[{"day":"01","corr_author":"1","license":"https://creativecommons.org/licenses/by/4.0/","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2022-09-12T08:14:50Z","creator":"dernst","access_level":"open_access","success":1,"file_size":2101656,"file_name":"2022_JBC_Artan.pdf","date_created":"2022-09-12T08:14:50Z","file_id":"12092","checksum":"e726c7b9315230e6710e0b1f1d1677e9"}],"date_updated":"2025-04-14T07:44:00Z","oa_version":"Published Version","issue":"9","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"month":"09","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.jbc.2022.102343","pmid":1,"ddc":["570"],"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"}],"publication_status":"published","date_published":"2022-09-01T00:00:00Z","status":"public","intvolume":"       298","publisher":"Elsevier","isi":1,"type":"journal_article","article_number":"102343","scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","citation":{"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>","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>.","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.","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.","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>.","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>","short":"M. Artan, M. Hartl, W. Chen, M. de Bono, Journal of Biological Chemistry 298 (2022)."},"_id":"12082","file_date_updated":"2022-09-12T08:14:50Z","author":[{"full_name":"Artan, Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","last_name":"Artan","orcid":"0000-0001-8945-6992","first_name":"Murat"},{"full_name":"Hartl, Markus","last_name":"Hartl","first_name":"Markus"},{"full_name":"Chen, Weiqiang","first_name":"Weiqiang","last_name":"Chen"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","first_name":"Mario","full_name":"De Bono, Mario"}],"article_processing_charge":"No","date_created":"2022-09-11T22:01:55Z","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).","acknowledged_ssus":[{"_id":"Bio"}],"publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"department":[{"_id":"MaDe"}],"volume":298,"title":"Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans","article_type":"original","external_id":{"pmid":["35933017"],"isi":["000884241800011"]},"project":[{"grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"publication":"Journal of Biological Chemistry","year":"2022"},{"issue":"8","oa_version":"Published Version","date_updated":"2025-04-14T07:26:59Z","arxiv":1,"language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"day":"25","corr_author":"1","file":[{"date_created":"2022-09-12T07:35:34Z","file_id":"12089","checksum":"e6fb0cf3f0327739c5e69a2cfc4020eb","success":1,"file_size":4552261,"file_name":"2022_JourMathPhysics_Rademacher.pdf","date_updated":"2022-09-12T07:35:34Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"publication_status":"published","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."}],"ddc":["510"],"date_published":"2022-08-25T00:00:00Z","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"08","doi":"10.1063/5.0086712","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","article_number":"081902","citation":{"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>","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>.","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.","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>.","short":"S.A.E. Rademacher, Journal of Mathematical Physics 63 (2022).","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>"},"author":[{"first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","last_name":"Rademacher","orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira"}],"file_date_updated":"2022-09-12T07:35:34Z","_id":"12083","intvolume":"        63","publisher":"AIP Publishing","type":"journal_article","isi":1,"external_id":{"isi":["000844402500001"],"arxiv":["2112.04817"]},"title":"Dependent random variables in quantum dynamics","article_type":"original","volume":63,"year":"2022","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"publication":"Journal of Mathematical Physics","date_created":"2022-09-11T22:01:56Z","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.","article_processing_charge":"No","publication_identifier":{"issn":["0022-2488"]},"department":[{"_id":"RoSe"}]},{"status":"public","date_published":"2022-08-15T00:00:00Z","publication_status":"published","abstract":[{"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.","lang":"eng"}],"ddc":["570"],"pmid":1,"doi":"10.1371/journal.pcbi.1010365","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"08","oa":1,"language":[{"iso":"eng"}],"issue":"8","oa_version":"Published Version","date_updated":"2025-06-11T13:51:21Z","file":[{"date_updated":"2022-09-12T07:47:55Z","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"12090","date_created":"2022-09-12T07:47:55Z","checksum":"8a81ab29f837991ee0ea770817c4a50e","file_size":2867337,"file_name":"2022_PLoSCompBio_Christodoulou.pdf","success":1}],"corr_author":"1","day":"15","year":"2022","publication":"PLoS Computational Biology","project":[{"grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."}],"title":"Regimes and mechanisms of transient amplification in abstract and biological neural networks","article_type":"original","external_id":{"isi":["000937227700001"],"pmid":["35969604"]},"volume":18,"department":[{"_id":"TiVo"}],"publication_identifier":{"eissn":["1553-7358"]},"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). ","date_created":"2022-09-11T22:01:56Z","article_processing_charge":"No","author":[{"full_name":"Christodoulou, Georgia","last_name":"Christodoulou","first_name":"Georgia"},{"first_name":"Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P"},{"last_name":"Agnes","first_name":"Everton J.","full_name":"Agnes, Everton J."}],"file_date_updated":"2022-09-12T07:47:55Z","_id":"12084","citation":{"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.","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.","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>.","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>","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>","short":"G. Christodoulou, T.P. Vogels, E.J. Agnes, PLoS Computational Biology 18 (2022).","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>."},"has_accepted_license":"1","quality_controlled":"1","article_number":"e1010365","scopus_import":"1","type":"journal_article","isi":1,"publisher":"Public Library of Science","intvolume":"        18"},{"type":"journal_article","isi":1,"publisher":"Springer Nature","intvolume":"        21","author":[{"full_name":"Mulla, Yuval","first_name":"Yuval","last_name":"Mulla"},{"last_name":"Avellaneda Sarrió","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","orcid":"0000-0001-6406-524X","first_name":"Mario","full_name":"Avellaneda Sarrió, Mario"},{"first_name":"Antoine","last_name":"Roland","full_name":"Roland, Antoine"},{"first_name":"Lucia","last_name":"Baldauf","full_name":"Baldauf, Lucia"},{"full_name":"Jung, Wonyeong","last_name":"Jung","first_name":"Wonyeong"},{"last_name":"Kim","first_name":"Taeyoon","full_name":"Kim, Taeyoon"},{"full_name":"Tans, Sander J.","first_name":"Sander J.","last_name":"Tans"},{"full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H.","last_name":"Koenderink"}],"_id":"12085","citation":{"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.","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>","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>.","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.","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>.","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.","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>"},"quality_controlled":"1","scopus_import":"1","department":[{"_id":"MiSi"}],"publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"date_created":"2022-09-11T22:01:57Z","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.).","article_processing_charge":"No","year":"2022","publication":"Nature Materials","article_type":"original","title":"Weak catch bonds make strong networks","external_id":{"pmid":["36008604"],"isi":["000844592000002"]},"volume":21,"page":"1019-1023","day":"01","language":[{"iso":"eng"}],"oa":1,"issue":"9","date_updated":"2023-08-03T14:08:47Z","oa_version":"Preprint","doi":"10.1038/s41563-022-01288-0","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.07.27.219618"}],"month":"09","status":"public","date_published":"2022-09-01T00:00:00Z","abstract":[{"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.","lang":"eng"}],"publication_status":"published"},{"year":"2022","status":"public","publication":"Conference on Lasers and Electro-Optics","title":"Realizing a quantum-enabled interconnect between microwave and telecom light","date_published":"2022-05-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"We present a quantum-enabled microwave-telecom interface with bidirectional conversion efficiencies up to 15% and added input noise quanta as low as 0.16. Moreover, we observe evidence for electro-optic laser cooling and vacuum amplification."}],"department":[{"_id":"JoFi"}],"doi":"10.1364/CLEO_QELS.2022.FW4D.4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"CLEO: QELS Fundamental Science","end_date":"2022-05-20","start_date":"2022-05-15","location":"San Jose, CA, United States"},"publication_identifier":{"isbn":["9781557528209"]},"date_created":"2022-09-11T22:01:58Z","article_processing_charge":"No","month":"05","author":[{"full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","orcid":"0000-0001-6264-2162","first_name":"Rishabh"},{"first_name":"William J","orcid":"0000-0001-9868-2166","last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J"},{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R"},{"orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","first_name":"Georg M","full_name":"Arnold, Georg M"},{"full_name":"Qiu, Liu","first_name":"Liu","orcid":"0000-0003-4345-4267","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu"},{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"_id":"12088","language":[{"iso":"eng"}],"citation":{"short":"R. Sahu, W.J. Hease, A.R. Rueda Sanchez, G.M. Arnold, L. Qiu, J.M. Fink, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2022.","apa":"Sahu, R., Hease, W. J., Rueda Sanchez, A. R., Arnold, G. M., Qiu, L., &#38; Fink, J. M. (2022). Realizing a quantum-enabled interconnect between microwave and telecom light. In <i>Conference on Lasers and Electro-Optics</i>. San Jose, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4\">https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4</a>","chicago":"Sahu, Rishabh, William J Hease, Alfredo R Rueda Sanchez, Georg M Arnold, Liu Qiu, and Johannes M Fink. “Realizing a Quantum-Enabled Interconnect between Microwave and Telecom Light.” In <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group, 2022. <a href=\"https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4\">https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4</a>.","ieee":"R. Sahu, W. J. Hease, A. R. Rueda Sanchez, G. M. Arnold, L. Qiu, and J. M. Fink, “Realizing a quantum-enabled interconnect between microwave and telecom light,” in <i>Conference on Lasers and Electro-Optics</i>, San Jose, CA, United States, 2022.","mla":"Sahu, Rishabh, et al. “Realizing a Quantum-Enabled Interconnect between Microwave and Telecom Light.” <i>Conference on Lasers and Electro-Optics</i>, FW4D.4, Optica Publishing Group, 2022, doi:<a href=\"https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4\">10.1364/CLEO_QELS.2022.FW4D.4</a>.","ista":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. 2022. Realizing a quantum-enabled interconnect between microwave and telecom light. Conference on Lasers and Electro-Optics. CLEO: QELS Fundamental Science, FW4D.4.","ama":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. Realizing a quantum-enabled interconnect between microwave and telecom light. In: <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group; 2022. doi:<a href=\"https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4\">10.1364/CLEO_QELS.2022.FW4D.4</a>"},"quality_controlled":"1","date_updated":"2024-10-09T21:03:27Z","oa_version":"None","scopus_import":"1","article_number":"FW4D.4","type":"conference","corr_author":"1","publisher":"Optica Publishing Group","day":"01"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       250","type":"conference","citation":{"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.","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>.","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. FSTTCS: 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>","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>."},"scopus_import":"1","quality_controlled":"1","article_number":"29","has_accepted_license":"1","_id":"12102","file_date_updated":"2023-01-20T10:39:44Z","author":[{"first_name":"Ali","last_name":"Ahmadi","full_name":"Ahmadi, Ali"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"},{"first_name":"Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias"},{"last_name":"Safavi Hemami","id":"72ed2640-8972-11ed-ae7b-f9c81ec75154","first_name":"Roodabeh","full_name":"Safavi Hemami, Roodabeh"},{"last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde","full_name":"Zikelic, Dorde"}],"publication_identifier":{"isbn":["9783959772617"],"issn":["1868-8969"]},"article_processing_charge":"No","date_created":"2023-01-01T23:00:50Z","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.","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","end_date":"2022-12-20","start_date":"2022-12-18","location":"Madras, India"},"project":[{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"publication":"42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","year":"2022","volume":250,"title":"Algorithms and hardness results for computing cores of Markov chains","day":"14","file":[{"file_id":"12324","date_created":"2023-01-20T10:39:44Z","checksum":"6660c802489013f034c9e8bd57f4d46e","file_name":"2022_LIPICs_Ahmadi.pdf","file_size":872534,"success":1,"date_updated":"2023-01-20T10:39:44Z","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf"}],"corr_author":"1","date_updated":"2025-07-10T11:50:23Z","oa_version":"Published Version","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"month":"12","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.4230/LIPIcs.FSTTCS.2022.29","ddc":["000"],"publication_status":"published","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"}],"status":"public","date_published":"2022-12-14T00:00:00Z"},{"isi":1,"type":"journal_article","publisher":"Wiley","intvolume":"        49","file_date_updated":"2023-01-20T10:52:31Z","_id":"12107","author":[{"full_name":"Roca, Rémy","first_name":"Rémy","last_name":"Roca"},{"full_name":"De Meyer, Victorien","first_name":"Victorien","last_name":"De Meyer"},{"full_name":"Muller, Caroline J","first_name":"Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"citation":{"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>.","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>","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>","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>.","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.","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."},"quality_controlled":"1","scopus_import":"1","article_number":"e2022GL100624","has_accepted_license":"1","department":[{"_id":"CaMu"}],"publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"article_processing_charge":"No","date_created":"2023-01-08T23:00:53Z","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":"Geophysical Research Letters","year":"2022","volume":49,"title":"Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans","external_id":{"isi":["000924587900001"]},"article_type":"letter_note","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2023-01-20T10:52:31Z","access_level":"open_access","creator":"dernst","file_size":875379,"file_name":"2022_GeophysicalResearchLetters_Roca.pdf","success":1,"file_id":"12326","date_created":"2023-01-20T10:52:31Z","checksum":"2c6325cea8938adeea7e3a6f5c2ab64e"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"28","language":[{"iso":"eng"}],"oa":1,"date_updated":"2023-08-03T14:10:27Z","oa_version":"Published Version","issue":"24","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1029/2022GL100624","month":"12","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"status":"public","date_published":"2022-12-28T00:00:00Z","ddc":["550"],"publication_status":"published","abstract":[{"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.","lang":"eng"}]},{"publication":"Physical Review Letters","project":[{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"},{"grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"grant_number":"96752","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes"}],"year":"2022","volume":129,"title":"Mechanochemical rules for shape-shifting filaments that remodel membranes","article_type":"original","external_id":{"isi":["000906721500001"],"pmid":["36608212"]},"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"article_processing_charge":"No","date_created":"2023-01-08T23:00:53Z","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). ","department":[{"_id":"AnSa"}],"citation":{"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>","short":"B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical Review Letters 129 (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>","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.","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.","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>."},"quality_controlled":"1","article_number":"268101","scopus_import":"1","_id":"12108","author":[{"full_name":"Meadowcroft, Billie","orcid":"0000-0003-3441-1337","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft","first_name":"Billie"},{"first_name":"Ivan","orcid":" 0000-0002-8843-9485 ","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","full_name":"Palaia, Ivan"},{"full_name":"Pfitzner, Anna Katharina","last_name":"Pfitzner","first_name":"Anna Katharina"},{"full_name":"Roux, Aurélien","first_name":"Aurélien","last_name":"Roux"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"publisher":"American Physical Society","intvolume":"       129","isi":1,"type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","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."}],"status":"public","date_published":"2022-12-23T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.05.10.490642 "}],"month":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"doi":"10.1103/PhysRevLett.129.268101","oa_version":"Preprint","date_updated":"2025-04-14T07:54:53Z","issue":"26","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"day":"23","corr_author":"1"},{"_id":"12110","file_date_updated":"2023-01-20T11:58:59Z","author":[{"last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","orcid":"0000-0003-1106-327X","first_name":"Sven Joscha","full_name":"Henheik, Sven Joscha"},{"full_name":"Tumulka, Roderich","first_name":"Roderich","last_name":"Tumulka"}],"quality_controlled":"1","article_number":"122302","scopus_import":"1","has_accepted_license":"1","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>.","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>","short":"S.J. Henheik, R. Tumulka, Journal of Mathematical Physics 63 (2022).","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.","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>.","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."},"isi":1,"type":"journal_article","intvolume":"        63","publisher":"AIP Publishing","volume":63,"article_type":"original","title":"Interior-boundary conditions for the Dirac equation at point sources in three dimensions","external_id":{"isi":["000900748900002"]},"project":[{"grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"publication":"Journal of Mathematical Physics","year":"2022","department":[{"_id":"LaEr"}],"article_processing_charge":"No","acknowledgement":"J.H. gratefully acknowledges the partial financial support by the ERC Advanced Grant “RMTBeyond” under Grant No. 101020331.\r\n","date_created":"2023-01-08T23:00:53Z","publication_identifier":{"issn":["0022-2488"]},"language":[{"iso":"eng"}],"oa":1,"ec_funded":1,"oa_version":"Published Version","date_updated":"2025-04-14T07:57:18Z","issue":"12","corr_author":"1","file":[{"file_name":"2022_JourMathPhysics_Henheik.pdf","file_size":5436804,"success":1,"checksum":"5150287295e0ce4f12462c990744d65d","file_id":"12327","date_created":"2023-01-20T11:58:59Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2023-01-20T11:58:59Z"}],"day":"01","date_published":"2022-12-01T00:00:00Z","status":"public","ddc":["510"],"publication_status":"published","abstract":[{"lang":"eng","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1063/5.0104675","month":"12","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"12","doi":"10.1103/PhysRevResearch.4.043177","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","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."}],"ddc":["530"],"date_published":"2022-12-01T00:00:00Z","status":"public","day":"01","file":[{"checksum":"556820cf6e4af77c8476e5b8f4114d1a","file_id":"12328","date_created":"2023-01-20T12:03:31Z","file_size":2941167,"file_name":"2022_PhysicalReviewResearch_Stocker.pdf","success":1,"access_level":"open_access","creator":"dernst","date_updated":"2023-01-20T12:03:31Z","relation":"main_file","content_type":"application/pdf"}],"issue":"4","oa_version":"Published Version","date_updated":"2023-02-13T09:08:28Z","oa":1,"language":[{"iso":"eng"}],"date_created":"2023-01-08T23:00:53Z","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].","article_processing_charge":"No","publication_identifier":{"issn":["2643-1564"]},"department":[{"_id":"MaSe"}],"title":"Entanglement-based observables for quantum impurities","article_type":"original","volume":4,"year":"2022","publication":"Physical Review Research","intvolume":"         4","publisher":"American Physical Society","type":"journal_article","has_accepted_license":"1","article_number":"043177","quality_controlled":"1","scopus_import":"1","citation":{"short":"L. Stocker, S. Sack, M.S. Ferguson, O. Zilberberg, Physical Review Research 4 (2022).","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>","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>.","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.","ista":"Stocker L, Sack S, Ferguson MS, Zilberberg O. 2022. Entanglement-based observables for quantum impurities. Physical Review Research. 4(4), 043177.","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>"},"author":[{"full_name":"Stocker, Lidia","last_name":"Stocker","first_name":"Lidia"},{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","first_name":"Stefan","full_name":"Sack, Stefan"},{"full_name":"Ferguson, Michael S.","last_name":"Ferguson","first_name":"Michael S."},{"first_name":"Oded","last_name":"Zilberberg","full_name":"Zilberberg, Oded"}],"file_date_updated":"2023-01-20T12:03:31Z","_id":"12111"},{"isi":1,"type":"journal_article","intvolume":"       378","publisher":"American Association for the Advancement of Science","_id":"12116","author":[{"last_name":"Chhugani","first_name":"Karishma","full_name":"Chhugani, Karishma"},{"last_name":"Frolova","first_name":"Alina","full_name":"Frolova, 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"},{"full_name":"Wolfsberger, Walter W.","last_name":"Wolfsberger","first_name":"Walter W."},{"first_name":"Oleksandra V.","last_name":"Ivashchenko","full_name":"Ivashchenko, Oleksandra V."},{"full_name":"Maci, Megi","last_name":"Maci","first_name":"Megi"},{"full_name":"Dziuba, Dmytro","first_name":"Dmytro","last_name":"Dziuba"},{"full_name":"Parkhomenko, Andrii","last_name":"Parkhomenko","first_name":"Andrii"},{"full_name":"Bortz, Eric","last_name":"Bortz","first_name":"Eric"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Paweł P.","last_name":"Łabaj","full_name":"Łabaj, Paweł P."},{"last_name":"Romero","first_name":"Veronika","full_name":"Romero, Veronika"},{"last_name":"Hlávka","first_name":"Jakub","full_name":"Hlávka, Jakub"},{"full_name":"Oleksyk, Taras K.","first_name":"Taras K.","last_name":"Oleksyk"},{"first_name":"Serghei","last_name":"Mangul","full_name":"Mangul, Serghei"}],"quality_controlled":"1","scopus_import":"1","citation":{"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>.","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>","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.","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>","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>.","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.","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."},"department":[{"_id":"FyKo"}],"article_processing_charge":"No","date_created":"2023-01-12T11:56:30Z","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"volume":378,"article_type":"letter_note","external_id":{"pmid":["36548425"],"isi":["000963463700023"]},"title":"Remote opportunities for scholars in Ukraine","publication":"Science","year":"2022","page":"1285-1286","day":"22","language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-06-11T13:39:17Z","oa_version":"Published Version","issue":"6626","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1126/science.adg0797","pmid":1,"month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adg0797"}],"date_published":"2022-12-22T00:00:00Z","status":"public","abstract":[{"lang":"eng","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."}],"publication_status":"published"},{"article_processing_charge":"No","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.","date_created":"2023-01-12T11:56:38Z","acknowledged_ssus":[{"_id":"Bio"}],"publication_identifier":{"issn":["2666-1667"]},"department":[{"_id":"SaSi"},{"_id":"GradSch"}],"related_material":{"record":[{"id":"11478","status":"public","relation":"other"}]},"volume":3,"article_type":"letter_note","external_id":{"pmid":["36595902"]},"title":"Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay","publication":"STAR Protocols","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571","call_identifier":"H2020"},{"_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","name":"How human microglia shape developing neurons during health and inflammation","grant_number":"SC19-017"}],"year":"2022","intvolume":"         3","publisher":"Elsevier","type":"journal_article","scopus_import":"1","article_number":"101866","quality_controlled":"1","has_accepted_license":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"citation":{"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>","short":"V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022).","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>.","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.","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>.","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>"},"_id":"12117","file_date_updated":"2023-01-23T09:50:51Z","author":[{"last_name":"Hübschmann","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","full_name":"Hübschmann, Verena"},{"full_name":"Korkut, Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","last_name":"Korkut","orcid":"0000-0003-4309-2251","first_name":"Medina"},{"full_name":"Siegert, Sandra","first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"month":"12","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1016/j.xpro.2022.101866","ddc":["570"],"publication_status":"published","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"}],"date_published":"2022-12-16T00:00:00Z","status":"public","day":"16","corr_author":"1","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2023-01-23T09:50:51Z","file_size":6251945,"file_name":"2022_STARProtocols_Huebschmann.pdf","success":1,"checksum":"3c71b8a60633d42c2f77c49025d5559b","file_id":"12340","date_created":"2023-01-23T09:50:51Z"}],"date_updated":"2025-06-11T13:58:47Z","oa_version":"Published Version","issue":"4","oa":1,"language":[{"iso":"eng"}],"ec_funded":1},{"publisher":"Elsevier","intvolume":"        55","type":"journal_article","isi":1,"citation":{"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>","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.","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>.","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.","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>.","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>","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."},"keyword":["Infectious Diseases","Immunology","Immunology and Allergy"],"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","author":[{"first_name":"Tobias","last_name":"Petzold","full_name":"Petzold, Tobias"},{"full_name":"Zhang, Zhe","last_name":"Zhang","first_name":"Zhe"},{"last_name":"Ballesteros","first_name":"Iván","full_name":"Ballesteros, Iván"},{"full_name":"Saleh, Inas","last_name":"Saleh","first_name":"Inas"},{"full_name":"Polzin, Amin","last_name":"Polzin","first_name":"Amin"},{"full_name":"Thienel, Manuela","first_name":"Manuela","last_name":"Thienel"},{"first_name":"Lulu","last_name":"Liu","full_name":"Liu, Lulu"},{"first_name":"Qurrat","last_name":"Ul Ain","full_name":"Ul Ain, Qurrat"},{"full_name":"Ehreiser, Vincent","last_name":"Ehreiser","first_name":"Vincent"},{"last_name":"Weber","first_name":"Christian","full_name":"Weber, Christian"},{"first_name":"Badr","last_name":"Kilani","full_name":"Kilani, Badr"},{"full_name":"Mertsch, Pontus","first_name":"Pontus","last_name":"Mertsch"},{"full_name":"Götschke, Jeremias","last_name":"Götschke","first_name":"Jeremias"},{"first_name":"Sophie","last_name":"Cremer","full_name":"Cremer, Sophie"},{"full_name":"Fu, Wenwen","last_name":"Fu","first_name":"Wenwen"},{"full_name":"Lorenz, Michael","last_name":"Lorenz","first_name":"Michael"},{"full_name":"Ishikawa-Ankerhold, Hellen","last_name":"Ishikawa-Ankerhold","first_name":"Hellen"},{"first_name":"Elisabeth","last_name":"Raatz","full_name":"Raatz, Elisabeth"},{"last_name":"El-Nemr","first_name":"Shaza","full_name":"El-Nemr, Shaza"},{"full_name":"Görlach, Agnes","first_name":"Agnes","last_name":"Görlach"},{"first_name":"Esther","last_name":"Marhuenda","full_name":"Marhuenda, Esther"},{"full_name":"Stark, Konstantin","first_name":"Konstantin","last_name":"Stark"},{"first_name":"Joachim","last_name":"Pircher","full_name":"Pircher, Joachim"},{"first_name":"David","last_name":"Stegner","full_name":"Stegner, David"},{"last_name":"Gieger","first_name":"Christian","full_name":"Gieger, Christian"},{"full_name":"Schmidt-Supprian, Marc","last_name":"Schmidt-Supprian","first_name":"Marc"},{"orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner","first_name":"Florian R","full_name":"Gärtner, Florian R"},{"full_name":"Almendros, Isaac","first_name":"Isaac","last_name":"Almendros"},{"full_name":"Kelm, Malte","first_name":"Malte","last_name":"Kelm"},{"first_name":"Christian","last_name":"Schulz","full_name":"Schulz, Christian"},{"full_name":"Hidalgo, Andrés","last_name":"Hidalgo","first_name":"Andrés"},{"full_name":"Massberg, Steffen","first_name":"Steffen","last_name":"Massberg"}],"_id":"12119","file_date_updated":"2023-01-23T10:18:48Z","publication_identifier":{"issn":["1074-7613"]},"date_created":"2023-01-12T11:56:54Z","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.","article_processing_charge":"No","department":[{"_id":"MiSi"}],"page":"2285-2299.e7","year":"2022","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","call_identifier":"H2020"}],"publication":"Immunity","title":"Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease","article_type":"original","external_id":{"pmid":["36272416"],"isi":["000922019600003"]},"volume":55,"day":"13","file":[{"content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2023-01-23T10:18:48Z","success":1,"file_name":"2022_Immunity_Petzold.pdf","file_size":5299475,"checksum":"073267a9c0ad9f85a650053bc7b23777","date_created":"2023-01-23T10:18:48Z","file_id":"12341"}],"issue":"12","date_updated":"2025-04-14T07:43:16Z","oa_version":"Published Version","ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"month":"12","pmid":1,"doi":"10.1016/j.immuni.2022.10.001","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","abstract":[{"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.","lang":"eng"}],"ddc":["570"],"status":"public","date_published":"2022-12-13T00:00:00Z"},{"status":"public","date_published":"2022-12-05T00:00:00Z","publication_status":"published","abstract":[{"text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.","lang":"eng"}],"pmid":1,"doi":"10.1016/j.devcel.2022.11.006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2022.11.006"}],"OA_type":"free access","month":"12","language":[{"iso":"eng"}],"oa":1,"issue":"23","oa_version":"Published Version","date_updated":"2025-06-25T07:29:52Z","day":"05","year":"2022","publication":"Developmental Cell","article_type":"original","external_id":{"isi":["000919603800005"],"pmid":["36473460"]},"title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","volume":57,"page":"2638-2651.e6","OA_place":"publisher","department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["1534-5807"]},"date_created":"2023-01-12T11:57:00Z","acknowledgement":"The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153).","article_processing_charge":"No","author":[{"full_name":"Xiao, Huixin","first_name":"Huixin","last_name":"Xiao"},{"full_name":"Hu, Yumei","last_name":"Hu","first_name":"Yumei"},{"full_name":"Wang, Yaping","first_name":"Yaping","last_name":"Wang"},{"last_name":"Cheng","first_name":"Jinkui","full_name":"Cheng, Jinkui"},{"first_name":"Jinyi","last_name":"Wang","full_name":"Wang, Jinyi"},{"full_name":"Chen, Guojingwei","first_name":"Guojingwei","last_name":"Chen"},{"full_name":"Li, Qian","first_name":"Qian","last_name":"Li"},{"first_name":"Shuwei","last_name":"Wang","full_name":"Wang, Shuwei"},{"full_name":"Wang, Yalu","first_name":"Yalu","last_name":"Wang"},{"full_name":"Wang, Shao-Shuai","first_name":"Shao-Shuai","last_name":"Wang"},{"full_name":"Wang, Yi","first_name":"Yi","last_name":"Wang"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"first_name":"Zhen","last_name":"Li","full_name":"Li, Zhen"},{"last_name":"Guo","first_name":"Yan","full_name":"Guo, Yan"},{"last_name":"Gong","first_name":"Zhizhong","full_name":"Gong, Zhizhong"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Zhang, Jing","first_name":"Jing","last_name":"Zhang"}],"_id":"12120","citation":{"short":"H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6.","apa":"Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>","chicago":"Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>.","mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>.","ieee":"H. Xiao <i>et al.</i>, “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” <i>Developmental Cell</i>, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.","ista":"Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6.","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. 2022;57(23):2638-2651.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>"},"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"quality_controlled":"1","scopus_import":"1","type":"journal_article","isi":1,"publisher":"Elsevier","intvolume":"        57"},{"intvolume":"       221","publisher":"Rockefeller University Press","type":"journal_article","isi":1,"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","article_number":"e202203139","citation":{"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>.","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>","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).","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>","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.","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.","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>."},"keyword":["Cell Biology"],"author":[{"last_name":"Zhao","first_name":"Jierui","full_name":"Zhao, Jierui"},{"full_name":"Bui, Mai Thu","last_name":"Bui","first_name":"Mai Thu"},{"full_name":"Ma, Juncai","last_name":"Ma","first_name":"Juncai"},{"last_name":"Künzl","first_name":"Fabian","full_name":"Künzl, Fabian"},{"full_name":"Picchianti, Lorenzo","first_name":"Lorenzo","last_name":"Picchianti"},{"full_name":"De La Concepcion, Juan Carlos","first_name":"Juan Carlos","last_name":"De La Concepcion"},{"full_name":"Chen, Yixuan","first_name":"Yixuan","last_name":"Chen"},{"full_name":"Petsangouraki, Sofia","last_name":"Petsangouraki","first_name":"Sofia"},{"last_name":"Mohseni","first_name":"Azadeh","full_name":"Mohseni, Azadeh"},{"full_name":"García-Leon, Marta","last_name":"García-Leon","first_name":"Marta"},{"last_name":"Gomez","first_name":"Marta Salas","full_name":"Gomez, Marta Salas"},{"full_name":"Giannini, Caterina","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini"},{"full_name":"Gwennogan, Dubois","first_name":"Dubois","last_name":"Gwennogan"},{"full_name":"Kobylinska, Roksolana","last_name":"Kobylinska","first_name":"Roksolana"},{"first_name":"Marion","last_name":"Clavel","full_name":"Clavel, Marion"},{"full_name":"Schellmann, Swen","last_name":"Schellmann","first_name":"Swen"},{"first_name":"Yvon","last_name":"Jaillais","full_name":"Jaillais, Yvon"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"Byung-Ho","last_name":"Kang","full_name":"Kang, Byung-Ho"},{"full_name":"Dagdas, Yasin","last_name":"Dagdas","first_name":"Yasin"}],"_id":"12121","file_date_updated":"2023-01-23T10:30:11Z","date_created":"2023-01-12T11:57:10Z","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.","article_processing_charge":"No","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"department":[{"_id":"JiFr"}],"title":"Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole","article_type":"original","external_id":{"pmid":["36260289"],"isi":["000932958800001"]},"volume":221,"year":"2022","publication":"Journal of Cell Biology","day":"01","file":[{"content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2023-01-23T10:30:11Z","success":1,"file_name":"2022_JCB_Zhao.pdf","file_size":10365777,"checksum":"050b5cc4b25e6b94fe3e3cbfe0f5c06b","date_created":"2023-01-23T10:30:11Z","file_id":"12342"}],"issue":"12","date_updated":"2023-08-03T14:20:15Z","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"12","doi":"10.1083/jcb.202203139","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","abstract":[{"lang":"eng","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."}],"ddc":["580"],"date_published":"2022-12-01T00:00:00Z","status":"public"},{"language":[{"iso":"eng"}],"oa":1,"issue":"12","oa_version":"Published Version","date_updated":"2025-04-15T08:37:41Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2023-08-16T11:24:53Z","success":1,"file_name":"2023_JCB_Weier.pdf","file_size":11090179,"checksum":"0c9af38f82af30c6ce528f2caece4246","date_created":"2023-08-16T11:24:53Z","file_id":"14065"}],"day":"05","date_published":"2022-12-05T00:00:00Z","status":"public","abstract":[{"lang":"eng","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."}],"publication_status":"published","ddc":["570"],"doi":"10.1083/jcb.202107134","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY-NC-SA (4.0)","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"},"month":"12","author":[{"full_name":"Weier, Ann-Kathrin","first_name":"Ann-Kathrin","last_name":"Weier"},{"first_name":"Mirka","last_name":"Homrich","full_name":"Homrich, Mirka"},{"full_name":"Ebbinghaus, Stephanie","first_name":"Stephanie","last_name":"Ebbinghaus"},{"last_name":"Juda","first_name":"Pavel","full_name":"Juda, Pavel"},{"full_name":"Miková, Eliška","first_name":"Eliška","last_name":"Miková"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"last_name":"Zhang","first_name":"Lili","full_name":"Zhang, Lili"},{"full_name":"Quast, Thomas","last_name":"Quast","first_name":"Thomas"},{"last_name":"Mass","first_name":"Elvira","full_name":"Mass, Elvira"},{"last_name":"Schlitzer","first_name":"Andreas","full_name":"Schlitzer, Andreas"},{"last_name":"Kolanus","first_name":"Waldemar","full_name":"Kolanus, Waldemar"},{"last_name":"Burgdorf","first_name":"Sven","full_name":"Burgdorf, Sven"},{"full_name":"Gruß, Oliver J.","first_name":"Oliver J.","last_name":"Gruß"},{"first_name":"Miroslav","last_name":"Hons","full_name":"Hons, Miroslav"},{"first_name":"Stefan","last_name":"Wieser","full_name":"Wieser, Stefan"},{"last_name":"Kiermaier","first_name":"Eva","full_name":"Kiermaier, Eva"}],"_id":"12122","file_date_updated":"2023-08-16T11:24:53Z","has_accepted_license":"1","quality_controlled":"1","article_number":"e202107134","scopus_import":"1","citation":{"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).","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>","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>.","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>"},"keyword":["Cell Biology"],"type":"journal_article","isi":1,"intvolume":"       221","publisher":"Rockefeller University Press","article_type":"original","external_id":{"pmid":["36214847 "],"isi":["000932941400001"]},"title":"Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells","volume":221,"year":"2022","project":[{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","name":"Tools for automation and feedback microscopy","grant_number":"CZI01"}],"publication":"Journal of Cell Biology","department":[{"_id":"Bio"}],"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.","date_created":"2023-01-12T12:01:09Z","article_processing_charge":"No","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]}},{"volume":3,"external_id":{"isi":["000886534000001"]},"article_type":"original","title":"BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale","publication":"Machine Learning: Science and Technology","year":"2022","related_material":{"link":[{"relation":"software","url":"https://github.com/capoe/benchml"}]},"department":[{"_id":"BiCh"}],"article_processing_charge":"No","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). ","date_created":"2023-01-12T12:02:21Z","publication_identifier":{"issn":["2632-2153"]},"_id":"12128","file_date_updated":"2023-01-23T10:42:04Z","author":[{"full_name":"Poelking, Carl","first_name":"Carl","last_name":"Poelking"},{"last_name":"Faber","first_name":"Felix A","full_name":"Faber, Felix A"},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"article_number":"040501","scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","keyword":["Artificial Intelligence","Human-Computer Interaction","Software"],"citation":{"short":"C. Poelking, F.A. Faber, B. Cheng, Machine Learning: Science and Technology 3 (2022).","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>","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>.","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.","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.","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>"},"isi":1,"type":"journal_article","intvolume":"         3","publisher":"IOP Publishing","date_published":"2022-11-17T00:00:00Z","status":"public","ddc":["000"],"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."}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1088/2632-2153/ac4d11","month":"11","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","date_updated":"2024-10-09T21:03:32Z","issue":"4","corr_author":"1","file":[{"file_name":"2022_MachLearning_Poelking.pdf","file_size":13814559,"success":1,"checksum":"8930d4ad6ed9b47358c6f1a68666adb6","file_id":"12343","date_created":"2023-01-23T10:42:04Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2023-01-23T10:42:04Z"}],"day":"17"},{"abstract":[{"lang":"eng","text":"Given a finite point set P in general position in the plane, a full triangulation of P is a maximal straight-line embedded plane graph on P. A partial triangulation of P is a full triangulation of some subset P′ of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge (called edge flip), removes a non-extreme point of degree 3, or adds a point in P∖P′ as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The edge flip graph is defined with full triangulations as vertices, and edge flips determining the adjacencies. Lawson showed in the early seventies that these graphs are connected. The goal of this paper is to investigate the structure of these graphs, with emphasis on their vertex connectivity. For sets P of n points in the plane in general position, we show that the edge flip graph is ⌈n/2−2⌉-vertex connected, and the bistellar flip graph is (n−3)-vertex connected; both results are tight. The latter bound matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points to 3-space and projecting back the lower convex hull), where (n−3)-vertex connectivity has been known since the late eighties through the secondary polytope due to Gelfand, Kapranov, & Zelevinsky and Balinski’s Theorem. For the edge flip-graph, we additionally show that the vertex connectivity is at least as large as (and hence equal to) the minimum degree (i.e., the minimum number of flippable edges in any full triangulation), provided that n is large enough. Our methods also yield several other results: (i) The edge flip graph can be covered by graphs of polytopes of dimension ⌈n/2−2⌉ (products of associahedra) and the bistellar flip graph can be covered by graphs of polytopes of dimension n−3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n−3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations of a point set are regular iff the partial order of partial subdivisions has height n−3. (iv) There are arbitrarily large sets P with non-regular partial triangulations and such that every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular triangulations."}],"publication_status":"published","ddc":["510"],"date_published":"2022-11-14T00:00:00Z","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"11","doi":"10.1007/s00454-022-00436-2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"4","oa_version":"Published Version","date_updated":"2025-07-10T11:54:56Z","language":[{"iso":"eng"}],"oa":1,"day":"14","corr_author":"1","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2023-01-23T11:10:03Z","creator":"dernst","access_level":"open_access","success":1,"file_name":"2022_DiscreteCompGeometry_Wagner.pdf","file_size":1747581,"date_created":"2023-01-23T11:10:03Z","file_id":"12345","checksum":"307e879d09e52eddf5b225d0aaa9213a"}],"page":"1227-1284","related_material":{"record":[{"id":"7807","status":"public","relation":"earlier_version"},{"relation":"earlier_version","id":"7990","status":"public"}]},"external_id":{"isi":["000883222200003"]},"title":"Connectivity of triangulation flip graphs in the plane","article_type":"original","volume":68,"year":"2022","publication":"Discrete & Computational Geometry","date_created":"2023-01-12T12:02:28Z","acknowledgement":"This is a full and revised version of [38] (on partial triangulations) in Proceedings of the 36th Annual International Symposium on Computational Geometry (SoCG‘20) and of some of the results in [37] (on full triangulations) in Proceedings of the 31st Annual ACM-SIAM Symposium on Discrete Algorithms (SODA‘20).\r\nThis research started at the 11th Gremo’s Workshop on Open Problems (GWOP), Alp Sellamatt, Switzerland, June 24–28, 2013, motivated by a question posed by Filip Mori´c on full triangulations. Research was supported by the Swiss National Science Foundation within the collaborative DACH project Arrangements and Drawings as SNSF Project 200021E-171681, and by IST Austria and Berlin Free University during a sabbatical stay of the second author. We thank Michael Joswig, Jesús De Loera, and Francisco Santos for helpful discussions on the topics of this paper, and Daniel Bertschinger and Valentin Stoppiello for carefully reading earlier versions and for many helpful comments.\r\nOpen access funding provided by the Swiss Federal Institute of Technology Zürich","article_processing_charge":"No","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"department":[{"_id":"UlWa"}],"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","citation":{"ama":"Wagner U, Welzl E. Connectivity of triangulation flip graphs in the plane. <i>Discrete &#38; Computational Geometry</i>. 2022;68(4):1227-1284. doi:<a href=\"https://doi.org/10.1007/s00454-022-00436-2\">10.1007/s00454-022-00436-2</a>","ieee":"U. Wagner and E. Welzl, “Connectivity of triangulation flip graphs in the plane,” <i>Discrete &#38; Computational Geometry</i>, vol. 68, no. 4. Springer Nature, pp. 1227–1284, 2022.","mla":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane.” <i>Discrete &#38; Computational Geometry</i>, vol. 68, no. 4, Springer Nature, 2022, pp. 1227–84, doi:<a href=\"https://doi.org/10.1007/s00454-022-00436-2\">10.1007/s00454-022-00436-2</a>.","ista":"Wagner U, Welzl E. 2022. Connectivity of triangulation flip graphs in the plane. Discrete &#38; Computational Geometry. 68(4), 1227–1284.","chicago":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-022-00436-2\">https://doi.org/10.1007/s00454-022-00436-2</a>.","apa":"Wagner, U., &#38; Welzl, E. (2022). Connectivity of triangulation flip graphs in the plane. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00436-2\">https://doi.org/10.1007/s00454-022-00436-2</a>","short":"U. Wagner, E. Welzl, Discrete &#38; Computational Geometry 68 (2022) 1227–1284."},"keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"author":[{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"},{"full_name":"Welzl, Emo","last_name":"Welzl","first_name":"Emo"}],"_id":"12129","file_date_updated":"2023-01-23T11:10:03Z","intvolume":"        68","publisher":"Springer Nature","type":"journal_article","isi":1},{"ddc":["580"],"publication_status":"published","abstract":[{"lang":"eng","text":"Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants."}],"status":"public","date_published":"2022-11-15T00:00:00Z","month":"11","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1038/s41467-022-34723-6","date_updated":"2025-07-08T09:01:02Z","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"day":"15","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2023-01-23T11:17:33Z","content_type":"application/pdf","relation":"main_file","checksum":"233922a7b9507d9d48591e6799e4526e","date_created":"2023-01-23T11:17:33Z","file_id":"12346","success":1,"file_name":"2022_NatureCommunications_Huang.pdf","file_size":3375249}],"publication":"Nature Communications","year":"2022","volume":13,"article_type":"original","title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","external_id":{"pmid":["36379956"],"isi":["000884426700001"]},"publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"No","date_created":"2023-01-12T12:02:41Z","acknowledgement":"We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari for critically reading the manuscript; E. Xiong and G. Zhang for preparing some experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1 cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP, pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP spl and pin1-5 seeds. This work was supported by the US National Science Foundation (NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796) and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist Award from the Greater Milwaukee Foundation, USDA National Institute of Food and Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System Applied Research Funding Programs.","department":[{"_id":"JiFr"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"citation":{"chicago":"Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>.","short":"J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022).","apa":"Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>","ama":"Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>","ista":"Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J, Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 13, 6960.","ieee":"J. Huang <i>et al.</i>, “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","mla":"Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>, vol. 13, 6960, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>."},"scopus_import":"1","quality_controlled":"1","article_number":"6960","has_accepted_license":"1","file_date_updated":"2023-01-23T11:17:33Z","_id":"12130","author":[{"last_name":"Huang","first_name":"Jian","full_name":"Huang, Jian"},{"first_name":"Lei","last_name":"Zhao","full_name":"Zhao, Lei"},{"full_name":"Malik, Shikha","last_name":"Malik","first_name":"Shikha"},{"full_name":"Gentile, Benjamin R.","first_name":"Benjamin R.","last_name":"Gentile"},{"full_name":"Xiong, Va","first_name":"Va","last_name":"Xiong"},{"full_name":"Arazi, Tzahi","first_name":"Tzahi","last_name":"Arazi"},{"first_name":"Heather A.","last_name":"Owen","full_name":"Owen, Heather A."},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"Dazhong","last_name":"Zhao","full_name":"Zhao, Dazhong"}],"publisher":"Springer Nature","intvolume":"        13","isi":1,"type":"journal_article"},{"language":[{"iso":"eng"}],"oa":1,"date_updated":"2023-08-04T08:52:40Z","oa_version":"Published Version","file":[{"success":1,"file_name":"2022_njpVaccines_Byazrova.pdf","file_size":1856046,"checksum":"ddaac096381565b2b4b7dcc34cdbc4ee","date_created":"2023-01-23T11:22:09Z","file_id":"12347","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2023-01-23T11:22:09Z"}],"day":"15","date_published":"2022-11-15T00:00:00Z","status":"public","ddc":["570"],"publication_status":"published","abstract":[{"text":"Replication-incompetent adenoviral vectors have been extensively used as a platform for vaccine design, with at least four anti-COVID-19 vaccines authorized to date. These vaccines elicit neutralizing antibody responses directed against SARS-CoV-2 Spike protein and confer significant level of protection against SARS-CoV-2 infection. Immunization with adenovirus-vectored vaccines is known to be accompanied by the production of anti-vector antibodies, which may translate into reduced efficacy of booster or repeated rounds of revaccination. Here, we used blood samples from patients who received an adenovirus-based Gam-COVID-Vac vaccine to address the question of whether anti-vector antibodies may influence the magnitude of SARS-CoV-2-specific humoral response after booster vaccination. We observed that rAd26-based prime vaccination with Gam-COVID-Vac induced the development of Ad26-neutralizing antibodies, which persisted in circulation for at least 9 months. Our analysis further indicates that high pre-boost Ad26 neutralizing antibody titers do not appear to affect the humoral immunogenicity of the Gam-COVID-Vac boost. The titers of anti-SARS-CoV-2 RBD IgGs and antibodies, which neutralized both the wild type and the circulating variants of concern of SARS-CoV-2 such as Delta and Omicron, were independent of the pre-boost levels of Ad26-neutralizing antibodies. Thus, our results support the development of repeated immunization schedule with adenovirus-based COVID-19 vaccines.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41541-022-00566-x","pmid":1,"month":"11","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-01-23T11:22:09Z","_id":"12131","author":[{"last_name":"Byazrova","first_name":"Maria G.","full_name":"Byazrova, Maria G."},{"first_name":"Ekaterina A.","last_name":"Astakhova","full_name":"Astakhova, Ekaterina A."},{"full_name":"Minnegalieva, Aygul","first_name":"Aygul","id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","last_name":"Minnegalieva"},{"full_name":"Sukhova, Maria M.","first_name":"Maria M.","last_name":"Sukhova"},{"full_name":"Mikhailov, Artem A.","first_name":"Artem A.","last_name":"Mikhailov"},{"full_name":"Prilipov, Alexey G.","first_name":"Alexey G.","last_name":"Prilipov"},{"last_name":"Gorchakov","first_name":"Andrey A.","full_name":"Gorchakov, Andrey A."},{"first_name":"Alexander V.","last_name":"Filatov","full_name":"Filatov, Alexander V."}],"article_number":"145","quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","keyword":["Pharmacology (medical)","Infectious Diseases","Pharmacology","Immunology","SARS-COV-2","COVID"],"citation":{"ista":"Byazrova MG, Astakhova EA, Minnegalieva A, Sukhova MM, Mikhailov AA, Prilipov AG, Gorchakov AA, Filatov AV. 2022. Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. npj Vaccines. 7, 145.","mla":"Byazrova, Maria G., et al. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.” <i>Npj Vaccines</i>, vol. 7, 145, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41541-022-00566-x\">10.1038/s41541-022-00566-x</a>.","ieee":"M. G. Byazrova <i>et al.</i>, “Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination,” <i>npj Vaccines</i>, vol. 7. Springer Nature, 2022.","ama":"Byazrova MG, Astakhova EA, Minnegalieva A, et al. Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. <i>npj Vaccines</i>. 2022;7. doi:<a href=\"https://doi.org/10.1038/s41541-022-00566-x\">10.1038/s41541-022-00566-x</a>","apa":"Byazrova, M. G., Astakhova, E. A., Minnegalieva, A., Sukhova, M. M., Mikhailov, A. A., Prilipov, A. G., … Filatov, A. V. (2022). Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. <i>Npj Vaccines</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41541-022-00566-x\">https://doi.org/10.1038/s41541-022-00566-x</a>","short":"M.G. Byazrova, E.A. Astakhova, A. Minnegalieva, M.M. Sukhova, A.A. Mikhailov, A.G. Prilipov, A.A. Gorchakov, A.V. Filatov, Npj Vaccines 7 (2022).","chicago":"Byazrova, Maria G., Ekaterina A. Astakhova, Aygul Minnegalieva, Maria M. Sukhova, Artem A. Mikhailov, Alexey G. Prilipov, Andrey A. Gorchakov, and Alexander V. Filatov. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.” <i>Npj Vaccines</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41541-022-00566-x\">https://doi.org/10.1038/s41541-022-00566-x</a>."},"isi":1,"type":"journal_article","intvolume":"         7","publisher":"Springer Nature","volume":7,"article_type":"original","external_id":{"pmid":["36379998"],"isi":["000884278600004"]},"title":"Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination","publication":"npj Vaccines","year":"2022","department":[{"_id":"FyKo"}],"article_processing_charge":"No","date_created":"2023-01-12T12:02:54Z","acknowledgement":"We thank Sergey Kulemzin, Grigory Efimov, Yuri Lebedin, Alexander Taranin and Rudolf Valenta for providing reagents. Figures were created with the help of BioRender.com. This work was supported by the Russian Science Foundation (Project 21-15-00286). Byazrova M.G. was supported by the RUDN University Strategic Academic Leadership Program.","publication_identifier":{"issn":["2059-0105"]}}]