Maidorn","first_name":"Manuel"},{"last_name":"Crzan","first_name":"Dagmar","full_name":"Crzan, Dagmar"},{"full_name":"Wildhagen, Hanna","last_name":"Wildhagen","first_name":"Hanna"},{"full_name":"Kabatas, Selda","first_name":"Selda","last_name":"Kabatas"},{"full_name":"Rizzoli, Silvio O","last_name":"Rizzoli","first_name":"Silvio O"}],"issue":"9","file_date_updated":"2020-07-14T12:47:32Z","date_created":"2019-05-28T13:16:08Z","scopus_import":"1","publisher":"EMBO","file":[{"file_name":"2018_embo_Truckenbrodt.pdf","file_size":2005572,"access_level":"open_access","date_updated":"2020-07-14T12:47:32Z","content_type":"application/pdf","creator":"kschuh","date_created":"2019-05-28T13:17:19Z","relation":"main_file","checksum":"6ec90abc637f09cca3a7b6424d7e7a26","file_id":"6500"}],"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"date_updated":"2023-09-19T14:52:32Z","ddc":["580"],"publication_status":"published","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"09","article_number":"e45836","has_accepted_license":"1","department":[{"_id":"JoDa"}],"quality_controlled":"1","intvolume":"        19","_id":"6499","external_id":{"isi":["000443682200009"]},"doi":"10.15252/embr.201845836","type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","isi":1,"citation":{"apa":"Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., &#38; Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO Reports</i>. EMBO. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>","mla":"Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>, vol. 19, no. 9, e45836, EMBO, 2018, doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>.","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO reports</i>. 2018;19(9). doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>","chicago":"Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>. EMBO, 2018. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>.","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” <i>EMBO reports</i>, vol. 19, no. 9. EMBO, 2018.","ista":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836."},"article_processing_charge":"No"},{"date_updated":"2021-01-12T08:07:52Z","publication_identifier":{"isbn":["9780198802013","9780191840500"]},"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","year":"2018","language":[{"iso":"eng"}],"publication":"Geometry and Physics: Volume I","oa_version":"None","month":"01","abstract":[{"lang":"eng","text":"This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal."}],"date_published":"2018-01-01T00:00:00Z","author":[{"full_name":"Hausel, Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamás"},{"last_name":"Mellit","first_name":"Anton","full_name":"Mellit, Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Du","last_name":"Pei","full_name":"Pei, Du"}],"department":[{"_id":"TaHa"}],"quality_controlled":"1","page":"189-218","_id":"6525","date_created":"2019-06-06T12:42:01Z","doi":"10.1093/oso/9780198802013.003.0009","status":"public","type":"book_chapter","scopus_import":1,"title":"Mirror symmetry with branes by equivariant verlinde formulas","publisher":"Oxford University Press","citation":{"ista":"Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.","ieee":"T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218.","ama":"Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: <i>Geometry and Physics: Volume I</i>. Oxford University Press; 2018:189-218. doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>","chicago":"Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In <i>Geometry and Physics: Volume I</i>, 189–218. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>.","short":"T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","mla":"Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218, doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>.","apa":"Hausel, T., Mellit, A., &#38; Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In <i>Geometry and Physics: Volume I</i> (pp. 189–218). Oxford University Press. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>"}},{"publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"year":"2018","day":"01","author":[{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Allen-Zhu","first_name":"Zeyuan","full_name":"Allen-Zhu, Zeyuan"},{"last_name":"Li","first_name":"Jerry","full_name":"Li, Jerry"}],"date_published":"2018-12-01T00:00:00Z","volume":2018,"abstract":[{"lang":"eng","text":"This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of m machines which allegedly compute stochastic gradients every iteration, an α-fraction are Byzantine, and may behave adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations. In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sample complexity and time complexity."}],"date_created":"2019-06-13T08:22:37Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08917"}],"publisher":"Neural Information Processing Systems Foundation","conference":{"end_date":"2018-12-08","name":"NeurIPS: Conference on Neural Information Processing Systems","start_date":"2018-12-02","location":"Montreal, Canada"},"publication_status":"published","oa":1,"date_updated":"2023-09-19T15:12:45Z","oa_version":"Published Version","month":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"quality_controlled":"1","department":[{"_id":"DaAl"}],"external_id":{"isi":["000461823304061"],"arxiv":["1803.08917"]},"intvolume":"      2018","page":"4613-4623","_id":"6558","title":"Byzantine stochastic gradient descent","status":"public","type":"conference","citation":{"ieee":"D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 2018, pp. 4613–4623.","ista":"Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 2018, 4613–4623.","mla":"Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” <i>Advances in Neural Information Processing Systems</i>, vol. 2018, Neural Information Processing Systems Foundation, 2018, pp. 4613–23.","apa":"Alistarh, D.-A., Allen-Zhu, Z., &#38; Li, J. (2018). Byzantine stochastic gradient descent. In <i>Advances in Neural Information Processing Systems</i> (Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems Foundation.","short":"D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018, pp. 4613–4623.","ama":"Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In: <i>Advances in Neural Information Processing Systems</i>. Vol 2018. Neural Information Processing Systems Foundation; 2018:4613-4623.","chicago":"Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic Gradient Descent.” In <i>Advances in Neural Information Processing Systems</i>, 2018:4613–23. Neural Information Processing Systems Foundation, 2018."},"article_processing_charge":"No","isi":1},{"department":[{"_id":"DaAl"},{"_id":"ChLa"}],"quality_controlled":"1","_id":"6589","page":"5973-5983","external_id":{"arxiv":["1809.10505"],"isi":["000461852000047"]},"status":"public","type":"conference","title":"The convergence of sparsified gradient methods","isi":1,"citation":{"ista":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems vol. Volume 2018, 5973–5983.","ieee":"D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat, and C. Renggli, “The convergence of sparsified gradient methods,” in <i>Advances in Neural Information Processing Systems 31</i>, Montreal, Canada, 2018, vol. Volume 2018, pp. 5973–5983.","apa":"Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat, S., &#38; Renggli, C. (2018). The convergence of sparsified gradient methods. In <i>Advances in Neural Information Processing Systems 31</i> (Vol. Volume 2018, pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.” <i>Advances in Neural Information Processing Systems 31</i>, vol. Volume 2018, Neural Information Processing Systems Foundation, 2018, pp. 5973–83.","short":"D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat, C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural Information Processing Systems Foundation, 2018, pp. 5973–5983.","ama":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. The convergence of sparsified gradient methods. In: <i>Advances in Neural Information Processing Systems 31</i>. Vol Volume 2018. Neural Information Processing Systems Foundation; 2018:5973-5983.","chicago":"Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov, Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.” In <i>Advances in Neural Information Processing Systems 31</i>, Volume 2018:5973–83. Neural Information Processing Systems Foundation, 2018."},"article_processing_charge":"No","date_updated":"2023-10-17T11:47:20Z","publication_status":"published","oa":1,"conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","start_date":"2018-12-02","end_date":"2018-12-08","location":"Montreal, Canada"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"12","arxiv":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"date_created":"2019-06-27T09:32:55Z","scopus_import":"1","publisher":"Neural Information Processing Systems Foundation","main_file_link":[{"url":"https://arxiv.org/abs/1809.10505","open_access":"1"}],"ec_funded":1,"day":"01","language":[{"iso":"eng"}],"year":"2018","publication":"Advances in Neural Information Processing Systems 31","abstract":[{"text":"Distributed training of massive machine learning models, in particular deep neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace. Several families of communication-reduction methods, such as quantization, large-batch methods, and gradient sparsification, have been proposed. To date, gradient sparsification methods--where each node sorts gradients by magnitude, and only communicates a subset of the components, accumulating the rest locally--are known to yield some of the largest practical gains. Such methods can reduce the amount of communication per step by up to \\emph{three orders of magnitude}, while preserving model accuracy. Yet, this family of methods currently has no theoretical justification. This is the question we address in this paper. We prove that, under analytic assumptions, sparsifying gradients by magnitude with local error correction provides convergence guarantees, for both convex and non-convex smooth objectives, for data-parallel SGD. The main insight is that sparsification methods implicitly maintain bounds on the maximum impact of stale updates, thanks to selection by magnitude. Our analysis and empirical validation also reveal that these methods do require analytical conditions to converge well, justifying existing heuristics.","lang":"eng"}],"volume":"Volume 2018","date_published":"2018-12-01T00:00:00Z","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Hoefler, Torsten","first_name":"Torsten","last_name":"Hoefler"},{"full_name":"Johansson, Mikael","first_name":"Mikael","last_name":"Johansson"},{"first_name":"Nikola H","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Khirirat, Sarit","last_name":"Khirirat","first_name":"Sarit"},{"first_name":"Cedric","last_name":"Renggli","full_name":"Renggli, Cedric"}]},{"department":[{"_id":"KrCh"}],"quality_controlled":"1","_id":"66","intvolume":"       118","doi":"10.4230/LIPIcs.CONCUR.2018.11","external_id":{"arxiv":["1806.03108"]},"status":"public","type":"conference","title":"Ergodic mean-payoff games for the analysis of attacks in crypto-currencies","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Yaron Velner. “Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.11</a>.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, Y. Velner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">10.4230/LIPIcs.CONCUR.2018.11</a>","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Velner, Y. (2018). Ergodic mean-payoff games for the analysis of attacks in crypto-currencies (Vol. 118). Presented at the CONCUR: Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.11</a>","mla":"Chatterjee, Krishnendu, et al. <i>Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies</i>. Vol. 118, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">10.4230/LIPIcs.CONCUR.2018.11</a>.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. 2018. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 118, 11.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and Y. Velner, “Ergodic mean-payoff games for the analysis of attacks in crypto-currencies,” presented at the CONCUR: Conference on Concurrency Theory, Beijing, China, 2018, vol. 118."},"article_processing_charge":"No","date_updated":"2025-06-02T08:53:46Z","ddc":["000"],"publication_identifier":{"isbn":["978-3-95977-087-3"]},"publication_status":"published","oa":1,"conference":{"location":"Beijing, China","start_date":"2018-09-04","name":"CONCUR: Conference on Concurrency Theory","end_date":"2018-09-07"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"publist_id":"7988","oa_version":"Published Version","month":"09","article_number":"11","arxiv":1,"alternative_title":["LIPIcs"],"has_accepted_license":"1","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"date_created":"2018-12-11T11:44:27Z","scopus_import":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file":[{"access_level":"open_access","file_size":1078309,"file_name":"2018_CONCUR_Chatterjee.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:34Z","relation":"main_file","checksum":"68a055b1aaa241cc38375083cf832a7d","date_created":"2018-12-17T12:08:00Z","creator":"dernst","file_id":"5696"}],"ec_funded":1,"day":"01","year":"2018","language":[{"iso":"eng"}],"volume":118,"abstract":[{"lang":"eng","text":"Crypto-currencies are digital assets designed to work as a medium of exchange, e.g., Bitcoin, but they are susceptible to attacks (dishonest behavior of participants). A framework for the analysis of attacks in crypto-currencies requires (a) modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior; (b) concurrent interactions between participants; and (c) analysis of long-term monetary gains. Traditional game-theoretic approaches for the analysis of security protocols consider either qualitative temporal properties such as safety and termination, or the very special class of one-shot (stateless) games. However, to analyze general attacks on protocols for crypto-currencies, both stateful analysis and quantitative objectives are necessary. In this work our main contributions are as follows: (a) we show how a class of concurrent mean-payo games, namely ergodic games, can model various attacks that arise naturally in crypto-currencies; (b) we present the first practical implementation of algorithms for ergodic games that scales to model realistic problems for crypto-currencies; and (c) we present experimental results showing that our framework can handle games with thousands of states and millions of transitions."}],"date_published":"2018-09-01T00:00:00Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir","full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"file_date_updated":"2020-07-14T12:47:34Z"},{"department":[{"_id":"FrLo"}],"_id":"14327","external_id":{"arxiv":["1804.11130"]},"doi":"10.48550/arXiv.1804.11130","date_created":"2023-09-13T12:20:49Z","type":"preprint","status":"public","title":"Competitive training of mixtures of independent deep generative models","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1804.11130"}],"extern":"1","article_processing_charge":"No","citation":{"ista":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130.","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” <i>arXiv</i>. .","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","ama":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., &#38; Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>","mla":"Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, 1804.11130, doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>."},"date_updated":"2023-09-13T12:23:03Z","publication_status":"submitted","oa":1,"language":[{"iso":"eng"}],"year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","oa_version":"Preprint","publication":"arXiv","month":"04","date_published":"2018-04-30T00:00:00Z","abstract":[{"lang":"eng","text":"A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples."}],"article_number":"1804.11130","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"full_name":"Vincent, Damien","last_name":"Vincent","first_name":"Damien"},{"full_name":"Tolstikhin, Ilya","last_name":"Tolstikhin","first_name":"Ilya"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"}],"arxiv":1},{"abstract":[{"text":"The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines.","lang":"eng"}],"volume":"Part F138033","date_published":"2018-07-09T00:00:00Z","author":[{"full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Saraç, Ege","last_name":"Saraç","first_name":"Ege"}],"alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"date_updated":"2023-09-08T11:49:13Z","publication_status":"published","conference":{"start_date":"2018-07-09","end_date":"2018-07-12","name":"LICS: Logic in Computer Science","location":"Oxford, UK"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"09","publist_id":"7779","year":"2018","language":[{"iso":"eng"}],"oa_version":"None","month":"07","status":"public","type":"conference","title":"A theory of register monitors","scopus_import":"1","isi":1,"publisher":"IEEE","citation":{"short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>.","ama":"Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>","mla":"Ferrere, Thomas, et al. <i>A Theory of Register Monitors</i>. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>.","apa":"Ferrere, T., Henzinger, T. A., &#38; Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>","ieee":"T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.","ista":"Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403."},"article_processing_charge":"No","department":[{"_id":"ToHe"}],"quality_controlled":"1","page":"394 - 403","_id":"144","date_created":"2018-12-11T11:44:52Z","doi":"10.1145/3209108.3209194","external_id":{"isi":["000545262800041"]}},{"volume":37,"abstract":[{"text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins.","lang":"eng"}],"date_published":"2018-08-01T00:00:00Z","author":[{"first_name":"Sven M","last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M"},{"full_name":"Viplav, Abhiyan","last_name":"Viplav","first_name":"Abhiyan"},{"full_name":"Jähne, Sebsatian","last_name":"Jähne","first_name":"Sebsatian"},{"last_name":"Vogts","first_name":"Angela","full_name":"Vogts, Angela"},{"full_name":"Denker, Annette","first_name":"Annette","last_name":"Denker"},{"first_name":"Hanna","last_name":"Wildhagen","full_name":"Wildhagen, Hanna"},{"first_name":"Eugenio","last_name":"Fornasiero","full_name":"Fornasiero, Eugenio"},{"first_name":"Silvio","last_name":"Rizzoli","full_name":"Rizzoli, Silvio"}],"issue":"15","file_date_updated":"2020-07-14T12:44:56Z","day":"01","year":"2018","language":[{"iso":"eng"}],"publication":"The EMBO Journal","scopus_import":"1","publisher":"Wiley","file":[{"date_created":"2018-12-17T14:17:29Z","creator":"dernst","checksum":"a540feb6c9af6aefc78de531461a8835","relation":"main_file","file_id":"5710","file_name":"2018_EMBO_Truckenbrodt.pdf","access_level":"open_access","file_size":2846470,"date_updated":"2020-07-14T12:44:56Z","content_type":"application/pdf"}],"pmid":1,"article_type":"original","date_created":"2018-12-11T11:44:52Z","article_number":"e98044","has_accepted_license":"1","ddc":["570"],"date_updated":"2023-09-13T09:02:48Z","publication_identifier":{"issn":["0261-4189"]},"publication_status":"published","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7778","oa_version":"Published Version","month":"08","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","isi":1,"citation":{"ieee":"S. M. Truckenbrodt <i>et al.</i>, “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” <i>The EMBO Journal</i>, vol. 37, no. 15. Wiley, 2018.","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>. Wiley, 2018. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. 2018;37(15). doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. Wiley. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>, vol. 37, no. 15, e98044, Wiley, 2018, doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>."},"article_processing_charge":"No","department":[{"_id":"JoDa"}],"acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","quality_controlled":"1","_id":"145","intvolume":"        37","doi":"10.15252/embj.201798044","external_id":{"isi":["000440416900005"],"pmid":["29950309"]}},{"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7777","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/","description":"News on IST Homepage","relation":"press_release"}]},"month":"07","oa_version":"Submitted Version","date_updated":"2023-09-19T10:08:45Z","ddc":["580"],"oa":1,"publication_status":"published","isi":1,"citation":{"ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. 2018;4(8):596-604. doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>.","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>","ieee":"C. L. Shi <i>et al.</i>, “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604."},"article_processing_charge":"No","type":"journal_article","status":"public","title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","intvolume":"         4","_id":"146","page":"596 - 604","external_id":{"pmid":["30061750"],"isi":["000443861300016"]},"doi":"10.1038/s41477-018-0212-z","department":[{"_id":"JiFr"}],"quality_controlled":"1","issue":"8","file_date_updated":"2020-07-14T12:44:56Z","date_published":"2018-07-30T00:00:00Z","volume":4,"abstract":[{"lang":"eng","text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity."}],"author":[{"last_name":"Shi","first_name":"Chun Lin","full_name":"Shi, Chun Lin"},{"first_name":"Daniel","last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Herrmann","first_name":"Ullrich","full_name":"Herrmann, Ullrich"},{"last_name":"Wildhagen","first_name":"Mari","full_name":"Wildhagen, Mari"},{"id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","full_name":"Kulik, Ivan","first_name":"Ivan","last_name":"Kulik"},{"first_name":"Andreas","last_name":"Kopf","full_name":"Kopf, Andreas"},{"first_name":"Takashi","last_name":"Ishida","full_name":"Ishida, Takashi"},{"full_name":"Olsson, Vilde","first_name":"Vilde","last_name":"Olsson"},{"last_name":"Anker","first_name":"Mari Kristine","full_name":"Anker, Mari Kristine"},{"last_name":"Albert","first_name":"Markus","full_name":"Albert, Markus"},{"full_name":"Butenko, Melinka A","first_name":"Melinka A","last_name":"Butenko"},{"full_name":"Felix, Georg","first_name":"Georg","last_name":"Felix"},{"first_name":"Shinichiro","last_name":"Sawa","full_name":"Sawa, Shinichiro"},{"full_name":"Claassen, Manfred","last_name":"Claassen","first_name":"Manfred"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"full_name":"Aalen, Reidunn B","last_name":"Aalen","first_name":"Reidunn B"}],"language":[{"iso":"eng"}],"year":"2018","day":"30","publication":"Nature Plants","pmid":1,"publisher":"Nature Publishing Group","file":[{"checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","relation":"main_file","creator":"dernst","date_created":"2019-11-18T16:24:07Z","file_id":"7043","file_size":226829,"access_level":"open_access","file_name":"2018_NaturePlants_Shi.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:56Z"}],"scopus_import":"1","article_type":"original","date_created":"2018-12-11T11:44:52Z"},{"date_created":"2018-12-11T11:44:52Z","article_type":"original","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"}],"main_file_link":[{"url":"https://doi.org/10.1105/tpc.18.00127","open_access":"1"}],"pmid":1,"publisher":"Oxford University Press","scopus_import":"1","year":"2018","language":[{"iso":"eng"}],"day":"12","publication":"The Plant Cell","ec_funded":1,"issue":"10","date_published":"2018-11-12T00:00:00Z","abstract":[{"text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development.","lang":"eng"}],"volume":30,"author":[{"full_name":"Kania, Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","last_name":"Kania"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"full_name":"Lu, Qing","first_name":"Qing","last_name":"Lu"},{"full_name":"Hicks, Glenn R","first_name":"Glenn R","last_name":"Hicks"},{"full_name":"Nerinckx, Wim","last_name":"Nerinckx","first_name":"Wim"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"full_name":"Peurois, Francois","last_name":"Peurois","first_name":"Francois"},{"full_name":"Cherfils, Jacqueline","first_name":"Jacqueline","last_name":"Cherfils"},{"first_name":"Rycke Riet Maria","last_name":"De","full_name":"De, Rycke Riet Maria"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"intvolume":"        30","page":"2553 - 2572","_id":"147","external_id":{"isi":["000450000500023"],"pmid":["30018156"]},"doi":"10.1105/tpc.18.00127","department":[{"_id":"JiFr"}],"quality_controlled":"1","acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","isi":1,"article_processing_charge":"No","citation":{"ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","ieee":"U. Kania <i>et al.</i>, “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” <i>The Plant Cell</i>, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. 2018;30(10):2553-2572. doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>.","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>"},"type":"journal_article","status":"public","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","publist_id":"7776","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"11","publication_identifier":{"issn":["1040-4651"]},"date_updated":"2025-05-07T11:12:30Z","oa":1,"publication_status":"published"},{"publist_id":"7774","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"07","date_updated":"2023-09-19T10:02:47Z","oa":1,"publication_status":"published","isi":1,"citation":{"ieee":"T. Nishiyama <i>et al.</i>, “The Chara genome: Secondary complexity and implications for plant terrestrialization,” <i>Cell</i>, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. 2018;174(2):448-464.e24. doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>.","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>."},"article_processing_charge":"No","type":"journal_article","status":"public","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","intvolume":"       174","page":"448 - 464.e24","_id":"148","external_id":{"pmid":["30007417"],"isi":["000438482800019"]},"doi":"10.1016/j.cell.2018.06.033","department":[{"_id":"JiFr"}],"quality_controlled":"1","acknowledgement":"In-Data-Review","issue":"2","date_published":"2018-07-12T00:00:00Z","volume":174,"abstract":[{"lang":"eng","text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote."}],"author":[{"first_name":"Tomoaki","last_name":"Nishiyama","full_name":"Nishiyama, Tomoaki"},{"last_name":"Sakayama","first_name":"Hidetoshi","full_name":"Sakayama, Hidetoshi"},{"full_name":"De Vries, Jan","last_name":"De Vries","first_name":"Jan"},{"first_name":"Henrik","last_name":"Buschmann","full_name":"Buschmann, Henrik"},{"full_name":"Saint Marcoux, Denis","last_name":"Saint Marcoux","first_name":"Denis"},{"first_name":"Kristian","last_name":"Ullrich","full_name":"Ullrich, Kristian"},{"first_name":"Fabian","last_name":"Haas","full_name":"Haas, Fabian"},{"first_name":"Lisa","last_name":"Vanderstraeten","full_name":"Vanderstraeten, Lisa"},{"full_name":"Becker, Dirk","first_name":"Dirk","last_name":"Becker"},{"full_name":"Lang, Daniel","first_name":"Daniel","last_name":"Lang"},{"last_name":"Vosolsobě","first_name":"Stanislav","full_name":"Vosolsobě, Stanislav"},{"full_name":"Rombauts, Stephane","last_name":"Rombauts","first_name":"Stephane"},{"last_name":"Wilhelmsson","first_name":"Per","full_name":"Wilhelmsson, Per"},{"first_name":"Philipp","last_name":"Janitza","full_name":"Janitza, Philipp"},{"full_name":"Kern, Ramona","last_name":"Kern","first_name":"Ramona"},{"last_name":"Heyl","first_name":"Alexander","full_name":"Heyl, Alexander"},{"full_name":"Rümpler, Florian","first_name":"Florian","last_name":"Rümpler"},{"full_name":"Calderón Villalobos, Luz","first_name":"Luz","last_name":"Calderón Villalobos"},{"full_name":"Clay, John","last_name":"Clay","first_name":"John"},{"full_name":"Skokan, Roman","last_name":"Skokan","first_name":"Roman"},{"last_name":"Toyoda","first_name":"Atsushi","full_name":"Toyoda, Atsushi"},{"first_name":"Yutaka","last_name":"Suzuki","full_name":"Suzuki, Yutaka"},{"full_name":"Kagoshima, Hiroshi","last_name":"Kagoshima","first_name":"Hiroshi"},{"full_name":"Schijlen, Elio","last_name":"Schijlen","first_name":"Elio"},{"full_name":"Tajeshwar, Navindra","last_name":"Tajeshwar","first_name":"Navindra"},{"full_name":"Catarino, Bruno","last_name":"Catarino","first_name":"Bruno"},{"full_name":"Hetherington, Alexander","first_name":"Alexander","last_name":"Hetherington"},{"full_name":"Saltykova, Assia","last_name":"Saltykova","first_name":"Assia"},{"first_name":"Clemence","last_name":"Bonnot","full_name":"Bonnot, Clemence"},{"full_name":"Breuninger, Holger","first_name":"Holger","last_name":"Breuninger"},{"full_name":"Symeonidi, Aikaterini","last_name":"Symeonidi","first_name":"Aikaterini"},{"last_name":"Radhakrishnan","first_name":"Guru","full_name":"Radhakrishnan, Guru"},{"full_name":"Van Nieuwerburgh, Filip","first_name":"Filip","last_name":"Van Nieuwerburgh"},{"full_name":"Deforce, Dieter","last_name":"Deforce","first_name":"Dieter"},{"first_name":"Caren","last_name":"Chang","full_name":"Chang, Caren"},{"full_name":"Karol, Kenneth","last_name":"Karol","first_name":"Kenneth"},{"full_name":"Hedrich, Rainer","last_name":"Hedrich","first_name":"Rainer"},{"first_name":"Peter","last_name":"Ulvskov","full_name":"Ulvskov, Peter"},{"full_name":"Glöckner, Gernot","last_name":"Glöckner","first_name":"Gernot"},{"last_name":"Delwiche","first_name":"Charles","full_name":"Delwiche, Charles"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"last_name":"Van De Peer","first_name":"Yves","full_name":"Van De Peer, Yves"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"last_name":"Beilby","first_name":"Mary","full_name":"Beilby, Mary"},{"full_name":"Dolan, Liam","last_name":"Dolan","first_name":"Liam"},{"last_name":"Kohara","first_name":"Yuji","full_name":"Kohara, Yuji"},{"first_name":"Sumio","last_name":"Sugano","full_name":"Sugano, Sumio"},{"full_name":"Fujiyama, Asao","last_name":"Fujiyama","first_name":"Asao"},{"last_name":"Delaux","first_name":"Pierre Marc","full_name":"Delaux, Pierre Marc"},{"first_name":"Marcel","last_name":"Quint","full_name":"Quint, Marcel"},{"full_name":"Theissen, Gunter","first_name":"Gunter","last_name":"Theissen"},{"full_name":"Hagemann, Martin","first_name":"Martin","last_name":"Hagemann"},{"first_name":"Jesper","last_name":"Harholt","full_name":"Harholt, Jesper"},{"first_name":"Christophe","last_name":"Dunand","full_name":"Dunand, Christophe"},{"last_name":"Zachgo","first_name":"Sabine","full_name":"Zachgo, Sabine"},{"full_name":"Langdale, Jane","first_name":"Jane","last_name":"Langdale"},{"full_name":"Maumus, Florian","first_name":"Florian","last_name":"Maumus"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"last_name":"Gould","first_name":"Sven B","full_name":"Gould, Sven B"},{"full_name":"Rensing, Stefan","first_name":"Stefan","last_name":"Rensing"}],"language":[{"iso":"eng"}],"year":"2018","day":"12","publication":"Cell","ec_funded":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"pmid":1,"publisher":"Cell Press","scopus_import":"1","project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"date_created":"2018-12-11T11:44:53Z"},{"ec_funded":1,"day":"12","language":[{"iso":"eng"}],"year":"2018","author":[{"first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes"}],"abstract":[{"lang":"eng","text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations."}],"date_published":"2018-07-12T00:00:00Z","file_date_updated":"2020-07-14T12:44:57Z","date_created":"2018-12-11T11:44:53Z","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7"}],"supervisor":[{"orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"}],"file":[{"file_id":"6241","relation":"main_file","checksum":"d4dad55a7513f345706aaaba90cb1bb8","date_created":"2019-04-08T13:55:20Z","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:44:57Z","access_level":"open_access","file_size":5801709,"file_name":"2018_thesis_Alt.pdf"},{"date_created":"2019-04-08T13:55:20Z","creator":"dernst","relation":"source_file","checksum":"d73fcf46300dce74c403f2b491148ab4","file_id":"6242","file_name":"2018_thesis_Alt_source.zip","file_size":3802059,"access_level":"closed","date_updated":"2020-07-14T12:44:57Z","content_type":"application/zip"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","oa":1,"date_updated":"2024-02-22T14:34:33Z","ddc":["515","519"],"publication_identifier":{"issn":["2663-337X"]},"month":"07","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7772","related_material":{"record":[{"status":"public","id":"1677","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"550"},{"relation":"part_of_dissertation","id":"6183","status":"public"},{"id":"566","relation":"part_of_dissertation","status":"public"},{"id":"1010","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"6240","relation":"part_of_dissertation"},{"status":"public","id":"6184","relation":"part_of_dissertation"}]},"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","department":[{"_id":"LaEr"}],"doi":"10.15479/AT:ISTA:TH_1040","page":"456","_id":"149","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Dyson equation and eigenvalue statistics of random matrices","status":"public","type":"dissertation","pubrep_id":"1040","article_processing_charge":"No","citation":{"short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">10.15479/AT:ISTA:TH_1040</a>","chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">https://doi.org/10.15479/AT:ISTA:TH_1040</a>.","apa":"Alt, J. (2018). <i>Dyson equation and eigenvalue statistics of random matrices</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">https://doi.org/10.15479/AT:ISTA:TH_1040</a>","mla":"Alt, Johannes. <i>Dyson Equation and Eigenvalue Statistics of Random Matrices</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">10.15479/AT:ISTA:TH_1040</a>.","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria."}}]