[{"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"publication_status":"published","status":"public","acknowledgement":"This work was supported by JSPS KAKENHI GRANT #18K062291, and the Takeda Science Foundation to J.Y. Toshima, as well as JSPS KAKENHI GRANT #19K065710, the Uehara Memorial Foundation, and Life Science Foundation of JAPAN to J. Toshima.","title":"Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway","author":[{"last_name":"Enshoji","full_name":"Enshoji, Mariko","first_name":"Mariko"},{"last_name":"Miyano","full_name":"Miyano, Yoshiko","first_name":"Yoshiko"},{"first_name":"Nao","last_name":"Yoshida","full_name":"Yoshida, Nao"},{"first_name":"Makoto","full_name":"Nagano, Makoto","last_name":"Nagano"},{"last_name":"Watanabe","full_name":"Watanabe, Minami","first_name":"Minami"},{"full_name":"Kunihiro, Mayumi","last_name":"Kunihiro","first_name":"Mayumi"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"first_name":"Junko Y.","full_name":"Toshima, Junko Y.","last_name":"Toshima"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"_id":"12080","abstract":[{"lang":"eng","text":"Endocytosis is a multistep process involving the sequential recruitment and action of numerous proteins. This process can be divided into two phases: an early phase, in which sites of endocytosis are formed, and a late phase in which clathrin-coated vesicles are formed and internalized into the cytosol, but how these phases link to each other remains unclear. In this study, we demonstrate that anchoring the yeast Eps15-like protein Pan1p to the peroxisome triggers most of the events occurring during the late phase at the peroxisome. At this ectopic location, Pan1p recruits most proteins that function in the late phases—including actin nucleation promoting factors—and then initiates actin polymerization. Pan1p also recruited Prk1 kinase and actin depolymerizing factors, thereby triggering disassembly immediately after actin assembly and inducing dissociation of endocytic proteins from the peroxisome. These observations suggest that Pan1p is a key regulator for initiating, processing, and completing the late phase of endocytosis."}],"issue":"10","doi":"10.1083/jcb.202112138","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"file":[{"date_created":"2023-01-20T09:32:53Z","file_id":"12321","embargo":"2023-02-20","file_size":7816875,"creator":"dernst","relation":"main_file","file_name":"2022_JCB_Enshoji.pdf","date_updated":"2023-02-21T23:30:39Z","checksum":"f2e581e66b5cdab9df81b56e850b3eaa","content_type":"application/pdf","access_level":"open_access"}],"has_accepted_license":"1","volume":221,"article_processing_charge":"No","citation":{"apa":"Enshoji, M., Miyano, Y., Yoshida, N., Nagano, M., Watanabe, M., Kunihiro, M., … Toshima, J. (2022). Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202112138\">https://doi.org/10.1083/jcb.202112138</a>","ieee":"M. Enshoji <i>et al.</i>, “Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway,” <i>Journal of Cell Biology</i>, vol. 221, no. 10. Rockefeller University Press, 2022.","short":"M. Enshoji, Y. Miyano, N. Yoshida, M. Nagano, M. Watanabe, M. Kunihiro, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Biology 221 (2022).","ama":"Enshoji M, Miyano Y, Yoshida N, et al. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. <i>Journal of Cell Biology</i>. 2022;221(10). doi:<a href=\"https://doi.org/10.1083/jcb.202112138\">10.1083/jcb.202112138</a>","ista":"Enshoji M, Miyano Y, Yoshida N, Nagano M, Watanabe M, Kunihiro M, Siekhaus DE, Toshima JY, Toshima J. 2022. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. Journal of Cell Biology. 221(10), e202112138.","mla":"Enshoji, Mariko, et al. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” <i>Journal of Cell Biology</i>, vol. 221, no. 10, e202112138, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202112138\">10.1083/jcb.202112138</a>.","chicago":"Enshoji, Mariko, Yoshiko Miyano, Nao Yoshida, Makoto Nagano, Minami Watanabe, Mayumi Kunihiro, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202112138\">https://doi.org/10.1083/jcb.202112138</a>."},"day":"19","ddc":["570"],"file_date_updated":"2023-02-21T23:30:39Z","pmid":1,"month":"08","oa_version":"Published Version","publication":"Journal of Cell Biology","date_updated":"2023-08-03T13:49:07Z","article_number":"e202112138","article_type":"original","oa":1,"year":"2022","publisher":"Rockefeller University Press","intvolume":"       221","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"DaSi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-08-19T00:00:00Z","external_id":{"pmid":["35984332"],"isi":["000932770500001"]},"date_created":"2022-09-11T22:01:54Z","scopus_import":"1"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_created":"2022-09-11T22:01:55Z","scopus_import":"1","external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"date_published":"2022-08-29T00:00:00Z","publisher":"Proceedings of the National Academy of Sciences","intvolume":"       119","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"oa":1,"year":"2022","date_updated":"2025-06-30T13:21:05Z","publication":"Proceedings of the National Academy of Sciences","article_number":"e2123152119","article_type":"original","related_material":{"record":[{"id":"15020","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2022-09-12T08:08:12Z","month":"08","ddc":["570"],"pmid":1,"citation":{"mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>.","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>.","apa":"Hledik, M., Barton, N. H., &#38; Tkačik, G. (2022). Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences</i>. 2022;119(36). doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022)."},"day":"29","oa_version":"Published Version","file":[{"date_created":"2022-09-12T08:08:12Z","file_id":"12091","date_updated":"2022-09-12T08:08:12Z","success":1,"checksum":"6dec51f6567da9039982a571508a8e4d","content_type":"application/pdf","access_level":"open_access","file_size":2165752,"relation":"main_file","creator":"dernst","file_name":"2022_PNAS_Hledik.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":119,"article_processing_charge":"No","has_accepted_license":"1","_id":"12081","title":"Accumulation and maintenance of information in evolution","author":[{"first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","full_name":"Hledik, Michal"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"1"}],"doi":"10.1073/pnas.2123152119","abstract":[{"text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.","lang":"eng"}],"issue":"36","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"ec_funded":1,"acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","publication_status":"published","status":"public"},{"abstract":[{"text":"Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest.","lang":"eng"}],"issue":"9","doi":"10.1016/j.jbc.2022.102343","title":"Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans","author":[{"id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat","full_name":"Artan, Murat","last_name":"Artan"},{"full_name":"Hartl, Markus","last_name":"Hartl","first_name":"Markus"},{"first_name":"Weiqiang","full_name":"Chen, Weiqiang","last_name":"Chen"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"De Bono, Mario","last_name":"De Bono","orcid":"0000-0001-8347-0443"}],"_id":"12082","publication_status":"published","status":"public","acknowledgement":"We thank de Bono laboratory members for helpful comments on the article and the Mass Spec Facilities at IST Austria and Max Perutz Labs for invaluable discussions and comments on how to optimize mass spec analyses of worm samples. We are grateful to Ekaterina Lashmanova for designing the degron knock-in constructs and preparing the injection mixes for CRISPR/Cas9-mediated genome editing. All LC–MS/MS analyses were performed on instruments of the Vienna BioCenter Core Facilities instrument pool.\r\nThis work was supported by a Wellcome Investigator Award (grant no.: 209504/Z/17/Z ) to M.d.B. and an ISTplus Fellowship to M.A. (Marie Sklodowska-Curie agreement no.: 754411).","ec_funded":1,"publication_identifier":{"issn":["0021-9258"],"eissn":["1083-351X"]},"project":[{"grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"oa_version":"Published Version","citation":{"mla":"Artan, Murat, et al. “Depletion of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.” <i>Journal of Biological Chemistry</i>, vol. 298, no. 9, 102343, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">10.1016/j.jbc.2022.102343</a>.","chicago":"Artan, Murat, Markus Hartl, Weiqiang Chen, and Mario de Bono. “Depletion of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.” <i>Journal of Biological Chemistry</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">https://doi.org/10.1016/j.jbc.2022.102343</a>.","ista":"Artan M, Hartl M, Chen W, de Bono M. 2022. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. Journal of Biological Chemistry. 298(9), 102343.","short":"M. Artan, M. Hartl, W. Chen, M. de Bono, Journal of Biological Chemistry 298 (2022).","ama":"Artan M, Hartl M, Chen W, de Bono M. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. <i>Journal of Biological Chemistry</i>. 2022;298(9). doi:<a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">10.1016/j.jbc.2022.102343</a>","ieee":"M. Artan, M. Hartl, W. Chen, and M. de Bono, “Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans,” <i>Journal of Biological Chemistry</i>, vol. 298, no. 9. Elsevier, 2022.","apa":"Artan, M., Hartl, M., Chen, W., &#38; de Bono, M. (2022). Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">https://doi.org/10.1016/j.jbc.2022.102343</a>"},"day":"01","pmid":1,"month":"09","file_date_updated":"2022-09-12T08:14:50Z","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","volume":298,"file":[{"creator":"dernst","relation":"main_file","file_size":2101656,"file_name":"2022_JBC_Artan.pdf","checksum":"e726c7b9315230e6710e0b1f1d1677e9","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-09-12T08:14:50Z","success":1,"date_created":"2022-09-12T08:14:50Z","file_id":"12092"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","oa":1,"article_number":"102343","article_type":"original","publication":"Journal of Biological Chemistry","date_updated":"2023-08-03T13:56:46Z","date_published":"2022-09-01T00:00:00Z","external_id":{"pmid":["35933017"],"isi":["000884241800011"]},"date_created":"2022-09-11T22:01:55Z","acknowledged_ssus":[{"_id":"Bio"}],"scopus_import":"1","department":[{"_id":"MaDe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Elsevier","intvolume":"       298"},{"date_published":"2022-08-25T00:00:00Z","external_id":{"arxiv":["2112.04817"],"isi":["000844402500001"]},"scopus_import":"1","date_created":"2022-09-11T22:01:56Z","department":[{"_id":"RoSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":"        63","publisher":"AIP Publishing","year":"2022","oa":1,"article_type":"original","article_number":"081902","publication":"Journal of Mathematical Physics","date_updated":"2023-08-03T13:57:19Z","oa_version":"Published Version","day":"25","citation":{"mla":"Rademacher, Simone Anna Elvira. “Dependent Random Variables in Quantum Dynamics.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 8, 081902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0086712\">10.1063/5.0086712</a>.","chicago":"Rademacher, Simone Anna Elvira. “Dependent Random Variables in Quantum Dynamics.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0086712\">https://doi.org/10.1063/5.0086712</a>.","apa":"Rademacher, S. A. E. (2022). Dependent random variables in quantum dynamics. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0086712\">https://doi.org/10.1063/5.0086712</a>","ieee":"S. A. E. Rademacher, “Dependent random variables in quantum dynamics,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 8. AIP Publishing, 2022.","ista":"Rademacher SAE. 2022. Dependent random variables in quantum dynamics. Journal of Mathematical Physics. 63(8), 081902.","ama":"Rademacher SAE. Dependent random variables in quantum dynamics. <i>Journal of Mathematical Physics</i>. 2022;63(8). doi:<a href=\"https://doi.org/10.1063/5.0086712\">10.1063/5.0086712</a>","short":"S.A.E. Rademacher, Journal of Mathematical Physics 63 (2022)."},"ddc":["510"],"file_date_updated":"2022-09-12T07:35:34Z","month":"08","has_accepted_license":"1","article_processing_charge":"No","volume":63,"file":[{"success":1,"date_updated":"2022-09-12T07:35:34Z","access_level":"open_access","checksum":"e6fb0cf3f0327739c5e69a2cfc4020eb","content_type":"application/pdf","file_name":"2022_JourMathPhysics_Rademacher.pdf","relation":"main_file","creator":"dernst","file_size":4552261,"file_id":"12089","date_created":"2022-09-12T07:35:34Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"issue":"8","abstract":[{"lang":"eng","text":"We consider the many-body time evolution of weakly interacting bosons in the mean field regime for initial coherent states. We show that bounded k-particle operators, corresponding to dependent random variables, satisfy both a law of large numbers and a central limit theorem."}],"doi":"10.1063/5.0086712","author":[{"orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira"}],"title":"Dependent random variables in quantum dynamics","_id":"12083","publication_status":"published","acknowledgement":"S.R. would like to thank Robert Seiringer and Benedikt Stufler for helpful discussions. Funding from the European Union’s Horizon 2020 Research and Innovation Program under the ERC grant (Grant Agreement No. 694227) and under the Marie Skłodowska-Curie grant (Agreement No. 754411) is acknowledged.","status":"public","ec_funded":1,"publication_identifier":{"issn":["0022-2488"]},"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}]},{"volume":18,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","file_size":2867337,"creator":"dernst","file_name":"2022_PLoSCompBio_Christodoulou.pdf","date_updated":"2022-09-12T07:47:55Z","success":1,"checksum":"8a81ab29f837991ee0ea770817c4a50e","content_type":"application/pdf","access_level":"open_access","date_created":"2022-09-12T07:47:55Z","file_id":"12090"}],"oa_version":"Published Version","month":"08","file_date_updated":"2022-09-12T07:47:55Z","ddc":["570"],"citation":{"apa":"Christodoulou, G., Vogels, T. P., &#38; Agnes, E. J. (2022). Regimes and mechanisms of transient amplification in abstract and biological neural networks. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">https://doi.org/10.1371/journal.pcbi.1010365</a>","ieee":"G. Christodoulou, T. P. Vogels, and E. J. Agnes, “Regimes and mechanisms of transient amplification in abstract and biological neural networks,” <i>PLoS Computational Biology</i>, vol. 18, no. 8. Public Library of Science, 2022.","short":"G. Christodoulou, T.P. Vogels, E.J. Agnes, PLoS Computational Biology 18 (2022).","ista":"Christodoulou G, Vogels TP, Agnes EJ. 2022. Regimes and mechanisms of transient amplification in abstract and biological neural networks. PLoS Computational Biology. 18(8), e1010365.","ama":"Christodoulou G, Vogels TP, Agnes EJ. Regimes and mechanisms of transient amplification in abstract and biological neural networks. <i>PLoS Computational Biology</i>. 2022;18(8). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">10.1371/journal.pcbi.1010365</a>","mla":"Christodoulou, Georgia, et al. “Regimes and Mechanisms of Transient Amplification in Abstract and Biological Neural Networks.” <i>PLoS Computational Biology</i>, vol. 18, no. 8, e1010365, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">10.1371/journal.pcbi.1010365</a>.","chicago":"Christodoulou, Georgia, Tim P Vogels, and Everton J. Agnes. “Regimes and Mechanisms of Transient Amplification in Abstract and Biological Neural Networks.” <i>PLoS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">https://doi.org/10.1371/journal.pcbi.1010365</a>."},"day":"15","acknowledgement":"We thank Friedemann Zenke for his comments, especially on the effect of the self loops on the spectrum. We also thank Ken Miller and Bill Podlaski for helpful comments. This research was funded by a Wellcome Trust and Royal Society Henry Dale Research Fellowship (WT100000; TPV), a Wellcome Senior Research Fellowship (214316/Z/18/Z; GC, EJA, and TPV), and a Research Project Grant by the Leverhulme Trust (RPG-2016-446; EJA and TPV). ","publication_status":"published","status":"public","project":[{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z"}],"publication_identifier":{"eissn":["1553-7358"]},"doi":"10.1371/journal.pcbi.1010365","abstract":[{"lang":"eng","text":"Neuronal networks encode information through patterns of activity that define the networks’ function. The neurons’ activity relies on specific connectivity structures, yet the link between structure and function is not fully understood. Here, we tackle this structure-function problem with a new conceptual approach. Instead of manipulating the connectivity directly, we focus on upper triangular matrices, which represent the network dynamics in a given orthonormal basis obtained by the Schur decomposition. This abstraction allows us to independently manipulate the eigenspectrum and feedforward structures of a connectivity matrix. Using this method, we describe a diverse repertoire of non-normal transient amplification, and to complement the analysis of the dynamical regimes, we quantify the geometry of output trajectories through the effective rank of both the eigenvector and the dynamics matrices. Counter-intuitively, we find that shrinking the eigenspectrum’s imaginary distribution leads to highly amplifying regimes in linear and long-lasting dynamics in nonlinear networks. We also find a trade-off between amplification and dimensionality of neuronal dynamics, i.e., trajectories in neuronal state-space. Networks that can amplify a large number of orthogonal initial conditions produce neuronal trajectories that lie in the same subspace of the neuronal state-space. Finally, we examine networks of excitatory and inhibitory neurons. We find that the strength of global inhibition is directly linked with the amplitude of amplification, such that weakening inhibitory weights also decreases amplification, and that the eigenspectrum’s imaginary distribution grows with an increase in the ratio between excitatory-to-inhibitory and excitatory-to-excitatory connectivity strengths. Consequently, the strength of global inhibition reveals itself as a strong signature for amplification and a potential control mechanism to switch dynamical regimes. Our results shed a light on how biological networks, i.e., networks constrained by Dale’s law, may be optimised for specific dynamical regimes."}],"issue":"8","_id":"12084","title":"Regimes and mechanisms of transient amplification in abstract and biological neural networks","author":[{"first_name":"Georgia","last_name":"Christodoulou","full_name":"Christodoulou, Georgia"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","full_name":"Vogels, Tim P","last_name":"Vogels","orcid":"0000-0003-3295-6181"},{"last_name":"Agnes","full_name":"Agnes, Everton J.","first_name":"Everton J."}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"Public Library of Science","intvolume":"        18","date_created":"2022-09-11T22:01:56Z","scopus_import":"1","date_published":"2022-08-15T00:00:00Z","external_id":{"isi":["000937227700001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TiVo"}],"article_number":"e1010365","article_type":"original","date_updated":"2023-08-03T14:06:29Z","publication":"PLoS Computational Biology","year":"2022","oa":1},{"date_updated":"2023-08-03T14:08:47Z","publication":"Nature Materials","page":"1019-1023","article_type":"original","oa":1,"year":"2022","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.07.27.219618"}],"intvolume":"        21","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiSi"}],"date_created":"2022-09-11T22:01:57Z","scopus_import":"1","external_id":{"isi":["000844592000002"],"pmid":["36008604"]},"date_published":"2022-09-01T00:00:00Z","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"status":"public","publication_status":"published","acknowledgement":"We thank M. van Hecke and C. Alkemade for critical reading of the manuscript. We thank P. R. ten Wolde, K. Storm, W. Ellenbroek, C. Broedersz, D. Brueckner and M. Berger for fruitful discussions. We thank W. Brieher and V. Tang from the University of Illinois for the kind gift of purified α-actinin-4 (WT and the K255E point mutant) and their plasmids; M. Kuit-Vinkenoog and J. den Haan for actin and further purification of α-actinin-4; A. Goutou and I. Isturiz-Petitjean for co-sedimentation measurements and V. Sunderlíková for the design, mutagenesis, cloning and purifying of the α-actinin-4 constructs used in the single-molecule experiments. We gratefully acknowledge financial support from the following sources: research program of the Netherlands Organization for Scientific Research (NWO) (S.J.T., A.R. and M.J.A.); ERC Starting Grant (335672-MINICELL) (G.H.K. and Y.M.). ‘BaSyC—Building a Synthetic Cell’ Gravitation grant (024.003.019) of the Netherlands Ministry of Education, Culture and Science (OCW) and the Netherlands Organisation for Scientific Research (G.H.K. and L.B.); and support from the National Institutes of Health (1R01GM126256) (T.K. and W.J.).","_id":"12085","title":"Weak catch bonds make strong networks","author":[{"first_name":"Yuval","full_name":"Mulla, Yuval","last_name":"Mulla"},{"full_name":"Avellaneda Sarrió, Mario","last_name":"Avellaneda Sarrió","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","first_name":"Mario","orcid":"0000-0001-6406-524X"},{"first_name":"Antoine","last_name":"Roland","full_name":"Roland, Antoine"},{"first_name":"Lucia","full_name":"Baldauf, Lucia","last_name":"Baldauf"},{"last_name":"Jung","full_name":"Jung, Wonyeong","first_name":"Wonyeong"},{"first_name":"Taeyoon","last_name":"Kim","full_name":"Kim, Taeyoon"},{"last_name":"Tans","full_name":"Tans, Sander J.","first_name":"Sander J."},{"full_name":"Koenderink, Gijsje H.","last_name":"Koenderink","first_name":"Gijsje H."}],"doi":"10.1038/s41563-022-01288-0","abstract":[{"lang":"eng","text":"Molecular catch bonds are ubiquitous in biology and essential for processes like leucocyte extravasion1 and cellular mechanosensing2. Unlike normal (slip) bonds, catch bonds strengthen under tension. The current paradigm is that this feature provides ‘strength on demand3’, thus enabling cells to increase rigidity under stress1,4,5,6. However, catch bonds are often weaker than slip bonds because they have cryptic binding sites that are usually buried7,8. Here we show that catch bonds render reconstituted cytoskeletal actin networks stronger than slip bonds, even though the individual bonds are weaker. Simulations show that slip bonds remain trapped in stress-free areas, whereas weak binding allows catch bonds to mitigate crack initiation by moving to high-tension areas. This ‘dissociation on demand’ explains how cells combine mechanical strength with the adaptability required for shape change, and is relevant to diseases where catch bonding is compromised7,9, including focal segmental glomerulosclerosis10 caused by the α-actinin-4 mutant studied here. We surmise that catch bonds are the key to create life-like materials."}],"issue":"9","article_processing_charge":"No","volume":21,"pmid":1,"month":"09","citation":{"apa":"Mulla, Y., Avellaneda Sarrió, M., Roland, A., Baldauf, L., Jung, W., Kim, T., … Koenderink, G. H. (2022). Weak catch bonds make strong networks. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41563-022-01288-0\">https://doi.org/10.1038/s41563-022-01288-0</a>","ieee":"Y. Mulla <i>et al.</i>, “Weak catch bonds make strong networks,” <i>Nature Materials</i>, vol. 21, no. 9. Springer Nature, pp. 1019–1023, 2022.","ista":"Mulla Y, Avellaneda Sarrió M, Roland A, Baldauf L, Jung W, Kim T, Tans SJ, Koenderink GH. 2022. Weak catch bonds make strong networks. Nature Materials. 21(9), 1019–1023.","short":"Y. Mulla, M. Avellaneda Sarrió, A. Roland, L. Baldauf, W. Jung, T. Kim, S.J. Tans, G.H. Koenderink, Nature Materials 21 (2022) 1019–1023.","ama":"Mulla Y, Avellaneda Sarrió M, Roland A, et al. Weak catch bonds make strong networks. <i>Nature Materials</i>. 2022;21(9):1019-1023. doi:<a href=\"https://doi.org/10.1038/s41563-022-01288-0\">10.1038/s41563-022-01288-0</a>","chicago":"Mulla, Yuval, Mario Avellaneda Sarrió, Antoine Roland, Lucia Baldauf, Wonyeong Jung, Taeyoon Kim, Sander J. Tans, and Gijsje H. Koenderink. “Weak Catch Bonds Make Strong Networks.” <i>Nature Materials</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41563-022-01288-0\">https://doi.org/10.1038/s41563-022-01288-0</a>.","mla":"Mulla, Yuval, et al. “Weak Catch Bonds Make Strong Networks.” <i>Nature Materials</i>, vol. 21, no. 9, Springer Nature, 2022, pp. 1019–23, doi:<a href=\"https://doi.org/10.1038/s41563-022-01288-0\">10.1038/s41563-022-01288-0</a>."},"day":"01","oa_version":"Preprint"},{"acknowledgement":"Krishnendu Chatterjee: The research was partially supported by the ERC CoG 863818\r\n(ForM-SMArt).\r\nIsmaël Jecker: The research was partially supported by the ERC grant 950398 (INFSYS).\r\nJakub Svoboda: The research was partially supported by the ERC CoG 863818 (ForM-SMArt)","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"isbn":["9783959772617"],"issn":["1868-8969"]},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"abstract":[{"text":"Spatial games form a widely-studied class of games from biology and physics modeling the evolution of social behavior. Formally, such a game is defined by a square (d by d) payoff matrix M and an undirected graph G. Each vertex of G represents an individual, that initially follows some strategy i ∈ {1,2,…,d}. In each round of the game, every individual plays the matrix game with each of its neighbors: An individual following strategy i meeting a neighbor following strategy j receives a payoff equal to the entry (i,j) of M. Then, each individual updates its strategy to its neighbors' strategy with the highest sum of payoffs, and the next round starts. The basic computational problems consist of reachability between configurations and the average frequency of a strategy. For general spatial games and graphs, these problems are in PSPACE. In this paper, we examine restricted setting: the game is a prisoner’s dilemma; and G is a subgraph of grid. We prove that basic computational problems for spatial games with prisoner’s dilemma on a subgraph of a grid are PSPACE-hard.","lang":"eng"}],"doi":"10.4230/LIPIcs.FSTTCS.2022.11","title":"Complexity of spatial games","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389"},{"full_name":"Jecker, Ismael R","last_name":"Jecker","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","first_name":"Ismael R"},{"orcid":"0000-0002-1419-3267","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","full_name":"Svoboda, Jakub"}],"_id":"12101","has_accepted_license":"1","volume":250,"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2023-01-20T10:19:19Z","file_id":"12323","checksum":"a21e3ba2421e2c4a06aa2cb6d530ede1","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-20T10:19:19Z","success":1,"relation":"main_file","creator":"dernst","file_size":657396,"file_name":"2022_LIPICs_Chatterjee.pdf"}],"oa_version":"Published Version","conference":{"name":"FSTTC: Foundations of Software Technology and Theoretical Computer Science","end_date":"2022-12-20","start_date":"2022-12-18","location":"Madras, India"},"citation":{"mla":"Chatterjee, Krishnendu, et al. “Complexity of Spatial Games.” <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, vol. 250, 11:1-11:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11\">10.4230/LIPIcs.FSTTCS.2022.11</a>.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Ismael R Jecker, and Jakub Svoboda. “Complexity of Spatial Games.” In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Vol. 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11</a>.","apa":"Chatterjee, K., Ibsen-Jensen, R., Jecker, I. R., &#38; Svoboda, J. (2022). Complexity of spatial games. In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i> (Vol. 250). Madras, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, I. R. Jecker, and J. Svoboda, “Complexity of spatial games,” in <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Madras, India, 2022, vol. 250.","short":"K. Chatterjee, R. Ibsen-Jensen, I.R. Jecker, J. Svoboda, in:, 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ama":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. Complexity of spatial games. In: <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>. Vol 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11\">10.4230/LIPIcs.FSTTCS.2022.11</a>","ista":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. 2022. Complexity of spatial games. 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTC: Foundations of Software Technology and Theoretical Computer Science vol. 250, 11:1-11:14."},"day":"14","ddc":["000"],"file_date_updated":"2023-01-20T10:19:19Z","month":"12","article_number":"11:1-11:14","publication":"42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","date_updated":"2025-07-14T09:09:55Z","year":"2022","oa":1,"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       250","date_published":"2022-12-14T00:00:00Z","date_created":"2023-01-01T23:00:50Z","scopus_import":"1","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"The research was partially supported by the Hong Kong Research Grants Council ECS\r\nProject No. 26208122, ERC CoG 863818 (FoRM-SMArt), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, HKUST– Kaisa Joint Research Institute Project Grant HKJRI3A-055 and HKUST Startup Grant R9272. Ali Ahmadi and Roodabeh Safavi were interns at HKUST.","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772617"]},"doi":"10.4230/LIPIcs.FSTTCS.2022.29","abstract":[{"text":"Given a Markov chain M = (V, v_0, δ), with state space V and a starting state v_0, and a probability threshold ε, an ε-core is a subset C of states that is left with probability at most ε. More formally, C ⊆ V is an ε-core, iff ℙ[reach (V\\C)] ≤ ε. Cores have been applied in a wide variety of verification problems over Markov chains, Markov decision processes, and probabilistic programs, as a means of discarding uninteresting and low-probability parts of a probabilistic system and instead being able to focus on the states that are likely to be encountered in a real-world run. In this work, we focus on the problem of computing a minimal ε-core in a Markov chain. Our contributions include both negative and positive results: (i) We show that the decision problem on the existence of an ε-core of a given size is NP-complete. This solves an open problem posed in [Jan Kretínský and Tobias Meggendorfer, 2020]. We additionally show that the problem remains NP-complete even when limited to acyclic Markov chains with bounded maximal vertex degree; (ii) We provide a polynomial time algorithm for computing a minimal ε-core on Markov chains over control-flow graphs of structured programs. A straightforward combination of our algorithm with standard branch prediction techniques allows one to apply the idea of cores to find a subset of program lines that are left with low probability and then focus any desired static analysis on this core subset.","lang":"eng"}],"_id":"12102","title":"Algorithms and hardness results for computing cores of Markov chains","author":[{"first_name":"Ali","full_name":"Ahmadi, Ali","last_name":"Ahmadi"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165"},{"first_name":"Roodabeh","id":"72ed2640-8972-11ed-ae7b-f9c81ec75154","last_name":"Safavi Hemami","full_name":"Safavi Hemami, Roodabeh"},{"full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","orcid":"0000-0002-4681-1699"}],"volume":250,"article_processing_charge":"No","has_accepted_license":"1","file":[{"relation":"main_file","creator":"dernst","file_size":872534,"file_name":"2022_LIPICs_Ahmadi.pdf","date_updated":"2023-01-20T10:39:44Z","success":1,"checksum":"6660c802489013f034c9e8bd57f4d46e","content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-20T10:39:44Z","file_id":"12324"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","conference":{"name":"FSTTC: Foundations of Software Technology and Theoretical Computer Science","end_date":"2022-12-20","start_date":"2022-12-18","location":"Madras, India"},"file_date_updated":"2023-01-20T10:39:44Z","month":"12","ddc":["000"],"citation":{"mla":"Ahmadi, Ali, et al. “Algorithms and Hardness Results for Computing Cores of Markov Chains.” <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, vol. 250, 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">10.4230/LIPIcs.FSTTCS.2022.29</a>.","chicago":"Ahmadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Tobias Meggendorfer, Roodabeh Safavi Hemami, and Dorde Zikelic. “Algorithms and Hardness Results for Computing Cores of Markov Chains.” In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Vol. 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29</a>.","ista":"Ahmadi A, Chatterjee K, Goharshady AK, Meggendorfer T, Safavi Hemami R, Zikelic D. 2022. Algorithms and hardness results for computing cores of Markov chains. 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTC: Foundations of Software Technology and Theoretical Computer Science vol. 250, 29.","ama":"Ahmadi A, Chatterjee K, Goharshady AK, Meggendorfer T, Safavi Hemami R, Zikelic D. Algorithms and hardness results for computing cores of Markov chains. In: <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>. Vol 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">10.4230/LIPIcs.FSTTCS.2022.29</a>","short":"A. Ahmadi, K. Chatterjee, A.K. Goharshady, T. Meggendorfer, R. Safavi Hemami, D. Zikelic, in:, 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","apa":"Ahmadi, A., Chatterjee, K., Goharshady, A. K., Meggendorfer, T., Safavi Hemami, R., &#38; Zikelic, D. (2022). Algorithms and hardness results for computing cores of Markov chains. In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i> (Vol. 250). Madras, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29</a>","ieee":"A. Ahmadi, K. Chatterjee, A. K. Goharshady, T. Meggendorfer, R. Safavi Hemami, and D. Zikelic, “Algorithms and hardness results for computing cores of Markov chains,” in <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Madras, India, 2022, vol. 250."},"day":"14","article_number":"29","date_updated":"2025-07-14T09:09:55Z","publication":"42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","year":"2022","oa":1,"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       250","date_created":"2023-01-01T23:00:50Z","scopus_import":"1","date_published":"2022-12-14T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"},{"_id":"GradSch"}]},{"publisher":"Wiley","intvolume":"        49","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"CaMu"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-12-28T00:00:00Z","external_id":{"isi":["000924587900001"]},"date_created":"2023-01-08T23:00:53Z","scopus_import":"1","publication":"Geophysical Research Letters","date_updated":"2023-08-03T14:10:27Z","article_number":"e2022GL100624","article_type":"letter_note","oa":1,"year":"2022","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_name":"2022_GeophysicalResearchLetters_Roca.pdf","file_size":875379,"creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"2c6325cea8938adeea7e3a6f5c2ab64e","content_type":"application/pdf","success":1,"date_updated":"2023-01-20T10:52:31Z","file_id":"12326","date_created":"2023-01-20T10:52:31Z"}],"has_accepted_license":"1","article_processing_charge":"No","volume":49,"citation":{"ieee":"R. Roca, V. De Meyer, and C. J. Muller, “Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans,” <i>Geophysical Research Letters</i>, vol. 49, no. 24. Wiley, 2022.","apa":"Roca, R., De Meyer, V., &#38; Muller, C. J. (2022). Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans. <i>Geophysical Research Letters</i>. Wiley. <a href=\"https://doi.org/10.1029/2022GL100624\">https://doi.org/10.1029/2022GL100624</a>","ista":"Roca R, De Meyer V, Muller CJ. 2022. Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans. Geophysical Research Letters. 49(24), e2022GL100624.","short":"R. Roca, V. De Meyer, C.J. Muller, Geophysical Research Letters 49 (2022).","ama":"Roca R, De Meyer V, Muller CJ. Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans. <i>Geophysical Research Letters</i>. 2022;49(24). doi:<a href=\"https://doi.org/10.1029/2022GL100624\">10.1029/2022GL100624</a>","chicago":"Roca, Rémy, Victorien De Meyer, and Caroline J Muller. “Precipitating Fraction, Not Intensity, Explains Extreme Coarse-Grained Precipitation Clausius-Clapeyron Scaling with Sea Surface Temperature over Tropical Oceans.” <i>Geophysical Research Letters</i>. Wiley, 2022. <a href=\"https://doi.org/10.1029/2022GL100624\">https://doi.org/10.1029/2022GL100624</a>.","mla":"Roca, Rémy, et al. “Precipitating Fraction, Not Intensity, Explains Extreme Coarse-Grained Precipitation Clausius-Clapeyron Scaling with Sea Surface Temperature over Tropical Oceans.” <i>Geophysical Research Letters</i>, vol. 49, no. 24, e2022GL100624, Wiley, 2022, doi:<a href=\"https://doi.org/10.1029/2022GL100624\">10.1029/2022GL100624</a>."},"day":"28","file_date_updated":"2023-01-20T10:52:31Z","month":"12","ddc":["550"],"oa_version":"Published Version","publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"status":"public","acknowledgement":"We thank S. Cloché for her support with the handling of these various data sets. This study benefited from the IPSL mesocenter ESPRI facility which is supported by CNRS, UPMC, Labex L-IPSL, CNES and Ecole Polytechnique. We thank Rômulo A. Jucá Oliveira and Thomas\r\nFiolleau for helpful discussions on satellite data and precipitation. The authors acknowledge the CNES and CNRS support under the Megha-Tropiques program. C.M. gratefully acknowledges\r\nfunding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Project CLUSTER, Grant agreement 805041). We further\r\nthank the reviewers for their insightful comments that improved the paper.","publication_status":"published","title":"Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans","author":[{"full_name":"Roca, Rémy","last_name":"Roca","first_name":"Rémy"},{"first_name":"Victorien","last_name":"De Meyer","full_name":"De Meyer, Victorien"},{"orcid":"0000-0001-5836-5350","last_name":"Muller","full_name":"Muller, Caroline J","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"_id":"12107","abstract":[{"lang":"eng","text":"The sensitivity of coarse-grained daily extreme precipitation to sea surface temperature is analyzed using satellite precipitation estimates over the 300–302.5 K range. A theoretical scaling is proposed, linking changes in coarse-grained precipitation to changes in fine-scale hourly precipitation area fraction and changes in conditional fine-scale precipitation rates. The analysis reveals that the extreme coarse-grained precipitation scaling with temperature (∼7%/K) is dominated by the fine-scale precipitating fraction scaling (∼6.5%/K) when using a 3 mm/h fine-scale threshold to delineate the precipitating fraction. These results are shown to be robust to the selection of the precipitation product and to the percentile used to characterize the extreme. This new coarse-grained scaling is further related to the well-known scaling for fine-scale precipitation extremes, and suggests a compensation between thermodynamic and dynamic contributions or that both contributions are small with respect to that of fractional coverage. These results suggest that processes responsible for the changes in fractional coverage are to be accounted for to assess the sensitivity of coarse-grained extreme daily precipitation to surface temperature."}],"issue":"24","doi":"10.1029/2022GL100624"},{"department":[{"_id":"AnSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-12-23T00:00:00Z","external_id":{"isi":["000906721500001"],"pmid":["36608212"]},"date_created":"2023-01-08T23:00:53Z","scopus_import":"1","publisher":"American Physical Society","intvolume":"       129","main_file_link":[{"url":"https://doi.org/10.1101/2022.05.10.490642 ","open_access":"1"}],"isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","oa":1,"year":"2022","publication":"Physical Review Letters","date_updated":"2023-08-03T14:10:59Z","article_number":"268101","article_type":"original","citation":{"mla":"Meadowcroft, Billie, et al. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” <i>Physical Review Letters</i>, vol. 129, no. 26, 268101, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">10.1103/PhysRevLett.129.268101</a>.","chicago":"Meadowcroft, Billie, Ivan Palaia, Anna Katharina Pfitzner, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">https://doi.org/10.1103/PhysRevLett.129.268101</a>.","apa":"Meadowcroft, B., Palaia, I., Pfitzner, A. K., Roux, A., Baum, B., &#38; Šarić, A. (2022). Mechanochemical rules for shape-shifting filaments that remodel membranes. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">https://doi.org/10.1103/PhysRevLett.129.268101</a>","ieee":"B. Meadowcroft, I. Palaia, A. K. Pfitzner, A. Roux, B. Baum, and A. Šarić, “Mechanochemical rules for shape-shifting filaments that remodel membranes,” <i>Physical Review Letters</i>, vol. 129, no. 26. American Physical Society, 2022.","ama":"Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. Mechanochemical rules for shape-shifting filaments that remodel membranes. <i>Physical Review Letters</i>. 2022;129(26). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">10.1103/PhysRevLett.129.268101</a>","short":"B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical Review Letters 129 (2022).","ista":"Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. 2022. Mechanochemical rules for shape-shifting filaments that remodel membranes. Physical Review Letters. 129(26), 268101."},"day":"23","month":"12","pmid":1,"oa_version":"Preprint","article_processing_charge":"No","volume":129,"title":"Mechanochemical rules for shape-shifting filaments that remodel membranes","author":[{"first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft","full_name":"Meadowcroft, Billie"},{"full_name":"Palaia, Ivan","last_name":"Palaia","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","first_name":"Ivan","orcid":" 0000-0002-8843-9485 "},{"last_name":"Pfitzner","full_name":"Pfitzner, Anna Katharina","first_name":"Anna Katharina"},{"last_name":"Roux","full_name":"Roux, Aurélien","first_name":"Aurélien"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela"}],"_id":"12108","abstract":[{"text":"The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how some biological polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein–membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism of sequential polymer assembly lowers the energetic barrier for membrane deformation.","lang":"eng"}],"issue":"26","doi":"10.1103/PhysRevLett.129.268101","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"},{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"},{"grant_number":"96752","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes"}],"publication_status":"published","status":"public","acknowledgement":"We thank T. C. T. Michaels and J. Palacci for useful discussions. We thank Claudia Flandoli for the illustrations in Fig. 1(b) and Fig. 2. We acknowledge funding by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant\r\nAgreement No. 101034413 (I. P.), the Royal Society Grant No. UF160266 (A. Š.), the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant No. 802960; B. M., I. P., and A. Š.), and the Volkswagen Foundation\r\nLife Grant (B. B. and A. Š). ","ec_funded":1},{"external_id":{"isi":["000908384800001"],"arxiv":["2209.01889"]},"date_published":"2022-12-29T00:00:00Z","scopus_import":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"date_created":"2023-01-08T23:00:53Z","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2209.01889","open_access":"1"}],"intvolume":"         6","publisher":"American Physical Society","year":"2022","oa":1,"article_type":"original","article_number":"125605","publication":"Physical Review Materials","date_updated":"2023-08-03T14:11:29Z","oa_version":"Preprint","day":"29","citation":{"chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>.","mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>.","ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” <i>Physical Review Materials</i>, vol. 6, no. 12. American Physical Society, 2022.","apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., &#38; Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>","ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. 2022;6(12). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>","short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605."},"month":"12","article_processing_charge":"No","volume":6,"arxiv":1,"issue":"12","abstract":[{"text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.","lang":"eng"}],"doi":"10.1103/PhysRevMaterials.6.125605","author":[{"full_name":"Pertl, Felix","last_name":"Pertl","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","first_name":"Felix"},{"first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","last_name":"Sobarzo Ponce","full_name":"Sobarzo Ponce, Juan Carlos A"},{"orcid":"0000-0001-7180-6050","full_name":"Shafeek, Lubuna B","last_name":"Shafeek","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","first_name":"Lubuna B"},{"last_name":"Cramer","full_name":"Cramer, Tobias","first_name":"Tobias"},{"orcid":"0000-0002-2299-3176","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"}],"title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","_id":"12109","status":"public","publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work.","ec_funded":1,"publication_identifier":{"eissn":["2475-9953"]},"project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"}]},{"department":[{"_id":"LaEr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-12-01T00:00:00Z","external_id":{"isi":["000900748900002"]},"date_created":"2023-01-08T23:00:53Z","scopus_import":"1","publisher":"AIP Publishing","intvolume":"        63","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"oa":1,"year":"2022","publication":"Journal of Mathematical Physics","date_updated":"2023-08-03T14:12:01Z","article_number":"122302","article_type":"original","citation":{"chicago":"Henheik, Sven Joscha, and Roderich Tumulka. “Interior-Boundary Conditions for the Dirac Equation at Point Sources in Three Dimensions.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0104675\">https://doi.org/10.1063/5.0104675</a>.","mla":"Henheik, Sven Joscha, and Roderich Tumulka. “Interior-Boundary Conditions for the Dirac Equation at Point Sources in Three Dimensions.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 12, 122302, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0104675\">10.1063/5.0104675</a>.","ama":"Henheik SJ, Tumulka R. Interior-boundary conditions for the Dirac equation at point sources in three dimensions. <i>Journal of Mathematical Physics</i>. 2022;63(12). doi:<a href=\"https://doi.org/10.1063/5.0104675\">10.1063/5.0104675</a>","ista":"Henheik SJ, Tumulka R. 2022. Interior-boundary conditions for the Dirac equation at point sources in three dimensions. Journal of Mathematical Physics. 63(12), 122302.","short":"S.J. Henheik, R. Tumulka, Journal of Mathematical Physics 63 (2022).","apa":"Henheik, S. J., &#38; Tumulka, R. (2022). Interior-boundary conditions for the Dirac equation at point sources in three dimensions. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0104675\">https://doi.org/10.1063/5.0104675</a>","ieee":"S. J. Henheik and R. Tumulka, “Interior-boundary conditions for the Dirac equation at point sources in three dimensions,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 12. AIP Publishing, 2022."},"day":"01","file_date_updated":"2023-01-20T11:58:59Z","month":"12","ddc":["510"],"oa_version":"Published Version","file":[{"date_created":"2023-01-20T11:58:59Z","file_id":"12327","creator":"dernst","relation":"main_file","file_size":5436804,"file_name":"2022_JourMathPhysics_Henheik.pdf","content_type":"application/pdf","checksum":"5150287295e0ce4f12462c990744d65d","access_level":"open_access","date_updated":"2023-01-20T11:58:59Z","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":63,"article_processing_charge":"No","title":"Interior-boundary conditions for the Dirac equation at point sources in three dimensions","author":[{"last_name":"Henheik","full_name":"Henheik, Sven Joscha","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","orcid":"0000-0003-1106-327X"},{"first_name":"Roderich","last_name":"Tumulka","full_name":"Tumulka, Roderich"}],"_id":"12110","abstract":[{"text":"A recently proposed approach for avoiding the ultraviolet divergence of Hamiltonians with particle creation is based on interior-boundary conditions (IBCs). The approach works well in the non-relativistic case, i.e., for the Laplacian operator. Here, we study how the approach can be applied to Dirac operators. While this has successfully been done already in one space dimension, and more generally for codimension-1 boundaries, the situation of point sources in three dimensions corresponds to a codimension-3 boundary. One would expect that, for such a boundary, Dirac operators do not allow for boundary conditions because they are known not to allow for point interactions in 3D, which also correspond to a boundary condition. Indeed, we confirm this expectation here by proving that there is no self-adjoint operator on a (truncated) Fock space that would correspond to a Dirac operator with an IBC at configurations with a particle at the origin. However, we also present a positive result showing that there are self-adjoint operators with an IBC (on the boundary consisting of configurations with a particle at the origin) that are away from those configurations, given by a Dirac operator plus a sufficiently strong Coulomb potential.","lang":"eng"}],"issue":"12","doi":"10.1063/5.0104675","publication_identifier":{"issn":["0022-2488"]},"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"publication_status":"published","acknowledgement":"J.H. gratefully acknowledges the partial financial support by the ERC Advanced Grant “RMTBeyond” under Grant No. 101020331.\r\n","status":"public","ec_funded":1},{"article_type":"original","article_number":"043177","date_updated":"2023-02-13T09:08:28Z","publication":"Physical Review Research","year":"2022","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":"         4","publisher":"American Physical Society","scopus_import":"1","date_created":"2023-01-08T23:00:53Z","date_published":"2022-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaSe"}],"publication_status":"published","status":"public","acknowledgement":"We thank G. Blatter, T. Ihn, K. Ensslin, M. Goldstein, C. Carisch, and J. del Pino for illuminating discussions and acknowledge financial support from the Swiss National Science Foundation (SNSF) through Project No. 190078, and from the Deutsche Forschungsgemeinschaft (DFG) - Project No. 449653034. Our numerical implementations are based on the ITensors JULIA library [64].","publication_identifier":{"issn":["2643-1564"]},"doi":"10.1103/PhysRevResearch.4.043177","issue":"4","abstract":[{"lang":"eng","text":"Quantum impurities exhibit fascinating many-body phenomena when the small interacting impurity changes the physics of a large noninteracting environment. The characterisation of such strongly correlated nonperturbative effects is particularly challenging due to the infinite size of the environment, and the inability of local correlators to capture the buildup of long-ranged entanglement in the system. Here, we harness an entanglement-based observable—the purity of the impurity—as a witness for the formation of strong correlations. We showcase the utility of our scheme by exactly solving the open Kondo box model in the small box limit, and thus describe all-electronic dot-cavity devices. Specifically, we conclusively characterize the metal-to-insulator phase transition in the system and identify how the (conducting) dot-lead Kondo singlet is quenched by an (insulating) intraimpurity singlet formation. Furthermore, we propose an experimentally feasible tomography protocol for the measurement of the purity, which motivates the observation of impurity physics through their entanglement build up."}],"_id":"12111","author":[{"first_name":"Lidia","last_name":"Stocker","full_name":"Stocker, Lidia"},{"full_name":"Sack, Stefan","last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan"},{"first_name":"Michael S.","full_name":"Ferguson, Michael S.","last_name":"Ferguson"},{"first_name":"Oded","full_name":"Zilberberg, Oded","last_name":"Zilberberg"}],"title":"Entanglement-based observables for quantum impurities","volume":4,"article_processing_charge":"No","has_accepted_license":"1","file":[{"file_id":"12328","date_created":"2023-01-20T12:03:31Z","file_name":"2022_PhysicalReviewResearch_Stocker.pdf","relation":"main_file","creator":"dernst","file_size":2941167,"access_level":"open_access","checksum":"556820cf6e4af77c8476e5b8f4114d1a","content_type":"application/pdf","success":1,"date_updated":"2023-01-20T12:03:31Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","month":"12","file_date_updated":"2023-01-20T12:03:31Z","ddc":["530"],"day":"01","citation":{"apa":"Stocker, L., Sack, S., Ferguson, M. S., &#38; Zilberberg, O. (2022). Entanglement-based observables for quantum impurities. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.043177\">https://doi.org/10.1103/PhysRevResearch.4.043177</a>","ieee":"L. Stocker, S. Sack, M. S. Ferguson, and O. Zilberberg, “Entanglement-based observables for quantum impurities,” <i>Physical Review Research</i>, vol. 4, no. 4. American Physical Society, 2022.","short":"L. Stocker, S. Sack, M.S. Ferguson, O. Zilberberg, Physical Review Research 4 (2022).","ama":"Stocker L, Sack S, Ferguson MS, Zilberberg O. Entanglement-based observables for quantum impurities. <i>Physical Review Research</i>. 2022;4(4). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.043177\">10.1103/PhysRevResearch.4.043177</a>","ista":"Stocker L, Sack S, Ferguson MS, Zilberberg O. 2022. Entanglement-based observables for quantum impurities. Physical Review Research. 4(4), 043177.","chicago":"Stocker, Lidia, Stefan Sack, Michael S. Ferguson, and Oded Zilberberg. “Entanglement-Based Observables for Quantum Impurities.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.043177\">https://doi.org/10.1103/PhysRevResearch.4.043177</a>.","mla":"Stocker, Lidia, et al. “Entanglement-Based Observables for Quantum Impurities.” <i>Physical Review Research</i>, vol. 4, no. 4, 043177, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.043177\">10.1103/PhysRevResearch.4.043177</a>."}},{"date_updated":"2023-10-03T11:01:06Z","publication":"Science","article_type":"letter_note","page":"1285-1286","oa":1,"year":"2022","intvolume":"       378","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adg0797"}],"publisher":"American Association for the Advancement of Science","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FyKo"}],"scopus_import":"1","date_created":"2023-01-12T11:56:30Z","external_id":{"isi":["000963463700023"]},"date_published":"2022-12-22T00:00:00Z","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","status":"public","_id":"12116","author":[{"full_name":"Chhugani, Karishma","last_name":"Chhugani","first_name":"Karishma"},{"last_name":"Frolova","full_name":"Frolova, Alina","first_name":"Alina"},{"first_name":"Yuriy","last_name":"Salyha","full_name":"Salyha, Yuriy"},{"full_name":"Fiscutean, Andrada","last_name":"Fiscutean","first_name":"Andrada"},{"first_name":"Oksana","last_name":"Zlenko","full_name":"Zlenko, Oksana"},{"first_name":"Sanita","last_name":"Reinsone","full_name":"Reinsone, Sanita"},{"first_name":"Walter W.","last_name":"Wolfsberger","full_name":"Wolfsberger, Walter W."},{"full_name":"Ivashchenko, Oleksandra V.","last_name":"Ivashchenko","first_name":"Oleksandra V."},{"last_name":"Maci","full_name":"Maci, Megi","first_name":"Megi"},{"first_name":"Dmytro","full_name":"Dziuba, Dmytro","last_name":"Dziuba"},{"first_name":"Andrii","full_name":"Parkhomenko, Andrii","last_name":"Parkhomenko"},{"first_name":"Eric","full_name":"Bortz, Eric","last_name":"Bortz"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"full_name":"Łabaj, Paweł P.","last_name":"Łabaj","first_name":"Paweł P."},{"full_name":"Romero, Veronika","last_name":"Romero","first_name":"Veronika"},{"first_name":"Jakub","last_name":"Hlávka","full_name":"Hlávka, Jakub"},{"full_name":"Oleksyk, Taras K.","last_name":"Oleksyk","first_name":"Taras K."},{"first_name":"Serghei","full_name":"Mangul, Serghei","last_name":"Mangul"}],"title":"Remote opportunities for scholars in Ukraine","doi":"10.1126/science.adg0797","issue":"6626","abstract":[{"text":"Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them.","lang":"eng"}],"article_processing_charge":"No","volume":378,"month":"12","day":"22","citation":{"apa":"Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, O., Reinsone, S., … Mangul, S. (2022). Remote opportunities for scholars in Ukraine. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg0797\">https://doi.org/10.1126/science.adg0797</a>","ieee":"K. Chhugani <i>et al.</i>, “Remote opportunities for scholars in Ukraine,” <i>Science</i>, vol. 378, no. 6626. American Association for the Advancement of Science, pp. 1285–1286, 2022.","ista":"Chhugani K, Frolova A, Salyha Y, Fiscutean A, Zlenko O, Reinsone S, Wolfsberger WW, Ivashchenko OV, Maci M, Dziuba D, Parkhomenko A, Bortz E, Kondrashov F, Łabaj PP, Romero V, Hlávka J, Oleksyk TK, Mangul S. 2022. Remote opportunities for scholars in Ukraine. Science. 378(6626), 1285–1286.","ama":"Chhugani K, Frolova A, Salyha Y, et al. Remote opportunities for scholars in Ukraine. <i>Science</i>. 2022;378(6626):1285-1286. doi:<a href=\"https://doi.org/10.1126/science.adg0797\">10.1126/science.adg0797</a>","short":"K. Chhugani, A. Frolova, Y. Salyha, A. Fiscutean, O. Zlenko, S. Reinsone, W.W. Wolfsberger, O.V. Ivashchenko, M. Maci, D. Dziuba, A. Parkhomenko, E. Bortz, F. Kondrashov, P.P. Łabaj, V. Romero, J. Hlávka, T.K. Oleksyk, S. Mangul, Science 378 (2022) 1285–1286.","chicago":"Chhugani, Karishma, Alina Frolova, Yuriy Salyha, Andrada Fiscutean, Oksana Zlenko, Sanita Reinsone, Walter W. Wolfsberger, et al. “Remote Opportunities for Scholars in Ukraine.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.adg0797\">https://doi.org/10.1126/science.adg0797</a>.","mla":"Chhugani, Karishma, et al. “Remote Opportunities for Scholars in Ukraine.” <i>Science</i>, vol. 378, no. 6626, American Association for the Advancement of Science, 2022, pp. 1285–86, doi:<a href=\"https://doi.org/10.1126/science.adg0797\">10.1126/science.adg0797</a>."},"oa_version":"Published Version"},{"file_date_updated":"2023-01-23T09:50:51Z","ddc":["570"],"month":"12","citation":{"chicago":"Hübschmann, Verena, Medina Korkut, and Sandra Siegert. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>.","mla":"Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation Assay.” <i>STAR Protocols</i>, vol. 3, no. 4, 101866, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>.","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022).","ama":"Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">10.1016/j.xpro.2022.101866</a>","ista":"Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. STAR Protocols. 3(4), 101866.","ieee":"V. Hübschmann, M. Korkut, and S. Siegert, “Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay,” <i>STAR Protocols</i>, vol. 3, no. 4. Elsevier, 2022.","apa":"Hübschmann, V., Korkut, M., &#38; Siegert, S. (2022). Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2022.101866\">https://doi.org/10.1016/j.xpro.2022.101866</a>"},"day":"16","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"date_created":"2023-01-23T09:50:51Z","file_id":"12340","file_size":6251945,"creator":"dernst","relation":"main_file","file_name":"2022_STARProtocols_Huebschmann.pdf","date_updated":"2023-01-23T09:50:51Z","success":1,"checksum":"3c71b8a60633d42c2f77c49025d5559b","content_type":"application/pdf","access_level":"open_access"}],"volume":3,"article_processing_charge":"No","has_accepted_license":"1","_id":"12117","title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","author":[{"id":"32B7C918-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","full_name":"Hübschmann, Verena","last_name":"Hübschmann"},{"orcid":"0000-0003-4309-2251","first_name":"Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","last_name":"Korkut","full_name":"Korkut, Medina"},{"orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra"}],"doi":"10.1016/j.xpro.2022.101866","abstract":[{"text":"To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.\r\nFor complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1","lang":"eng"}],"issue":"4","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020"},{"_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017","name":"How human microglia shape developing neurons during health and inflammation"}],"publication_identifier":{"issn":["2666-1667"]},"ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.). We thank Rouven Schulz and Alessandro Venturino for their insights into functional assays and data analysis, Verena Seiboth for insights into necessary institutional permission, and ISTA imaging & optics facility (IOF) especially Bernhard Hochreiter for their support.","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"date_created":"2023-01-12T11:56:38Z","acknowledged_ssus":[{"_id":"Bio"}],"scopus_import":"1","date_published":"2022-12-16T00:00:00Z","publisher":"Elsevier","intvolume":"         3","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"year":"2022","date_updated":"2023-11-02T12:21:32Z","publication":"STAR Protocols","article_number":"101866","article_type":"letter_note","related_material":{"record":[{"relation":"other","status":"public","id":"11478"}]}},{"oa":1,"keyword":["Multidisciplinary"],"year":"2022","date_updated":"2024-02-21T12:35:33Z","publication":"Nature","article_type":"original","page":"442-447","related_material":{"record":[{"id":"13286","relation":"dissertation_contains","status":"public"},{"relation":"research_data","status":"public","id":"12522"}],"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/imposter-particles-revealed-and-explained/","relation":"press_release"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GeKa"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"scopus_import":"1","date_created":"2023-01-12T11:56:45Z","date_published":"2022-12-15T00:00:00Z","external_id":{"arxiv":["2203.07829"],"isi":["000899725400001"]},"intvolume":"       612","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2203.07829"}],"publisher":"Springer Nature","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"_id":"12118","author":[{"full_name":"Valentini, Marco","last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco"},{"last_name":"Borovkov","full_name":"Borovkov, Maksim","first_name":"Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087"},{"first_name":"Elsa","full_name":"Prada, Elsa","last_name":"Prada"},{"full_name":"Martí-Sánchez, Sara","last_name":"Martí-Sánchez","first_name":"Sara"},{"first_name":"Marc","full_name":"Botifoll, Marc","last_name":"Botifoll"},{"full_name":"Hofmann, Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Aguado","full_name":"Aguado, Ramón","first_name":"Ramón"},{"first_name":"Pablo","full_name":"San-Jose, Pablo","last_name":"San-Jose"},{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"title":"Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks","doi":"10.1038/s41586-022-05382-w","issue":"7940","abstract":[{"lang":"eng","text":"Hybrid semiconductor–superconductor devices hold great promise for realizing topological quantum computing with Majorana zero modes1,2,3,4,5. However, multiple claims of Majorana detection, based on either tunnelling6,7,8,9,10 or Coulomb blockade (CB) spectroscopy11,12, remain disputed. Here we devise an experimental protocol that allows us to perform both types of measurement on the same hybrid island by adjusting its charging energy via tunable junctions to the normal leads. This method reduces ambiguities of Majorana detections by checking the consistency between CB spectroscopy and zero-bias peaks in non-blockaded transport. Specifically, we observe junction-dependent, even–odd modulated, single-electron CB peaks in InAs/Al hybrid nanowires without concomitant low-bias peaks in tunnelling spectroscopy. We provide a theoretical interpretation of the experimental observations in terms of low-energy, longitudinally confined island states rather than overlapping Majorana modes. Our results highlight the importance of combined measurements on the same device for the identification of topological Majorana zero modes."}],"project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"We thank P. Krogstrup for providing us with the NW materials. We thank A. Higginbotham, E. J. H. Lee, C. Marcus and S. Vaitiekėnas for helpful discussions and G. Steffensen for his input on the diffusive Little-Parks theory. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility; the NOMIS Foundation; the CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). A.H. acknowledges support from H2020-MSCA-IF-2018/844511. ICN2 also acknowledges funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa Program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD programme. Authors acknowledge the use of instrumentation as well as the technical advice provided by the National Facility ELECMI ICTS, node ‘Laboratorio de Microscopías Avanzadas’ at University of Zaragoza. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 823717-ESTEEM3. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. This research is part of the CSIC programme for the Spanish Recovery, Transformation and Resilience Plan funded by the Recovery and Resilience Facility of the European Union, established by the Regulation (EU) 2020/2094. We thank support from Grant PGC2018-097018-BI00, project FlagERA TOPOGRAPH (PCI2018-093026) and project NANOGEN (PID2020-116093RB-C43), funded by MCIN/AEI/10.13039/501100011033/ and by ‘ERDF A way of making Europe’, by the European Union. M. Botifoll acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund (project ref. 2020 FI 00103).","month":"12","day":"15","citation":{"ama":"Valentini M, Borovkov M, Prada E, et al. Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks. <i>Nature</i>. 2022;612(7940):442-447. doi:<a href=\"https://doi.org/10.1038/s41586-022-05382-w\">10.1038/s41586-022-05382-w</a>","short":"M. Valentini, M. Borovkov, E. Prada, S. Martí-Sánchez, M. Botifoll, A.C. Hofmann, J. Arbiol, R. Aguado, P. San-Jose, G. Katsaros, Nature 612 (2022) 442–447.","ista":"Valentini M, Borovkov M, Prada E, Martí-Sánchez S, Botifoll M, Hofmann AC, Arbiol J, Aguado R, San-Jose P, Katsaros G. 2022. Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks. Nature. 612(7940), 442–447.","ieee":"M. Valentini <i>et al.</i>, “Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks,” <i>Nature</i>, vol. 612, no. 7940. Springer Nature, pp. 442–447, 2022.","apa":"Valentini, M., Borovkov, M., Prada, E., Martí-Sánchez, S., Botifoll, M., Hofmann, A. C., … Katsaros, G. (2022). Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05382-w\">https://doi.org/10.1038/s41586-022-05382-w</a>","chicago":"Valentini, Marco, Maksim Borovkov, Elsa Prada, Sara Martí-Sánchez, Marc Botifoll, Andrea C Hofmann, Jordi Arbiol, Ramón Aguado, Pablo San-Jose, and Georgios Katsaros. “Majorana-like Coulomb Spectroscopy in the Absence of Zero-Bias Peaks.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05382-w\">https://doi.org/10.1038/s41586-022-05382-w</a>.","mla":"Valentini, Marco, et al. “Majorana-like Coulomb Spectroscopy in the Absence of Zero-Bias Peaks.” <i>Nature</i>, vol. 612, no. 7940, Springer Nature, 2022, pp. 442–47, doi:<a href=\"https://doi.org/10.1038/s41586-022-05382-w\">10.1038/s41586-022-05382-w</a>."},"oa_version":"Preprint","arxiv":1,"article_processing_charge":"No","volume":612},{"project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020"}],"publication_identifier":{"issn":["1074-7613"]},"ec_funded":1,"acknowledgement":"We thank Coung Kieu and Dominik van den Heuvel for excellent technical assistance. This work was supported by the German Research Foundation (PE2704/2-1, PE2704/3-1 to T.P., SFB 1123-project B06 to S.M., SFB1525 project A07 to D.S, TRR 332 project A7 to C.S., PO 2247/2-1 to A.P., SFB1116-project B11 to A.P. and B12 to M.K.), LMU Munich’s Institutional\r\nStrategy LMUexcellent within the framework of the German Excellence Initiative (No. 806 32 006 to T.P.), and by the German Centre for Cardiovascular Research (DZHK) to T.P. (Postdoc Start-up grant No. 100378833). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 833440 to S.M.). F.G. received funding from the European Union’s\r\nHorizon 2020 research and innovation program under the Marie Sk1odowska-Curie grant agreement no. 747687. A.H. was funded by RTI2018-095497-B-I00 from Ministerio de Ciencia e Innovacio´ n (MICINN), HR17_00527 from Fundacion La Caixa, and Transatlantic Network of Excellence (TNE-18CVD04) from the Leducq Foundation. The CNIC is supported by the MICINN and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (CEX2020-001041-S). A.P. was supported by the Forschungskommission of the Medical Faculty of the Heinrich-Heine-Universität Düsseldorf (No. 18-2019 to A.P.). C.G. was supported by the Helmholtz Alliance ‘Aging and Metabolic Programming, AMPro,’ by the German Federal\r\nMinistry of Education and Research to the German Center for Diabetes Research (DZD), and by the Bavarian State Ministry of Health and Care through the research project DigiMed Bayern.","status":"public","publication_status":"published","_id":"12119","title":"Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease","author":[{"last_name":"Petzold","full_name":"Petzold, Tobias","first_name":"Tobias"},{"first_name":"Zhe","full_name":"Zhang, Zhe","last_name":"Zhang"},{"full_name":"Ballesteros, Iván","last_name":"Ballesteros","first_name":"Iván"},{"last_name":"Saleh","full_name":"Saleh, Inas","first_name":"Inas"},{"first_name":"Amin","last_name":"Polzin","full_name":"Polzin, Amin"},{"first_name":"Manuela","full_name":"Thienel, Manuela","last_name":"Thienel"},{"full_name":"Liu, Lulu","last_name":"Liu","first_name":"Lulu"},{"first_name":"Qurrat","last_name":"Ul Ain","full_name":"Ul Ain, Qurrat"},{"last_name":"Ehreiser","full_name":"Ehreiser, Vincent","first_name":"Vincent"},{"first_name":"Christian","full_name":"Weber, Christian","last_name":"Weber"},{"first_name":"Badr","last_name":"Kilani","full_name":"Kilani, Badr"},{"first_name":"Pontus","full_name":"Mertsch, Pontus","last_name":"Mertsch"},{"last_name":"Götschke","full_name":"Götschke, Jeremias","first_name":"Jeremias"},{"full_name":"Cremer, Sophie","last_name":"Cremer","first_name":"Sophie"},{"full_name":"Fu, Wenwen","last_name":"Fu","first_name":"Wenwen"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"last_name":"Ishikawa-Ankerhold","full_name":"Ishikawa-Ankerhold, Hellen","first_name":"Hellen"},{"last_name":"Raatz","full_name":"Raatz, Elisabeth","first_name":"Elisabeth"},{"full_name":"El-Nemr, Shaza","last_name":"El-Nemr","first_name":"Shaza"},{"full_name":"Görlach, Agnes","last_name":"Görlach","first_name":"Agnes"},{"full_name":"Marhuenda, Esther","last_name":"Marhuenda","first_name":"Esther"},{"last_name":"Stark","full_name":"Stark, Konstantin","first_name":"Konstantin"},{"last_name":"Pircher","full_name":"Pircher, Joachim","first_name":"Joachim"},{"last_name":"Stegner","full_name":"Stegner, David","first_name":"David"},{"last_name":"Gieger","full_name":"Gieger, Christian","first_name":"Christian"},{"first_name":"Marc","full_name":"Schmidt-Supprian, Marc","last_name":"Schmidt-Supprian"},{"full_name":"Gärtner, Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","orcid":"0000-0001-6120-3723"},{"full_name":"Almendros, Isaac","last_name":"Almendros","first_name":"Isaac"},{"first_name":"Malte","full_name":"Kelm, Malte","last_name":"Kelm"},{"first_name":"Christian","full_name":"Schulz, Christian","last_name":"Schulz"},{"last_name":"Hidalgo","full_name":"Hidalgo, Andrés","first_name":"Andrés"},{"last_name":"Massberg","full_name":"Massberg, Steffen","first_name":"Steffen"}],"doi":"10.1016/j.immuni.2022.10.001","abstract":[{"lang":"eng","text":"Intravascular neutrophils and platelets collaborate in maintaining host integrity, but their interaction can also trigger thrombotic complications. We report here that cooperation between neutrophil and platelet lineages extends to the earliest stages of platelet formation by megakaryocytes in the bone marrow. Using intravital microscopy, we show that neutrophils “plucked” intravascular megakaryocyte extensions, termed proplatelets, to control platelet production. Following CXCR4-CXCL12-dependent migration towards perisinusoidal megakaryocytes, plucking neutrophils actively pulled on proplatelets and triggered myosin light chain and extracellular-signal-regulated kinase activation through reactive oxygen species. By these mechanisms, neutrophils accelerate proplatelet growth and facilitate continuous release of platelets in steady state. Following myocardial infarction, plucking neutrophils drove excessive release of young, reticulated platelets and boosted the risk of recurrent ischemia. Ablation of neutrophil plucking normalized thrombopoiesis and reduced recurrent thrombosis after myocardial infarction and thrombus burden in venous thrombosis. We establish neutrophil plucking as a target to reduce thromboischemic events."}],"issue":"12","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"content_type":"application/pdf","checksum":"073267a9c0ad9f85a650053bc7b23777","access_level":"open_access","date_updated":"2023-01-23T10:18:48Z","success":1,"file_size":5299475,"creator":"dernst","relation":"main_file","file_name":"2022_Immunity_Petzold.pdf","date_created":"2023-01-23T10:18:48Z","file_id":"12341"}],"volume":55,"article_processing_charge":"No","has_accepted_license":"1","month":"12","pmid":1,"ddc":["570"],"file_date_updated":"2023-01-23T10:18:48Z","citation":{"chicago":"Petzold, Tobias, Zhe Zhang, Iván Ballesteros, Inas Saleh, Amin Polzin, Manuela Thienel, Lulu Liu, et al. “Neutrophil ‘Plucking’ on Megakaryocytes Drives Platelet Production and Boosts Cardiovascular Disease.” <i>Immunity</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.immuni.2022.10.001\">https://doi.org/10.1016/j.immuni.2022.10.001</a>.","mla":"Petzold, Tobias, et al. “Neutrophil ‘Plucking’ on Megakaryocytes Drives Platelet Production and Boosts Cardiovascular Disease.” <i>Immunity</i>, vol. 55, no. 12, Elsevier, 2022, p. 2285–2299.e7, doi:<a href=\"https://doi.org/10.1016/j.immuni.2022.10.001\">10.1016/j.immuni.2022.10.001</a>.","ama":"Petzold T, Zhang Z, Ballesteros I, et al. Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease. <i>Immunity</i>. 2022;55(12):2285-2299.e7. doi:<a href=\"https://doi.org/10.1016/j.immuni.2022.10.001\">10.1016/j.immuni.2022.10.001</a>","ista":"Petzold T, Zhang Z, Ballesteros I, Saleh I, Polzin A, Thienel M, Liu L, Ul Ain Q, Ehreiser V, Weber C, Kilani B, Mertsch P, Götschke J, Cremer S, Fu W, Lorenz M, Ishikawa-Ankerhold H, Raatz E, El-Nemr S, Görlach A, Marhuenda E, Stark K, Pircher J, Stegner D, Gieger C, Schmidt-Supprian M, Gärtner FR, Almendros I, Kelm M, Schulz C, Hidalgo A, Massberg S. 2022. Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease. Immunity. 55(12), 2285–2299.e7.","short":"T. Petzold, Z. Zhang, I. Ballesteros, I. Saleh, A. Polzin, M. Thienel, L. Liu, Q. Ul Ain, V. Ehreiser, C. Weber, B. Kilani, P. Mertsch, J. Götschke, S. Cremer, W. Fu, M. Lorenz, H. Ishikawa-Ankerhold, E. Raatz, S. El-Nemr, A. Görlach, E. Marhuenda, K. Stark, J. Pircher, D. Stegner, C. Gieger, M. Schmidt-Supprian, F.R. Gärtner, I. Almendros, M. Kelm, C. Schulz, A. Hidalgo, S. Massberg, Immunity 55 (2022) 2285–2299.e7.","ieee":"T. Petzold <i>et al.</i>, “Neutrophil ‘plucking’ on megakaryocytes drives platelet production and boosts cardiovascular disease,” <i>Immunity</i>, vol. 55, no. 12. Elsevier, p. 2285–2299.e7, 2022.","apa":"Petzold, T., Zhang, Z., Ballesteros, I., Saleh, I., Polzin, A., Thienel, M., … Massberg, S. (2022). Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease. <i>Immunity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.immuni.2022.10.001\">https://doi.org/10.1016/j.immuni.2022.10.001</a>"},"day":"13","oa_version":"Published Version","date_updated":"2023-08-03T14:21:51Z","publication":"Immunity","page":"2285-2299.e7","article_type":"original","oa":1,"keyword":["Infectious Diseases","Immunology","Immunology and Allergy"],"year":"2022","publisher":"Elsevier","intvolume":"        55","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiSi"}],"date_created":"2023-01-12T11:56:54Z","scopus_import":"1","external_id":{"pmid":["36272416"],"isi":["000922019600003"]},"date_published":"2022-12-13T00:00:00Z"},{"keyword":["Cell Biology"],"year":"2022","oa":1,"article_type":"original","article_number":"e202203139","date_updated":"2023-08-03T14:20:15Z","publication":"Journal of Cell Biology","scopus_import":"1","date_created":"2023-01-12T11:57:10Z","external_id":{"pmid":["36260289"],"isi":["000932958800001"]},"date_published":"2022-12-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":"       221","publisher":"Rockefeller University Press","doi":"10.1083/jcb.202203139","issue":"12","abstract":[{"text":"Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants.","lang":"eng"}],"_id":"12121","author":[{"first_name":"Jierui","full_name":"Zhao, Jierui","last_name":"Zhao"},{"full_name":"Bui, Mai Thu","last_name":"Bui","first_name":"Mai Thu"},{"last_name":"Ma","full_name":"Ma, Juncai","first_name":"Juncai"},{"first_name":"Fabian","full_name":"Künzl, Fabian","last_name":"Künzl"},{"first_name":"Lorenzo","full_name":"Picchianti, Lorenzo","last_name":"Picchianti"},{"first_name":"Juan Carlos","full_name":"De La Concepcion, Juan Carlos","last_name":"De La Concepcion"},{"first_name":"Yixuan","full_name":"Chen, Yixuan","last_name":"Chen"},{"full_name":"Petsangouraki, Sofia","last_name":"Petsangouraki","first_name":"Sofia"},{"first_name":"Azadeh","full_name":"Mohseni, Azadeh","last_name":"Mohseni"},{"first_name":"Marta","last_name":"García-Leon","full_name":"García-Leon, Marta"},{"first_name":"Marta Salas","full_name":"Gomez, Marta Salas","last_name":"Gomez"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","full_name":"Giannini, Caterina","last_name":"Giannini"},{"first_name":"Dubois","last_name":"Gwennogan","full_name":"Gwennogan, Dubois"},{"last_name":"Kobylinska","full_name":"Kobylinska, Roksolana","first_name":"Roksolana"},{"full_name":"Clavel, Marion","last_name":"Clavel","first_name":"Marion"},{"full_name":"Schellmann, Swen","last_name":"Schellmann","first_name":"Swen"},{"full_name":"Jaillais, Yvon","last_name":"Jaillais","first_name":"Yvon"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"last_name":"Kang","full_name":"Kang, Byung-Ho","first_name":"Byung-Ho"},{"first_name":"Yasin","last_name":"Dagdas","full_name":"Dagdas, Yasin"}],"title":"Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole","publication_status":"published","status":"public","acknowledgement":"We thank Suayip Ustün, Karin Schumacher, Erika Isono, Gerd Juergens, Takashi Ueda, Daniel Hofius, and Liwen Jiang for sharing published materials.\r\nWe acknowledge funding from Austrian Academy of Sciences, Austrian Science Fund (FWF, P 32355, P 34944), Austrian Science Fund (FWF-SFB F79), Vienna Science and Technology\r\nFund (WWTF, LS17-047) to Y. Dagdas; Austrian Academy of Sciences DOC Fellowship to J. Zhao, Marie Curie VIP2 Fellowship to J.C. De La Concepcion and M. Clavel; Hong Kong Research Grant Council (GRF14121019, 14113921, AoE/M-05/12, C4002-17G) to B.-H. Kang. We thank Vienna Biocenter Core Facilities (VBCF) Protein Chemistry, Biooptics, Plant Sciences, Molecular Biology, and Protein Technologies. We thank J. Matthew Watson\r\nand members of the Dagdas lab for the critical reading and editing of the manuscript.","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"oa_version":"Published Version","ddc":["580"],"file_date_updated":"2023-01-23T10:30:11Z","pmid":1,"month":"12","day":"01","citation":{"mla":"Zhao, Jierui, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” <i>Journal of Cell Biology</i>, vol. 221, no. 12, e202203139, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202203139\">10.1083/jcb.202203139</a>.","chicago":"Zhao, Jierui, Mai Thu Bui, Juncai Ma, Fabian Künzl, Lorenzo Picchianti, Juan Carlos De La Concepcion, Yixuan Chen, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202203139\">https://doi.org/10.1083/jcb.202203139</a>.","ieee":"J. Zhao <i>et al.</i>, “Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole,” <i>Journal of Cell Biology</i>, vol. 221, no. 12. Rockefeller University Press, 2022.","apa":"Zhao, J., Bui, M. T., Ma, J., Künzl, F., Picchianti, L., De La Concepcion, J. C., … Dagdas, Y. (2022). Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202203139\">https://doi.org/10.1083/jcb.202203139</a>","ama":"Zhao J, Bui MT, Ma J, et al. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. <i>Journal of Cell Biology</i>. 2022;221(12). doi:<a href=\"https://doi.org/10.1083/jcb.202203139\">10.1083/jcb.202203139</a>","ista":"Zhao J, Bui MT, Ma J, Künzl F, Picchianti L, De La Concepcion JC, Chen Y, Petsangouraki S, Mohseni A, García-Leon M, Gomez MS, Giannini C, Gwennogan D, Kobylinska R, Clavel M, Schellmann S, Jaillais Y, Friml J, Kang B-H, Dagdas Y. 2022. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 221(12), e202203139.","short":"J. Zhao, M.T. Bui, J. Ma, F. Künzl, L. Picchianti, J.C. De La Concepcion, Y. Chen, S. Petsangouraki, A. Mohseni, M. García-Leon, M.S. Gomez, C. Giannini, D. Gwennogan, R. Kobylinska, M. Clavel, S. Schellmann, Y. Jaillais, J. Friml, B.-H. Kang, Y. Dagdas, Journal of Cell Biology 221 (2022)."},"article_processing_charge":"No","volume":221,"has_accepted_license":"1","file":[{"file_size":10365777,"relation":"main_file","creator":"dernst","file_name":"2022_JCB_Zhao.pdf","date_updated":"2023-01-23T10:30:11Z","success":1,"checksum":"050b5cc4b25e6b94fe3e3cbfe0f5c06b","content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-23T10:30:11Z","file_id":"12342"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"file":[{"relation":"main_file","creator":"dernst","file_size":11090179,"file_name":"2023_JCB_Weier.pdf","checksum":"0c9af38f82af30c6ce528f2caece4246","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-08-16T11:24:53Z","success":1,"date_created":"2023-08-16T11:24:53Z","file_id":"14065"}],"volume":221,"article_processing_charge":"No","has_accepted_license":"1","month":"12","pmid":1,"ddc":["570"],"file_date_updated":"2023-08-16T11:24:53Z","citation":{"apa":"Weier, A.-K., Homrich, M., Ebbinghaus, S., Juda, P., Miková, E., Hauschild, R., … Kiermaier, E. (2022). Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202107134\">https://doi.org/10.1083/jcb.202107134</a>","ieee":"A.-K. Weier <i>et al.</i>, “Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells,” <i>Journal of Cell Biology</i>, vol. 221, no. 12. Rockefeller University Press, 2022.","ista":"Weier A-K, Homrich M, Ebbinghaus S, Juda P, Miková E, Hauschild R, Zhang L, Quast T, Mass E, Schlitzer A, Kolanus W, Burgdorf S, Gruß OJ, Hons M, Wieser S, Kiermaier E. 2022. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. Journal of Cell Biology. 221(12), e202107134.","ama":"Weier A-K, Homrich M, Ebbinghaus S, et al. Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells. <i>Journal of Cell Biology</i>. 2022;221(12). doi:<a href=\"https://doi.org/10.1083/jcb.202107134\">10.1083/jcb.202107134</a>","short":"A.-K. Weier, M. Homrich, S. Ebbinghaus, P. Juda, E. Miková, R. Hauschild, L. Zhang, T. Quast, E. Mass, A. Schlitzer, W. Kolanus, S. Burgdorf, O.J. Gruß, M. Hons, S. Wieser, E. Kiermaier, Journal of Cell Biology 221 (2022).","chicago":"Weier, Ann-Kathrin, Mirka Homrich, Stephanie Ebbinghaus, Pavel Juda, Eliška Miková, Robert Hauschild, Lili Zhang, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202107134\">https://doi.org/10.1083/jcb.202107134</a>.","mla":"Weier, Ann-Kathrin, et al. “Multiple Centrosomes Enhance Migration and Immune Cell Effector Functions of Mature Dendritic Cells.” <i>Journal of Cell Biology</i>, vol. 221, no. 12, e202107134, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202107134\">10.1083/jcb.202107134</a>."},"day":"05","oa_version":"Published Version","project":[{"name":"Tools for automation and feedback microscopy","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01"}],"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"status":"public","acknowledgement":"We thank Markéta Dalecká and Irena Krejzová for their support with FIB-SEM imaging, the Imaging Methods Core Facility at BIOCEV supported by the Ministry of Education, Youth and Sports Czech Republic (Large RI Project LM2018129 Czech-BioImaging), and European Regional Development Fund (project No. CZ.02.1.01/0.0/0.0/18_046/0016045) for their support with obtaining imaging data presented in this paper. The authors further thank Andreas Villunger, Florian Gärtner, Frank Bradke, and Sarah Förster for helpful discussions; Andy Zielinski for help with statistics; and Björn Weiershausen for assisting with figure illustration.\r\n\r\nThis work was funded by a fellowship of the Ministry of Innovation, Science and Research of North-Rhine-Westphalia (AZ: 421-8.03.03.02-137069) to E. Kiermaier and the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy – EXC 2151 – 390873048. R. Hauschild was funded by grant number 2020-225401 from the Chan Zuckerberg Initiative Donor-Advised Fund, an advised fund of Silicon Valley Community Foundation. M. Hons is supported by Czech Science Foundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","publication_status":"published","_id":"12122","title":"Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells","author":[{"full_name":"Weier, Ann-Kathrin","last_name":"Weier","first_name":"Ann-Kathrin"},{"first_name":"Mirka","last_name":"Homrich","full_name":"Homrich, Mirka"},{"last_name":"Ebbinghaus","full_name":"Ebbinghaus, Stephanie","first_name":"Stephanie"},{"first_name":"Pavel","full_name":"Juda, Pavel","last_name":"Juda"},{"first_name":"Eliška","last_name":"Miková","full_name":"Miková, Eliška"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Zhang, Lili","last_name":"Zhang","first_name":"Lili"},{"last_name":"Quast","full_name":"Quast, Thomas","first_name":"Thomas"},{"last_name":"Mass","full_name":"Mass, Elvira","first_name":"Elvira"},{"full_name":"Schlitzer, Andreas","last_name":"Schlitzer","first_name":"Andreas"},{"first_name":"Waldemar","last_name":"Kolanus","full_name":"Kolanus, Waldemar"},{"full_name":"Burgdorf, Sven","last_name":"Burgdorf","first_name":"Sven"},{"first_name":"Oliver J.","last_name":"Gruß","full_name":"Gruß, Oliver J."},{"first_name":"Miroslav","last_name":"Hons","full_name":"Hons, Miroslav"},{"first_name":"Stefan","last_name":"Wieser","full_name":"Wieser, Stefan"},{"first_name":"Eva","last_name":"Kiermaier","full_name":"Kiermaier, Eva"}],"doi":"10.1083/jcb.202107134","abstract":[{"text":"Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis.","lang":"eng"}],"issue":"12","publisher":"Rockefeller University Press","intvolume":"       221","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"Bio"}],"date_created":"2023-01-12T12:01:09Z","scopus_import":"1","external_id":{"isi":["000932941400001"],"pmid":["36214847 "]},"date_published":"2022-12-05T00:00:00Z","date_updated":"2023-08-16T11:29:12Z","publication":"Journal of Cell Biology","article_number":"e202107134","article_type":"original","oa":1,"keyword":["Cell Biology"],"year":"2022"},{"article_number":"040501","article_type":"original","related_material":{"link":[{"url":"https://github.com/capoe/benchml","relation":"software"}]},"date_updated":"2023-08-04T08:49:53Z","publication":"Machine Learning: Science and Technology","keyword":["Artificial Intelligence","Human-Computer Interaction","Software"],"year":"2022","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"IOP Publishing","intvolume":"         3","date_created":"2023-01-12T12:02:21Z","scopus_import":"1","external_id":{"isi":["000886534000001"]},"date_published":"2022-11-17T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BiCh"}],"acknowledgement":"C P acknowledges funding from Astex through the Sustaining Innovation Program under the Milner Consortium. B C acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant EP/P020259/1. F A F acknowledges funding from the Swiss National Science Foundation (Grant No. P2BSP2_191736). ","publication_status":"published","status":"public","publication_identifier":{"issn":["2632-2153"]},"doi":"10.1088/2632-2153/ac4d11","abstract":[{"lang":"eng","text":"We introduce a machine-learning (ML) framework for high-throughput benchmarking of diverse representations of chemical systems against datasets of materials and molecules. The guiding principle underlying the benchmarking approach is to evaluate raw descriptor performance by limiting model complexity to simple regression schemes while enforcing best ML practices, allowing for unbiased hyperparameter optimization, and assessing learning progress through learning curves along series of synchronized train-test splits. The resulting models are intended as baselines that can inform future method development, in addition to indicating how easily a given dataset can be learnt. Through a comparative analysis of the training outcome across a diverse set of physicochemical, topological and geometric representations, we glean insight into the relative merits of these representations as well as their interrelatedness."}],"issue":"4","_id":"12128","title":"BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale","author":[{"full_name":"Poelking, Carl","last_name":"Poelking","first_name":"Carl"},{"last_name":"Faber","full_name":"Faber, Felix A","first_name":"Felix A"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632"}],"volume":3,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","file_size":13814559,"creator":"dernst","file_name":"2022_MachLearning_Poelking.pdf","date_updated":"2023-01-23T10:42:04Z","success":1,"checksum":"8930d4ad6ed9b47358c6f1a68666adb6","content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-23T10:42:04Z","file_id":"12343"}],"oa_version":"Published Version","file_date_updated":"2023-01-23T10:42:04Z","month":"11","ddc":["000"],"citation":{"chicago":"Poelking, Carl, Felix A Faber, and Bingqing Cheng. “BenchML: An Extensible Pipelining Framework for Benchmarking Representations of Materials and Molecules at Scale.” <i>Machine Learning: Science and Technology</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">https://doi.org/10.1088/2632-2153/ac4d11</a>.","mla":"Poelking, Carl, et al. “BenchML: An Extensible Pipelining Framework for Benchmarking Representations of Materials and Molecules at Scale.” <i>Machine Learning: Science and Technology</i>, vol. 3, no. 4, 040501, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">10.1088/2632-2153/ac4d11</a>.","apa":"Poelking, C., Faber, F. A., &#38; Cheng, B. (2022). BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. <i>Machine Learning: Science and Technology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">https://doi.org/10.1088/2632-2153/ac4d11</a>","ieee":"C. Poelking, F. A. Faber, and B. Cheng, “BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale,” <i>Machine Learning: Science and Technology</i>, vol. 3, no. 4. IOP Publishing, 2022.","ama":"Poelking C, Faber FA, Cheng B. BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. <i>Machine Learning: Science and Technology</i>. 2022;3(4). doi:<a href=\"https://doi.org/10.1088/2632-2153/ac4d11\">10.1088/2632-2153/ac4d11</a>","ista":"Poelking C, Faber FA, Cheng B. 2022. BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale. Machine Learning: Science and Technology. 3(4), 040501.","short":"C. Poelking, F.A. Faber, B. Cheng, Machine Learning: Science and Technology 3 (2022)."},"day":"17"}]