[{"language":[{"iso":"eng"}],"publication_status":"published","pmid":1,"citation":{"ista":"Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2022. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233(1), 329–343.","mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist, vol. 233, no. 1, Wiley, 2022, pp. 329–43, doi:10.1111/nph.17792.","chicago":"Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist. Wiley, 2022. https://doi.org/10.1111/nph.17792.","apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2022). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.17792","short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2022) 329–343.","ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 2022;233(1):329-343. doi:10.1111/nph.17792","ieee":"I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New Phytologist, vol. 233, no. 1. Wiley, pp. 329–343, 2022."},"oa":1,"external_id":{"pmid":["34637542"],"isi":["000714678100001"]},"isi":1,"page":"329-343","intvolume":" 233","date_created":"2021-11-14T23:01:24Z","acknowledgement":"We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests.","article_processing_charge":"No","volume":233,"publisher":"Wiley","type":"journal_article","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"oa_version":"Preprint","doi":"10.1111/nph.17792","date_published":"2022-01-01T00:00:00Z","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","issue":"1","date_updated":"2024-05-22T11:33:15Z","quality_controlled":"1","article_type":"original","author":[{"last_name":"Kashkan","first_name":"Ivan","full_name":"Kashkan, Ivan"},{"last_name":"Hrtyan","full_name":"Hrtyan, Mónika","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Retzer","full_name":"Retzer, Katarzyna","first_name":"Katarzyna"},{"first_name":"Jana","full_name":"Humpolíčková, Jana","last_name":"Humpolíčková"},{"last_name":"Jayasree","full_name":"Jayasree, Aswathy","first_name":"Aswathy"},{"first_name":"Roberta","full_name":"Filepová, Roberta","last_name":"Filepová"},{"last_name":"Vondráková","full_name":"Vondráková, Zuzana","first_name":"Zuzana"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","last_name":"Simon","first_name":"Sibu","full_name":"Simon, Sibu"},{"last_name":"Rombaut","first_name":"Debbie","full_name":"Rombaut, Debbie"},{"last_name":"Jacobs","full_name":"Jacobs, Thomas B.","first_name":"Thomas B."},{"first_name":"Mikko J.","full_name":"Frilander, Mikko J.","last_name":"Frilander"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"last_name":"Růžička","full_name":"Růžička, Kamil","first_name":"Kamil"}],"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2","open_access":"1"}],"year":"2022","_id":"10282","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development."}],"publication":"New Phytologist","month":"01"},{"issue":"1","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2022-01-01T00:00:00Z","doi":"10.1111/ele.13907","oa_version":"Published Version","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"01","publication":"Ecology Letters","abstract":[{"lang":"eng","text":"Infections early in life can have enduring effects on an organism's development and immunity. In this study, we show that this equally applies to developing ‘superorganisms’––incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen's immune system to suppress pathogen proliferation. Early-life queen pathogen exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen's pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism."}],"department":[{"_id":"SyCr"}],"license":"https://creativecommons.org/licenses/by/4.0/","related_material":{"record":[{"id":"13061","status":"public","relation":"research_data"}]},"_id":"10284","year":"2022","file_date_updated":"2022-02-03T13:37:11Z","scopus_import":"1","author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"},{"orcid":"0000-0003-1122-3982","last_name":"Pull","full_name":"Pull, Christopher","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Naiser","full_name":"Naiser, Filip","first_name":"Filip"},{"last_name":"Naderlinger","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Matas","first_name":"Jiri","full_name":"Matas, Jiri"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","quality_controlled":"1","file":[{"access_level":"open_access","date_updated":"2022-02-03T13:37:11Z","file_name":"2021_EcologyLetters_CasillasPerez.pdf","file_size":700087,"file_id":"10721","content_type":"application/pdf","creator":"cchlebak","success":1,"relation":"main_file","date_created":"2022-02-03T13:37:11Z","checksum":"0bd4210400e9876609b7c538ab4f9a3c"}],"date_updated":"2025-04-14T13:55:31Z","corr_author":"1","page":"89-100","isi":1,"external_id":{"isi":["000713396100001"],"pmid":["34725912"]},"oa":1,"citation":{"ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2022. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Ecology Letters. 25(1), 89–100.","mla":"Casillas Perez, Barbara E., et al. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Ecology Letters, vol. 25, no. 1, Wiley, 2022, pp. 89–100, doi:10.1111/ele.13907.","chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Ecology Letters. Wiley, 2022. https://doi.org/10.1111/ele.13907.","apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., & Cremer, S. (2022). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13907","ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies,” Ecology Letters, vol. 25, no. 1. Wiley, pp. 89–100, 2022.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, Ecology Letters 25 (2022) 89–100.","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Ecology Letters. 2022;25(1):89-100. doi:10.1111/ele.13907"},"publication_status":"published","language":[{"iso":"eng"}],"pmid":1,"article_processing_charge":"Yes (via OA deal)","publisher":"Wiley","ec_funded":1,"volume":25,"type":"journal_article","acknowledgement":"The authors are grateful to G. Tkačik and V. Mireles for advice on data analyses and to A. Schloegl for help using the IST Austria HPC cluster for data processing. The authors thank J. Eilenberg for providing the fungal strain and A.V. Grasse for support with the molecular analysis. The authors also thank the Social Immunity group at IST Austria, in particular B. Milutinović, for discussions throughout and comments on the manuscript.","has_accepted_license":"1","date_created":"2021-11-14T23:01:25Z","ddc":["573"],"project":[{"grant_number":"771402","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"intvolume":" 25"},{"date_created":"2021-11-25T13:49:16Z","type":"journal_article","volume":42,"article_processing_charge":"No","publisher":"Springer Nature","acknowledgement":"V. K. gratefully acknowledges the support of Austrian Science Fund (FWF): P 30902-N35. This work was done mostly while he was employed at the University of Innsbruck. During the early stage of this research, V. K. was partially supported by Charles University project GAUK 926416. M. T. is supported by the grant no. 19-04113Y of the Czech Science Foundation(GA ˇCR) and partially supported by Charles University project UNCE/SCI/004.","ddc":["514","516"],"intvolume":" 42","external_id":{"isi":["000798210100003"],"arxiv":["1907.05055"]},"oa":1,"isi":1,"page":"1317-1345","language":[{"iso":"eng"}],"publication_status":"published","citation":{"ieee":"V. Kaluza and M. Tancer, “Even maps, the Colin de Verdière number and representations of graphs,” Combinatorica, vol. 42. Springer Nature, pp. 1317–1345, 2022.","short":"V. Kaluza, M. Tancer, Combinatorica 42 (2022) 1317–1345.","ama":"Kaluza V, Tancer M. Even maps, the Colin de Verdière number and representations of graphs. Combinatorica. 2022;42:1317-1345. doi:10.1007/s00493-021-4443-7","ista":"Kaluza V, Tancer M. 2022. Even maps, the Colin de Verdière number and representations of graphs. Combinatorica. 42, 1317–1345.","chicago":"Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” Combinatorica. Springer Nature, 2022. https://doi.org/10.1007/s00493-021-4443-7.","apa":"Kaluza, V., & Tancer, M. (2022). Even maps, the Colin de Verdière number and representations of graphs. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-021-4443-7","mla":"Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” Combinatorica, vol. 42, Springer Nature, 2022, pp. 1317–45, doi:10.1007/s00493-021-4443-7."},"arxiv":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1907.05055","open_access":"1"}],"year":"2022","scopus_import":"1","_id":"10335","department":[{"_id":"UlWa"}],"month":"12","publication":"Combinatorica","abstract":[{"text":"Van der Holst and Pendavingh introduced a graph parameter σ, which coincides with the more famous Colin de Verdière graph parameter μ for small values. However, the definition of a is much more geometric/topological directly reflecting embeddability properties of the graph. They proved μ(G) ≤ σ(G) + 2 and conjectured σ(G) ≤ σ(G) for any graph G. We confirm this conjecture. As far as we know, this is the first topological upper bound on σ(G) which is, in general, tight.\r\nEquality between μ and σ does not hold in general as van der Holst and Pendavingh showed that there is a graph G with μ(G) ≤ 18 and σ(G) ≥ 20. We show that the gap appears at much smaller values, namely, we exhibit a graph H for which μ(H) ≥ 7 and σ(H) ≥ 8. We also prove that, in general, the gap can be large: The incidence graphs Hq of finite projective planes of order q satisfy μ(Hq) ∈ O(q3/2) and σ(Hq) ≥ q2.","lang":"eng"}],"corr_author":"1","date_updated":"2024-10-09T20:53:51Z","author":[{"first_name":"Vojtech","full_name":"Kaluza, Vojtech","last_name":"Kaluza","orcid":"0000-0002-2512-8698","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E"},{"orcid":"0000-0002-1191-6714","last_name":"Tancer","full_name":"Tancer, Martin","first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","quality_controlled":"1","oa_version":"Preprint","date_published":"2022-12-01T00:00:00Z","doi":"10.1007/s00493-021-4443-7","day":"01","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Even maps, the Colin de Verdière number and representations of graphs","publication_identifier":{"issn":["0209-9683"]}},{"oa_version":"Preprint","doi":"10.1109/TWC.2021.3125626","date_published":"2022-06-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","issue":"6","title":"Parallelism versus latency in simplified successive-cancellation decoding of polar codes","publication_identifier":{"issn":["1536-1276"],"eissn":["1558-2248"]},"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2012.13378","open_access":"1"}],"year":"2022","_id":"10364","related_material":{"record":[{"status":"public","id":"10053","relation":"earlier_version"}]},"department":[{"_id":"MaMo"}],"abstract":[{"lang":"eng","text":"This paper characterizes the latency of the simplified successive-cancellation (SSC) decoding scheme for polar codes under hardware resource constraints. In particular, when the number of processing elements P that can perform SSC decoding operations in parallel is limited, as is the case in practice, the latency of SSC decoding is O(N1-1/μ + N/P log2 log2 N/P), where N is the block length of the code and μ is the scaling exponent of the channel. Three direct consequences of this bound are presented. First, in a fully-parallel implementation where P = N/2, the latency of SSC decoding is O(N1-1/μ), which is sublinear in the block length. This recovers a result from our earlier work. Second, in a fully-serial implementation where P = 1, the latency of SSC decoding scales as O(N log2 log2 N). The multiplicative constant is also calculated: we show that the latency of SSC decoding when P = 1 is given by (2 + o(1))N log2 log2 N. Third, in a semi-parallel implementation, the smallest P that gives the same latency as that of the fully-parallel implementation is P = N1/μ. The tightness of our bound on SSC decoding latency and the applicability of the foregoing results is validated through extensive simulations."}],"month":"06","publication":"IEEE Transactions on Wireless Communications","date_updated":"2025-04-15T07:50:11Z","article_type":"original","quality_controlled":"1","author":[{"last_name":"Hashemi","full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali"},{"last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"last_name":"Fazeli","first_name":"Arman","full_name":"Fazeli, Arman"},{"first_name":"Alexander","full_name":"Vardy, Alexander","last_name":"Vardy"},{"full_name":"Cioffi, John","first_name":"John","last_name":"Cioffi"},{"last_name":"Goldsmith","first_name":"Andrea","full_name":"Goldsmith, Andrea"}],"external_id":{"isi":["000809406400028"],"arxiv":["2012.13378"]},"oa":1,"isi":1,"page":"3909-3920","publication_status":"published","language":[{"iso":"eng"}],"citation":{"chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” IEEE Transactions on Wireless Communications. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/TWC.2021.3125626.","apa":"Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., & Goldsmith, A. (2022). Parallelism versus latency in simplified successive-cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TWC.2021.3125626","mla":"Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” IEEE Transactions on Wireless Communications, vol. 21, no. 6, Institute of Electrical and Electronics Engineers, 2022, pp. 3909–20, doi:10.1109/TWC.2021.3125626.","ista":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2022. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 21(6), 3909–3920.","ama":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 2022;21(6):3909-3920. doi:10.1109/TWC.2021.3125626","short":"S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 21 (2022) 3909–3920.","ieee":"S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith, “Parallelism versus latency in simplified successive-cancellation decoding of polar codes,” IEEE Transactions on Wireless Communications, vol. 21, no. 6. Institute of Electrical and Electronics Engineers, pp. 3909–3920, 2022."},"arxiv":1,"date_created":"2021-11-28T23:01:29Z","acknowledgement":"S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC) and by Huawei. M. Mondelli is partially\r\nsupported by the 2019 Lopez-Loreta Prize. A. Fazeli and A. Vardy were supported in part by\r\nthe National Science Foundation under Grant CCF-1764104.","publisher":"Institute of Electrical and Electronics Engineers","article_processing_charge":"No","volume":21,"type":"journal_article","intvolume":" 21","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}]},{"citation":{"ieee":"D. Dikranjan, A. Giordano Bruno, H. P. Künzi, N. Zava, and D. Toller, “Generalized quasi-metric semilattices,” Topology and its Applications, vol. 309. Elsevier, 2022.","ama":"Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. Generalized quasi-metric semilattices. Topology and its Applications. 2022;309. doi:10.1016/j.topol.2021.107916","short":"D. Dikranjan, A. Giordano Bruno, H.P. Künzi, N. Zava, D. Toller, Topology and Its Applications 309 (2022).","mla":"Dikranjan, Dikran, et al. “Generalized Quasi-Metric Semilattices.” Topology and Its Applications, vol. 309, 107916, Elsevier, 2022, doi:10.1016/j.topol.2021.107916.","chicago":"Dikranjan, Dikran, Anna Giordano Bruno, Hans Peter Künzi, Nicolò Zava, and Daniele Toller. “Generalized Quasi-Metric Semilattices.” Topology and Its Applications. Elsevier, 2022. https://doi.org/10.1016/j.topol.2021.107916.","apa":"Dikranjan, D., Giordano Bruno, A., Künzi, H. P., Zava, N., & Toller, D. (2022). Generalized quasi-metric semilattices. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2021.107916","ista":"Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. 2022. Generalized quasi-metric semilattices. Topology and its Applications. 309, 107916."},"publication_status":"published","language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["000791838800012"]},"article_number":"107916","intvolume":" 309","article_processing_charge":"No","publisher":"Elsevier","volume":309,"type":"journal_article","acknowledgement":"Dedicated to the memory of Hans-Peter Künzi.","date_created":"2021-12-05T23:01:44Z","publication_identifier":{"issn":["0166-8641"]},"title":"Generalized quasi-metric semilattices","day":"15","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-03-15T00:00:00Z","doi":"10.1016/j.topol.2021.107916","oa_version":"None","author":[{"full_name":"Dikranjan, Dikran","first_name":"Dikran","last_name":"Dikranjan"},{"first_name":"Anna","full_name":"Giordano Bruno, Anna","last_name":"Giordano Bruno"},{"last_name":"Künzi","first_name":"Hans Peter","full_name":"Künzi, Hans Peter"},{"id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","full_name":"Zava, Nicolò","first_name":"Nicolò","last_name":"Zava","orcid":"0000-0001-8686-1888"},{"full_name":"Toller, Daniele","first_name":"Daniele","last_name":"Toller"}],"quality_controlled":"1","article_type":"original","date_updated":"2024-10-09T21:01:16Z","corr_author":"1","month":"03","publication":"Topology and its Applications","abstract":[{"lang":"eng","text":"Motivated by the recent introduction of the intrinsic semilattice entropy, we study generalized quasi-metric semilattices and their categories. We investigate the relationship between these objects and generalized semivaluations, extending Nakamura and Schellekens' approach. Finally, we use this correspondence to compare the intrinsic semilattice entropy and the semigroup entropy induced in particular situations, like sets, torsion abelian groups and vector spaces."}],"department":[{"_id":"HeEd"}],"_id":"10413","year":"2022","scopus_import":"1"},{"issue":"1","day":"04","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-01-04T00:00:00Z","doi":"10.1016/j.bpj.2021.12.006","oa_version":"Published Version","publication_identifier":{"issn":["0006-3495"]},"title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"month":"01","publication":"Biophysical Journal","abstract":[{"text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n","lang":"eng"}],"department":[{"_id":"EdHa"},{"_id":"GaTk"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"10530","year":"2022","scopus_import":"1","file_date_updated":"2022-07-29T10:17:10Z","author":[{"first_name":"Themistoklis","full_name":"Zisis, Themistoklis","last_name":"Zisis"},{"orcid":"0000-0001-7205-2975","last_name":"Brückner","full_name":"Brückner, David","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"last_name":"Brandstätter","first_name":"Tom","full_name":"Brandstätter, Tom"},{"last_name":"Siow","full_name":"Siow, Wei Xiong","first_name":"Wei Xiong"},{"full_name":"d’Alessandro, Joseph","first_name":"Joseph","last_name":"d’Alessandro"},{"first_name":"Angelika M.","full_name":"Vollmar, Angelika M.","last_name":"Vollmar"},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."},{"last_name":"Zahler","first_name":"Stefan","full_name":"Zahler, Stefan"}],"file":[{"date_updated":"2022-07-29T10:17:10Z","access_level":"open_access","file_name":"2022_BiophysicalJour_Zisis.pdf","file_size":4475504,"creator":"dernst","content_type":"application/pdf","file_id":"11697","date_created":"2022-07-29T10:17:10Z","relation":"main_file","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","success":1}],"quality_controlled":"1","article_type":"original","date_updated":"2025-06-11T13:59:29Z","page":"P44-60","keyword":["Biophysics"],"isi":1,"oa":1,"external_id":{"isi":["000740815400007"],"pmid":["34890578"]},"citation":{"short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.","ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 2022;121(1):P44-60. doi:10.1016/j.bpj.2021.12.006","ieee":"T. Zisis et al., “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” Biophysical Journal, vol. 121, no. 1. Elsevier, pp. P44-60, 2022.","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.","mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” Biophysical Journal, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:10.1016/j.bpj.2021.12.006.","chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” Biophysical Journal. Elsevier, 2022. https://doi.org/10.1016/j.bpj.2021.12.006.","apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2021.12.006"},"language":[{"iso":"eng"}],"pmid":1,"publication_status":"published","article_processing_charge":"No","volume":121,"publisher":"Elsevier","type":"journal_article","acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","has_accepted_license":"1","date_created":"2021-12-10T09:48:19Z","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"ddc":["570"],"intvolume":" 121"},{"publication_identifier":{"issn":["1424-0637"]},"title":"Bosonization of fermionic many-body dynamics","doi":"10.1007/s00023-021-01136-y","date_published":"2022-05-01T00:00:00Z","oa_version":"Preprint","issue":"5","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","day":"01","article_type":"original","quality_controlled":"1","author":[{"orcid":"0000-0002-1071-6091","last_name":"Benedikter","first_name":"Niels P","full_name":"Benedikter, Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nam","first_name":"Phan Thành","full_name":"Nam, Phan Thành"},{"first_name":"Marcello","full_name":"Porta, Marcello","last_name":"Porta"},{"last_name":"Schlein","first_name":"Benjamin","full_name":"Schlein, Benjamin"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-04-14T07:26:53Z","_id":"10537","scopus_import":"1","year":"2022","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.08224"}],"abstract":[{"lang":"eng","text":"We consider the quantum many-body evolution of a homogeneous Fermi gas in three dimensions in the coupled semiclassical and mean-field scaling regime. We study a class of initial data describing collective particle–hole pair excitations on the Fermi ball. Using a rigorous version of approximate bosonization, we prove that the many-body evolution can be approximated in Fock space norm by a quasi-free bosonic evolution of the collective particle–hole excitations."}],"month":"05","publication":"Annales Henri Poincaré","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"publication_status":"published","arxiv":1,"citation":{"ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2022. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. 23(5), 1725–1764.","mla":"Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré, vol. 23, no. 5, Springer Nature, 2022, pp. 1725–64, doi:10.1007/s00023-021-01136-y.","chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré. Springer Nature, 2022. https://doi.org/10.1007/s00023-021-01136-y.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R. (2022). Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. Springer Nature. https://doi.org/10.1007/s00023-021-01136-y","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré 23 (2022) 1725–1764.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. 2022;23(5):1725-1764. doi:10.1007/s00023-021-01136-y","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization of fermionic many-body dynamics,” Annales Henri Poincaré, vol. 23, no. 5. Springer Nature, pp. 1725–1764, 2022."},"isi":1,"external_id":{"arxiv":["2103.08224"],"isi":["000725405700001"]},"oa":1,"page":"1725-1764","intvolume":" 23","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"}],"date_created":"2021-12-12T23:01:28Z","acknowledgement":"NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM). RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates,” and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program through the ERC-AdG CLaQS (Grant Agreement No. 834782).","ec_funded":1,"volume":23,"publisher":"Springer Nature","article_processing_charge":"No","type":"journal_article"},{"language":[{"iso":"eng"}],"publication_status":"published","arxiv":1,"citation":{"mla":"Fischer, Julian L., et al. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” SIAM Journal on Mathematical Analysis, vol. 54, no. 1, Society for Industrial and Applied Mathematics, 2022, pp. 220–67, doi:10.1137/20M1387237.","chicago":"Fischer, Julian L, Katharina Hopf, Michael Kniely, and Alexander Mielke. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2022. https://doi.org/10.1137/20M1387237.","apa":"Fischer, J. L., Hopf, K., Kniely, M., & Mielke, A. (2022). Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1387237","ista":"Fischer JL, Hopf K, Kniely M, Mielke A. 2022. Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. 54(1), 220–267.","ieee":"J. L. Fischer, K. Hopf, M. Kniely, and A. Mielke, “Global existence analysis of energy-reaction-diffusion systems,” SIAM Journal on Mathematical Analysis, vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 220–267, 2022.","ama":"Fischer JL, Hopf K, Kniely M, Mielke A. Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. 2022;54(1):220-267. doi:10.1137/20M1387237","short":"J.L. Fischer, K. Hopf, M. Kniely, A. Mielke, SIAM Journal on Mathematical Analysis 54 (2022) 220–267."},"isi":1,"external_id":{"arxiv":["2012.03792 "],"isi":["000762768000006"]},"oa":1,"page":"220-267","keyword":["Energy-Reaction-Diffusion Systems","Cross Diffusion","Global-In-Time Existence of Weak/Renormalised Solutions","Entropy Method","Onsager System","Soret/Dufour Effect"],"intvolume":" 54","date_created":"2021-12-16T12:08:56Z","acknowledgement":"M.K. gratefully acknowledges the hospitality of WIAS Berlin, where a major part of the project was carried out. The research stay of M.K. at WIAS Berlin was funded by the Austrian Federal Ministry of Education, Science and Research through a research fellowship for graduates of a promotio sub auspiciis. The research of A.M. has been partially supported by Deutsche Forschungsgemeinschaft (DFG) through the Collaborative Research Center SFB 1114 “Scaling Cascades in Complex Systems” (Project no. 235221301), Subproject C05 “Effective models for materials and interfaces with multiple scales”. J.F. and A.M. are grateful for the hospitality of the Erwin Schrödinger Institute in Vienna, where some ideas for this work have been developed. The authors are grateful to two anonymous referees for several helpful comments, in particular for the short proof of estimate (2.7).","type":"journal_article","publisher":"Society for Industrial and Applied Mathematics","article_processing_charge":"No","volume":54,"publication_identifier":{"issn":["0036-1410"]},"title":"Global existence analysis of energy-reaction-diffusion systems","doi":"10.1137/20M1387237","date_published":"2022-01-04T00:00:00Z","oa_version":"Preprint","issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","day":"04","quality_controlled":"1","article_type":"original","author":[{"full_name":"Fischer, Julian L","first_name":"Julian L","last_name":"Fischer","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hopf","full_name":"Hopf, Katharina","first_name":"Katharina"},{"id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","full_name":"Kniely, Michael","first_name":"Michael","orcid":"0000-0001-5645-4333"},{"first_name":"Alexander","full_name":"Mielke, Alexander","last_name":"Mielke"}],"date_updated":"2023-08-02T13:37:03Z","_id":"10547","scopus_import":"1","year":"2022","main_file_link":[{"url":"https://arxiv.org/abs/2012.03792","open_access":"1"}],"abstract":[{"text":"We establish global-in-time existence results for thermodynamically consistent reaction-(cross-)diffusion systems coupled to an equation describing heat transfer. Our main interest is to model species-dependent diffusivities,\r\nwhile at the same time ensuring thermodynamic consistency. A key difficulty of the non-isothermal case lies in the intrinsic presence of cross-diffusion type phenomena like the Soret and the Dufour effect: due to the temperature/energy dependence of the thermodynamic equilibria, a nonvanishing temperature gradient may drive a concentration flux even in a situation with constant concentrations; likewise, a nonvanishing concentration gradient may drive a heat flux even in a case of spatially constant temperature. We use time discretisation and regularisation techniques and derive a priori estimates based on a suitable entropy and the associated entropy production. Renormalised solutions are used in cases where non-integrable diffusion fluxes or reaction terms appear.","lang":"eng"}],"month":"01","publication":"SIAM Journal on Mathematical Analysis","department":[{"_id":"JuFi"}]},{"volume":32,"type":"journal_article","publisher":"Institute of Mathematical Statistics","article_processing_charge":"No","acknowledgement":"The authors thank Ivan Nourdin and Felix Otto for inspiring discussions. The work of MD is financially supported by the CNRS-Momentum program. Financial support of AG is acknowledged from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2014-2019 Grant Agreement QUANTHOM 335410).","date_created":"2021-12-16T12:10:16Z","intvolume":" 32","page":"1179-1209","isi":1,"external_id":{"arxiv":["1910.04088"],"isi":["000791003700011"]},"oa":1,"arxiv":1,"citation":{"short":"M. Duerinckx, J.L. Fischer, A. Gloria, Annals of Applied Probability 32 (2022) 1179–1209.","ama":"Duerinckx M, Fischer JL, Gloria A. Scaling limit of the homogenization commutator for Gaussian coefficient fields. Annals of applied probability. 2022;32(2):1179-1209. doi:10.1214/21-AAP1705","ieee":"M. Duerinckx, J. L. Fischer, and A. Gloria, “Scaling limit of the homogenization commutator for Gaussian coefficient fields,” Annals of applied probability, vol. 32, no. 2. Institute of Mathematical Statistics, pp. 1179–1209, 2022.","ista":"Duerinckx M, Fischer JL, Gloria A. 2022. Scaling limit of the homogenization commutator for Gaussian coefficient fields. Annals of applied probability. 32(2), 1179–1209.","chicago":"Duerinckx, Mitia, Julian L Fischer, and Antoine Gloria. “Scaling Limit of the Homogenization Commutator for Gaussian Coefficient Fields.” Annals of Applied Probability. Institute of Mathematical Statistics, 2022. https://doi.org/10.1214/21-AAP1705.","apa":"Duerinckx, M., Fischer, J. L., & Gloria, A. (2022). Scaling limit of the homogenization commutator for Gaussian coefficient fields. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-AAP1705","mla":"Duerinckx, Mitia, et al. “Scaling Limit of the Homogenization Commutator for Gaussian Coefficient Fields.” Annals of Applied Probability, vol. 32, no. 2, Institute of Mathematical Statistics, 2022, pp. 1179–209, doi:10.1214/21-AAP1705."},"publication_status":"published","language":[{"iso":"eng"}],"publication":"Annals of applied probability","month":"04","abstract":[{"lang":"eng","text":"Consider a linear elliptic partial differential equation in divergence form with a random coefficient field. The solution operator displays fluctuations around its expectation. The recently developed pathwise theory of fluctuations in stochastic homogenization reduces the characterization of these fluctuations to those of the so-called standard homogenization commutator. In this contribution, we investigate the scaling limit of this key quantity: starting\r\nfrom a Gaussian-like coefficient field with possibly strong correlations, we establish the convergence of the rescaled commutator to a fractional Gaussian field, depending on the decay of correlations of the coefficient field, and we\r\ninvestigate the (non)degeneracy of the limit. This extends to general dimension $d\\ge1$ previous results so far limited to dimension $d=1$, and to the continuum setting with strong correlations recent results in the discrete iid case."}],"department":[{"_id":"JuFi"}],"_id":"10548","main_file_link":[{"url":"https://arxiv.org/abs/1910.04088","open_access":"1"}],"year":"2022","scopus_import":"1","author":[{"last_name":"Duerinckx","first_name":"Mitia","full_name":"Duerinckx, Mitia"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","last_name":"Fischer","full_name":"Fischer, Julian L","first_name":"Julian L"},{"first_name":"Antoine","full_name":"Gloria, Antoine","last_name":"Gloria"}],"article_type":"original","quality_controlled":"1","date_updated":"2024-10-09T21:01:17Z","corr_author":"1","issue":"2","day":"28","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2022-04-28T00:00:00Z","doi":"10.1214/21-AAP1705","oa_version":"Preprint","publication_identifier":{"issn":["1050-5164"]},"title":"Scaling limit of the homogenization commutator for Gaussian coefficient fields"},{"citation":{"ista":"Shute AL. 2022. On the leading constant in the Manin-type conjecture for Campana points. Acta Arithmetica. 204(4), 317–346.","apa":"Shute, A. L. (2022). On the leading constant in the Manin-type conjecture for Campana points. Acta Arithmetica. Institute of Mathematics. https://doi.org/10.4064/aa210430-1-7","chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” Acta Arithmetica. Institute of Mathematics, 2022. https://doi.org/10.4064/aa210430-1-7.","mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” Acta Arithmetica, vol. 204, no. 4, Institute of Mathematics, 2022, pp. 317–46, doi:10.4064/aa210430-1-7.","short":"A.L. Shute, Acta Arithmetica 204 (2022) 317–346.","ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. Acta Arithmetica. 2022;204(4):317-346. doi:10.4064/aa210430-1-7","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” Acta Arithmetica, vol. 204, no. 4. Institute of Mathematics, pp. 317–346, 2022."},"arxiv":1,"language":[{"iso":"eng"}],"publication_status":"published","page":"317-346","oa":1,"external_id":{"isi":["000844789100001"],"arxiv":["2104.14946"]},"isi":1,"intvolume":" 204","article_processing_charge":"No","publisher":"Institute of Mathematics","type":"journal_article","volume":204,"date_created":"2024-05-28T13:39:26Z","title":"On the leading constant in the Manin-type conjecture for Campana points","publication_identifier":{"eissn":["1730-6264"],"issn":["0065-1036"]},"day":"22","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"4","oa_version":"Preprint","date_published":"2022-08-22T00:00:00Z","doi":"10.4064/aa210430-1-7","date_updated":"2025-09-10T09:57:03Z","author":[{"last_name":"Shute","full_name":"Shute, Alec L","first_name":"Alec L","orcid":"0000-0002-1812-2810","id":"440EB050-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","article_type":"original","corr_author":"1","department":[{"_id":"TiBr"}],"related_material":{"record":[{"id":"12077","status":"public","relation":"earlier_version"}]},"month":"08","publication":"Acta Arithmetica","abstract":[{"lang":"eng","text":"We compare the Manin-type conjecture for Campana points recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado with an alternative prediction of Browning and Van Valckenborgh in the special case of the orbifold (P1,D), where D=1/2[0]+1/2[1]+1/2[∞]. We find that the two predicted leading constants do not agree, and we discuss whether thin sets could explain this discrepancy. Motivated by this, we provide a counterexample to the Manin-type conjecture for Campana points, by considering orbifolds corresponding to squareful values of binary quadratic forms."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2104.14946","open_access":"1"}],"year":"2022","scopus_import":"1","_id":"17058"},{"oa_version":"Published Version","date_published":"2022-07-20T00:00:00Z","day":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"SPDY: Accurate pruning with speedup guarantees","year":"2022","scopus_import":"1","file_date_updated":"2024-08-19T06:54:41Z","_id":"17059","department":[{"_id":"DaAl"}],"publication":"39th International Conference on Machine Learning","month":"07","abstract":[{"lang":"eng","text":"The recent focus on the efficiency of deep neural networks (DNNs) has led to significant work on model compression approaches, of which weight pruning is one of the most popular. At the same time, there is rapidly-growing computational support for efficiently executing the unstructured-sparse models obtained via pruning. Yet, most existing pruning methods minimize just the number of remaining weights, i.e. the size of the model, rather than optimizing for inference time. We address this gap by introducing SPDY, a new compression method which automatically determines layer-wise sparsity targets achieving a desired inference speedup on a given system, while minimizing accuracy loss. SPDY is the composition of two new techniques. The first is an efficient and general dynamic programming algorithm for solving constrained layer-wise compression problems, given a set of layer-wise error scores. The second technique is a local search procedure for automatically determining such scores in an accurate and robust manner. Experiments across popular vision and language models show that SPDY guarantees speedups while recovering higher accuracy relative to existing strategies, both for one-shot and gradual pruning scenarios, and is compatible with most existing pruning approaches. We also extend our approach to the recently-proposed task of pruning with very little data, where we achieve the best known accuracy recovery when pruning to the GPU-supported 2:4 sparsity pattern."}],"corr_author":"1","date_updated":"2025-04-14T07:49:14Z","author":[{"id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias","first_name":"Elias","last_name":"Frantar"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"}],"file":[{"success":1,"checksum":"5179a1e4dfc0fbfab6674907299e414a","relation":"main_file","date_created":"2024-08-19T06:54:41Z","content_type":"application/pdf","file_id":"17440","creator":"dernst","file_size":615916,"file_name":"2022_PMLR_Frantar.pdf","access_level":"open_access","date_updated":"2024-08-19T06:54:41Z"}],"quality_controlled":"1","oa":1,"external_id":{"isi":["000922378801029"]},"alternative_title":["PMLR"],"conference":{"location":"Baltimore, MD, United States","end_date":"2022-07-23","name":"ICML: International Conference on Machine Learning","start_date":"2022-07-17"},"isi":1,"page":"6726-6743","language":[{"iso":"eng"}],"publication_status":"published","citation":{"ieee":"E. Frantar and D.-A. Alistarh, “SPDY: Accurate pruning with speedup guarantees,” in 39th International Conference on Machine Learning, Baltimore, MD, United States, 2022, vol. 162, pp. 6726–6743.","short":"E. Frantar, D.-A. Alistarh, in:, 39th International Conference on Machine Learning, ML Research Press, 2022, pp. 6726–6743.","ama":"Frantar E, Alistarh D-A. SPDY: Accurate pruning with speedup guarantees. In: 39th International Conference on Machine Learning. Vol 162. ML Research Press; 2022:6726-6743.","ista":"Frantar E, Alistarh D-A. 2022. SPDY: Accurate pruning with speedup guarantees. 39th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 162, 6726–6743.","mla":"Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with Speedup Guarantees.” 39th International Conference on Machine Learning, vol. 162, ML Research Press, 2022, pp. 6726–43.","chicago":"Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with Speedup Guarantees.” In 39th International Conference on Machine Learning, 162:6726–43. ML Research Press, 2022.","apa":"Frantar, E., & Alistarh, D.-A. (2022). SPDY: Accurate pruning with speedup guarantees. In 39th International Conference on Machine Learning (Vol. 162, pp. 6726–6743). Baltimore, MD, United States: ML Research Press."},"date_created":"2024-05-28T13:45:20Z","has_accepted_license":"1","volume":162,"publisher":"ML Research Press","article_processing_charge":"Yes","ec_funded":1,"type":"conference","acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement No 805223 ScaleML),\r\nas well as computational support from AWS EC2. We thank Eldar Kurtic for code and hyper-parameters for BERT pruning, and the Neural Magic Team, notably Michael Goin and\r\nMark Kurtz, for support with their software.","ddc":["000"],"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"intvolume":" 162"},{"page":"217-231","conference":{"location":"Cambridge, MA, United States","end_date":"2022-09-21","start_date":"2022-09-19","name":"AFT: Conference on Advances in Financial Technologies"},"isi":1,"external_id":{"isi":["001041852800015"],"arxiv":["2205.11597"]},"oa":1,"arxiv":1,"citation":{"chicago":"Tiwari, Samarth, Michelle X Yeo, Zeta Avarikioti, Iosif Salem, Krzysztof Z Pietrzak, and Stefan Schmid. “Wiser: Increasing Throughput in Payment Channel Networks with Transaction Aggregation.” In Proceedings of the 4th ACM Conference on Advances in Financial Technologies, 217–31. Association for Computing Machinery, 2022. https://doi.org/10.1145/3558535.3559775.","apa":"Tiwari, S., Yeo, M. X., Avarikioti, Z., Salem, I., Pietrzak, K. Z., & Schmid, S. (2022). Wiser: Increasing throughput in payment channel networks with transaction aggregation. In Proceedings of the 4th ACM Conference on Advances in Financial Technologies (pp. 217–231). Cambridge, MA, United States: Association for Computing Machinery. https://doi.org/10.1145/3558535.3559775","mla":"Tiwari, Samarth, et al. “Wiser: Increasing Throughput in Payment Channel Networks with Transaction Aggregation.” Proceedings of the 4th ACM Conference on Advances in Financial Technologies, Association for Computing Machinery, 2022, pp. 217–31, doi:10.1145/3558535.3559775.","ista":"Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. 2022. Wiser: Increasing throughput in payment channel networks with transaction aggregation. Proceedings of the 4th ACM Conference on Advances in Financial Technologies. AFT: Conference on Advances in Financial Technologies, 217–231.","ieee":"S. Tiwari, M. X. Yeo, Z. Avarikioti, I. Salem, K. Z. Pietrzak, and S. Schmid, “Wiser: Increasing throughput in payment channel networks with transaction aggregation,” in Proceedings of the 4th ACM Conference on Advances in Financial Technologies, Cambridge, MA, United States, 2022, pp. 217–231.","ama":"Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. Wiser: Increasing throughput in payment channel networks with transaction aggregation. In: Proceedings of the 4th ACM Conference on Advances in Financial Technologies. Association for Computing Machinery; 2022:217-231. doi:10.1145/3558535.3559775","short":"S. Tiwari, M.X. Yeo, Z. Avarikioti, I. Salem, K.Z. Pietrzak, S. Schmid, in:, Proceedings of the 4th ACM Conference on Advances in Financial Technologies, Association for Computing Machinery, 2022, pp. 217–231."},"publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","publisher":"Association for Computing Machinery","type":"conference","acknowledgement":"This work was supported partially by ERC Starting Grant QIP–805241, by the Vienna business agency (Wirtschaftsagentur) through the Vienna Cybersecurity and Privacy Research Center\r\n(ViSP) and by the Austrian Science Fund (FWF) project I 4800-N (ADVISE).\r\nThe first author would like to thank Daniel Dadush for suggesting the use of discrepancy techniques to solve the transaction aggregation problem.","date_created":"2024-05-28T13:58:35Z","has_accepted_license":"1","ddc":["000"],"day":"19","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","date_published":"2022-09-19T00:00:00Z","doi":"10.1145/3558535.3559775","oa_version":"Published Version","publication_identifier":{"isbn":["9781450398619"]},"title":"Wiser: Increasing throughput in payment channel networks with transaction aggregation","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"09","publication":"Proceedings of the 4th ACM Conference on Advances in Financial Technologies","abstract":[{"text":"Payment channel networks (PCNs) are one of the most prominent solutions to the limited transaction throughput of blockchains. Nevertheless, PCNs suffer themselves from a throughput limitation due to the capital constraints of their channels. A similar dependence on high capital is also found in inter-bank payment settlements, where the so-called netting technique is used to mitigate liquidity demands.\r\nIn this work, we alleviate this limitation by introducing the notion of transaction aggregation: instead of executing transactions sequentially through a PCN, we enable senders to aggregate multiple transactions and execute them simultaneously to benefit from several amounts that may \"cancel out\". Two direct advantages of our proposal is the decrease in intermediary fees paid by senders as well as the obfuscation of the transaction data from the intermediaries.\r\nWe formulate the transaction aggregation as a computational problem, a generalization of the Bank Clearing Problem. We present a generic framework for the transaction aggregation execution, and thereafter we propose Wiser as an implementation of this framework in a specific hub-based setting. To overcome the NP-hardness of the transaction aggregation problem, in Wiser we propose a fixed-parameter linear algorithm for a special case of transaction aggregation as well as the Bank Clearing Problem. Wiser can also be seen as a modern variant of the Hawala money transfer system, as well as a decentralized implementation of the overseas remittance service of Wise.","lang":"eng"}],"department":[{"_id":"KrPi"}],"_id":"17060","year":"2022","scopus_import":"1","file_date_updated":"2024-08-19T06:45:21Z","author":[{"last_name":"Tiwari","first_name":"Samarth","full_name":"Tiwari, Samarth"},{"orcid":"0009-0001-3676-4809","last_name":"Yeo","first_name":"Michelle X","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zeta","full_name":"Avarikioti, Zeta","last_name":"Avarikioti"},{"last_name":"Salem","full_name":"Salem, Iosif","first_name":"Iosif"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"quality_controlled":"1","file":[{"access_level":"open_access","date_updated":"2024-08-19T06:45:21Z","file_name":"2022_AFT_Tiwari.pdf","file_size":574728,"file_id":"17439","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2024-08-19T06:45:21Z","relation":"main_file","checksum":"54a7d405f8e57dba24728599ca63818c"}],"date_updated":"2025-09-10T09:57:48Z"},{"date_published":"2022-09-01T00:00:00Z","doi":"10.1093/pnasnexus/pgac141","oa_version":"Published Version","issue":"4","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["2752-6542"]},"title":"Evolutionary instability of selfish learning in repeated games","_id":"17061","year":"2022","scopus_import":"1","file_date_updated":"2024-08-06T07:33:30Z","publication":"PNAS Nexus","month":"09","abstract":[{"text":"Across many domains of interaction, both natural and artificial, individuals use past experience to shape future behaviors. The results of such learning processes depend on what individuals wish to maximize. A natural objective is one’s own success. However, when two such “selfish” learners interact with each other, the outcome can be detrimental to both, especially when there are conflicts of interest. Here, we explore how a learner can align incentives with a selfish opponent. Moreover, we consider the dynamics that arise when learning rules themselves are subject to evolutionary pressure. By combining extensive simulations and analytical techniques, we demonstrate that selfish learning is unstable in most classical two-player repeated games. If evolution operates on the level of long-run payoffs, selection instead favors learning rules that incorporate social (other-regarding) preferences. To further corroborate these results, we analyze data from a repeated prisoner’s dilemma experiment. We find that selfish learning is insufficient to explain human behavior when there is a trade-off between payoff maximization and fairness.","lang":"eng"}],"department":[{"_id":"KrCh"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/alexmcavoy/fmtl/"}]},"author":[{"last_name":"McAvoy","first_name":"Alex","full_name":"McAvoy, Alex"},{"full_name":"Kates-Harbeck, Julian","first_name":"Julian","last_name":"Kates-Harbeck"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian"}],"quality_controlled":"1","file":[{"success":1,"relation":"main_file","date_created":"2024-08-06T07:33:30Z","checksum":"79a8e3e4be7e8a2b407b4efddd65f3f3","file_size":2410962,"creator":"dernst","file_id":"17400","content_type":"application/pdf","file_name":"2022_PNASNexus_McAvoy.pdf","access_level":"open_access","date_updated":"2024-08-06T07:33:30Z"}],"article_type":"original","date_updated":"2025-06-11T13:54:20Z","external_id":{"pmid":["36714856"],"arxiv":["2105.06199"]},"oa":1,"article_number":"pgac141","pmid":1,"publication_status":"published","language":[{"iso":"eng"}],"arxiv":1,"citation":{"apa":"McAvoy, A., Kates-Harbeck, J., Chatterjee, K., & Hilbe, C. (2022). Evolutionary instability of selfish learning in repeated games. PNAS Nexus. Oxford University Press. https://doi.org/10.1093/pnasnexus/pgac141","mla":"McAvoy, Alex, et al. “Evolutionary Instability of Selfish Learning in Repeated Games.” PNAS Nexus, vol. 1, no. 4, pgac141, Oxford University Press, 2022, doi:10.1093/pnasnexus/pgac141.","chicago":"McAvoy, Alex, Julian Kates-Harbeck, Krishnendu Chatterjee, and Christian Hilbe. “Evolutionary Instability of Selfish Learning in Repeated Games.” PNAS Nexus. Oxford University Press, 2022. https://doi.org/10.1093/pnasnexus/pgac141.","ista":"McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. 2022. Evolutionary instability of selfish learning in repeated games. PNAS Nexus. 1(4), pgac141.","ama":"McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. Evolutionary instability of selfish learning in repeated games. PNAS Nexus. 2022;1(4). doi:10.1093/pnasnexus/pgac141","short":"A. McAvoy, J. Kates-Harbeck, K. Chatterjee, C. Hilbe, PNAS Nexus 1 (2022).","ieee":"A. McAvoy, J. Kates-Harbeck, K. Chatterjee, and C. Hilbe, “Evolutionary instability of selfish learning in repeated games,” PNAS Nexus, vol. 1, no. 4. Oxford University Press, 2022."},"date_created":"2024-05-28T14:23:12Z","has_accepted_license":"1","type":"journal_article","publisher":"Oxford University Press","ec_funded":1,"article_processing_charge":"Yes","volume":1,"acknowledgement":"The authors are grateful to Jörg Oechssler for many helpful comments. A.M. was supported by a Simons Postdoctoral Fellowship (Math+X) at the University of Pennsylvania; K.C. was supported by the European Research Council Consolidator Grant 863818 (ForM-SMArt); and C.H. was supported by the European Research Council Starting Grant 850529 (E-DIRECT).","ddc":["000"],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"intvolume":" 1"},{"oa":1,"external_id":{"arxiv":["2107.12265"]},"article_number":"32","language":[{"iso":"eng"}],"publication_status":"published","citation":{"chicago":"Zhao, Haisen, Max Willsey, Amy Zhu, Chandrakana Nandi, Zachary Tatlock, Justin Solomon, and Adriana Schulz. “Co-Optimization of Design and Fabrication Plans for Carpentry.” ACM Transactions on Graphics. Association for Computing Machinery, 2022. https://doi.org/10.1145/3508499.","apa":"Zhao, H., Willsey, M., Zhu, A., Nandi, C., Tatlock, Z., Solomon, J., & Schulz, A. (2022). Co-optimization of design and fabrication plans for carpentry. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3508499","mla":"Zhao, Haisen, et al. “Co-Optimization of Design and Fabrication Plans for Carpentry.” ACM Transactions on Graphics, vol. 41, no. 3, 32, Association for Computing Machinery, 2022, doi:10.1145/3508499.","ista":"Zhao H, Willsey M, Zhu A, Nandi C, Tatlock Z, Solomon J, Schulz A. 2022. Co-optimization of design and fabrication plans for carpentry. ACM Transactions on Graphics. 41(3), 32.","ieee":"H. Zhao et al., “Co-optimization of design and fabrication plans for carpentry,” ACM Transactions on Graphics, vol. 41, no. 3. Association for Computing Machinery, 2022.","ama":"Zhao H, Willsey M, Zhu A, et al. Co-optimization of design and fabrication plans for carpentry. ACM Transactions on Graphics. 2022;41(3). doi:10.1145/3508499","short":"H. Zhao, M. Willsey, A. Zhu, C. Nandi, Z. Tatlock, J. Solomon, A. Schulz, ACM Transactions on Graphics 41 (2022)."},"arxiv":1,"date_created":"2024-05-29T06:09:23Z","publisher":"Association for Computing Machinery","type":"journal_article","volume":41,"article_processing_charge":"No","acknowledgement":"The authors would like to thank anonymous reviewers for their helpful feedback; Haomiao Wu for her contribution to the algorithm development in the early stage of the project; Elias Baldwin, David Tsay, Alexander Lefort, and Qiyang Tan for helping the experiments.","intvolume":" 41","oa_version":"Preprint","date_published":"2022-03-09T00:00:00Z","doi":"10.1145/3508499","day":"09","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","title":"Co-optimization of design and fabrication plans for carpentry","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2107.12265"}],"year":"2022","scopus_import":"1","_id":"17065","department":[{"_id":"BeBi"}],"month":"03","publication":"ACM Transactions on Graphics","abstract":[{"lang":"eng","text":"Past work on optimizing fabrication plans given a carpentry design can provide Pareto-optimal plans trading off between material waste, fabrication time, precision, and other considerations. However, when developing fabrication plans, experts rarely restrict to a single design, instead considering families of design variations, sometimes adjusting designs to simplify fabrication. Jointly exploring the design and fabrication plan spaces for each design is intractable using current techniques. We present a new approach to jointly optimize design and fabrication plans for carpentered objects. To make this bi-level optimization tractable, we adapt recent work from program synthesis based on equality graphs (e-graphs), which encode sets of equivalent programs. Our insight is that subproblems within our bi-level problem share significant substructures. By representing both designs and fabrication plans in a new bag of parts (BOP) e-graph, we amortize the cost of optimizing design components shared among multiple candidates. Even using BOP e-graphs, the optimization space grows quickly in practice. Hence, we also show how a feedback-guided search strategy dubbed Iterative Contraction and Expansion on E-graphs (ICEE) can keep the size of the e-graph manageable and direct the search towards promising candidates. We illustrate the advantages of our pipeline through examples from the carpentry domain."}],"date_updated":"2024-08-06T07:03:14Z","author":[{"orcid":"0000-0002-6389-1045","last_name":"Zhao","first_name":"Haisen","full_name":"Zhao, Haisen","id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4"},{"first_name":"Max","full_name":"Willsey, Max","last_name":"Willsey"},{"full_name":"Zhu, Amy","first_name":"Amy","last_name":"Zhu"},{"first_name":"Chandrakana","full_name":"Nandi, Chandrakana","last_name":"Nandi"},{"last_name":"Tatlock","first_name":"Zachary","full_name":"Tatlock, Zachary"},{"first_name":"Justin","full_name":"Solomon, Justin","last_name":"Solomon"},{"first_name":"Adriana","full_name":"Schulz, Adriana","last_name":"Schulz"}],"article_type":"original","quality_controlled":"1"},{"article_number":"e3001786","oa":1,"external_id":{"pmid":["36201522"]},"pmid":1,"publication_status":"published","language":[{"iso":"eng"}],"citation":{"short":"A. Sethi, H. Wei, N. Mishra, I. Segos, E.J. Lambie, E. Zanin, B. Conradt, PLOS Biology 20 (2022).","ama":"Sethi A, Wei H, Mishra N, et al. A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. PLOS Biology. 2022;20(10). doi:10.1371/journal.pbio.3001786","ieee":"A. Sethi et al., “A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans,” PLOS Biology, vol. 20, no. 10. Public Library of Science, 2022.","ista":"Sethi A, Wei H, Mishra N, Segos I, Lambie EJ, Zanin E, Conradt B. 2022. A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. PLOS Biology. 20(10), e3001786.","mla":"Sethi, Aditya, et al. “A Caspase–RhoGEF Axis Contributes to the Cell Size Threshold for Apoptotic Death in Developing Caenorhabditis Elegans.” PLOS Biology, vol. 20, no. 10, e3001786, Public Library of Science, 2022, doi:10.1371/journal.pbio.3001786.","chicago":"Sethi, Aditya, Hai Wei, Nikhil Mishra, Ioannis Segos, Eric J. Lambie, Esther Zanin, and Barbara Conradt. “A Caspase–RhoGEF Axis Contributes to the Cell Size Threshold for Apoptotic Death in Developing Caenorhabditis Elegans.” PLOS Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pbio.3001786.","apa":"Sethi, A., Wei, H., Mishra, N., Segos, I., Lambie, E. J., Zanin, E., & Conradt, B. (2022). A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans. PLOS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001786"},"has_accepted_license":"1","date_created":"2024-05-29T06:09:34Z","acknowledgement":"We thank members of the Conradt, Lambie, and Hajnal labs for discussions and comments on the manuscript. We thank M. Bauer, L. Jocham, N. Lebedeva, and L. McGuinness for excellent technical support; A. Hajnal and T. Kohlbrenner (University of Zurich, Switzerland) for allele zh135; and H.R. Horvitz (Massachusetts of Technology, USA) for plasmid pET-CED-3.\r\nSome strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (https://orip.nih.gov/) (P40 OD010440). This work was supported by UCL (Capital Equipment Fund, CEF2), a predoctoral fellowship from the China Scholarship Council (https://www.csc.edu.cn/) to HW, a predoctoral fellowship from the Studienstiftung des Deutschen Volkes (https://www.studienstiftung.de/) to NM, a Wolfson Fellowship from the Royal Society (https://royalsociety.org/) to BC (RSWF\\R1\\180008), the Deutsche Forschungsgemeinschaft (https://www.dfg.de/en/index.jsp) (ZA619/3-1 and ZA619/3-2 to EZ; C0204/10-1 and EXC114 to BC), and the Biotechnology and Biological Sciences Research Council (https://bbsrc.ukri.org/) (BB/V007572/1 to BC). ","type":"journal_article","publisher":"Public Library of Science","article_processing_charge":"Yes","volume":20,"intvolume":" 20","ddc":["570"],"doi":"10.1371/journal.pbio.3001786","date_published":"2022-10-06T00:00:00Z","oa_version":"Published Version","issue":"10","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["1545-7885"]},"title":"A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death in developing Caenorhabditis elegans","_id":"17066","scopus_import":"1","file_date_updated":"2024-08-06T07:07:52Z","year":"2022","abstract":[{"text":"A cell’s size affects the likelihood that it will die. But how is cell size controlled in this context and how does cell size impact commitment to the cell death fate? We present evidence that the caspase CED-3 interacts with the RhoGEF ECT-2 in Caenorhabditis elegans neuroblasts that generate “unwanted” cells. We propose that this interaction promotes polar actomyosin contractility, which leads to unequal neuroblast division and the generation of a daughter cell that is below the critical “lethal” size threshold. Furthermore, we find that hyperactivation of ECT-2 RhoGEF reduces the sizes of unwanted cells. Importantly, this suppresses the “cell death abnormal” phenotype caused by the partial loss of ced-3 caspase and therefore increases the likelihood that unwanted cells die. A putative null mutation of ced-3 caspase, however, is not suppressed, which indicates that cell size affects CED-3 caspase activation and/or activity. Therefore, we have uncovered novel sequential and reciprocal interactions between the apoptosis pathway and cell size that impact a cell’s commitment to the cell death fate.","lang":"eng"}],"month":"10","publication":"PLOS Biology","department":[{"_id":"CaHe"}],"article_type":"original","quality_controlled":"1","file":[{"file_size":2515388,"content_type":"application/pdf","file_id":"17399","creator":"dernst","date_created":"2024-08-06T07:07:52Z","relation":"main_file","checksum":"a7b46460b7819c196028481cc18a7c85","success":1,"date_updated":"2024-08-06T07:07:52Z","access_level":"open_access","file_name":"2022_PlosBio_Sethi.pdf"}],"author":[{"first_name":"Aditya","full_name":"Sethi, Aditya","last_name":"Sethi"},{"full_name":"Wei, Hai","first_name":"Hai","last_name":"Wei"},{"last_name":"Mishra","first_name":"Nikhil","full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E"},{"full_name":"Segos, Ioannis","first_name":"Ioannis","last_name":"Segos"},{"full_name":"Lambie, Eric J.","first_name":"Eric J.","last_name":"Lambie"},{"first_name":"Esther","full_name":"Zanin, Esther","last_name":"Zanin"},{"last_name":"Conradt","first_name":"Barbara","full_name":"Conradt, Barbara"}],"date_updated":"2024-08-06T07:08:54Z"},{"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"title":"Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells","publication_identifier":{"issn":["0969-9961"]},"oa_version":"Published Version","doi":"10.1016/j.nbd.2022.105702","date_published":"2022-06-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"15","date_updated":"2024-08-06T06:57:39Z","article_type":"original","quality_controlled":"1","file":[{"success":1,"date_created":"2024-08-06T06:54:24Z","relation":"main_file","checksum":"b705d3d23d0b424ba29920be7ab64c23","file_size":8890818,"content_type":"application/pdf","creator":"dernst","file_id":"17398","file_name":"2022_NeurobioDisease_Stouffer.pdf","access_level":"open_access","date_updated":"2024-08-06T06:54:24Z"}],"author":[{"id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","last_name":"Stouffer","full_name":"Stouffer, Melissa A","first_name":"Melissa A"},{"full_name":"Khalaf-Nazzal, R.","first_name":"R.","last_name":"Khalaf-Nazzal"},{"first_name":"C.","full_name":"Cifuentes-Diaz, C.","last_name":"Cifuentes-Diaz"},{"last_name":"Albertini","first_name":"G.","full_name":"Albertini, G."},{"last_name":"Bandet","full_name":"Bandet, E.","first_name":"E."},{"last_name":"Grannec","first_name":"G.","full_name":"Grannec, G."},{"last_name":"Lavilla","full_name":"Lavilla, V.","first_name":"V."},{"last_name":"Deleuze","first_name":"J.-F.","full_name":"Deleuze, J.-F."},{"full_name":"Olaso, R.","first_name":"R.","last_name":"Olaso"},{"first_name":"M.","full_name":"Nosten-Bertrand, M.","last_name":"Nosten-Bertrand"},{"last_name":"Francis","full_name":"Francis, F.","first_name":"F."}],"file_date_updated":"2024-08-06T06:54:24Z","scopus_import":"1","year":"2022","_id":"17067","department":[{"_id":"SiHi"}],"abstract":[{"lang":"eng","text":"Human doublecortin (DCX) mutations are associated with severe brain malformations leading to aberrant neuron positioning (heterotopia), intellectual disability and epilepsy. DCX is a microtubule-associated protein which plays a key role during neurodevelopment in neuronal migration and differentiation. Dcx knockout (KO) mice show disorganized hippocampal pyramidal neurons. The CA2/CA3 pyramidal cell layer is present as two abnormal layers and disorganized CA3 KO pyramidal neurons are also more excitable than wild-type (WT) cells. To further identify abnormalities, we characterized Dcx KO hippocampal neurons at subcellular, molecular and ultrastructural levels. Severe defects were observed in mitochondria, affecting number and distribution. Also, the Golgi apparatus was visibly abnormal, increased in volume and abnormally organized. Transcriptome analyses from laser microdissected hippocampal tissue at postnatal day 60 (P60) highlighted organelle abnormalities. Ultrastructural studies of CA3 cells performed in P60 (young adult) and > 9 months (mature) tissue showed that organelle defects are persistent throughout life. Locomotor activity and fear memory of young and mature adults were also abnormal: Dcx KO mice consistently performed less well than WT littermates, with defects becoming more severe with age. Thus, we show that disruption of a neurodevelopmentally-regulated gene can lead to permanent organelle anomalies contributing to abnormal adult behavior."}],"publication":"Neurobiology of Disease","month":"06","publication_status":"published","pmid":1,"language":[{"iso":"eng"}],"citation":{"short":"M.A. Stouffer, R. Khalaf-Nazzal, C. Cifuentes-Diaz, G. Albertini, E. Bandet, G. Grannec, V. Lavilla, J.-F. Deleuze, R. Olaso, M. Nosten-Bertrand, F. Francis, Neurobiology of Disease 168 (2022).","ama":"Stouffer MA, Khalaf-Nazzal R, Cifuentes-Diaz C, et al. Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells. Neurobiology of Disease. 2022;168. doi:10.1016/j.nbd.2022.105702","ieee":"M. A. Stouffer et al., “Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells,” Neurobiology of Disease, vol. 168. Elsevier, 2022.","ista":"Stouffer MA, Khalaf-Nazzal R, Cifuentes-Diaz C, Albertini G, Bandet E, Grannec G, Lavilla V, Deleuze J-F, Olaso R, Nosten-Bertrand M, Francis F. 2022. Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells. Neurobiology of Disease. 168, 105702.","apa":"Stouffer, M. A., Khalaf-Nazzal, R., Cifuentes-Diaz, C., Albertini, G., Bandet, E., Grannec, G., … Francis, F. (2022). Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells. Neurobiology of Disease. Elsevier. https://doi.org/10.1016/j.nbd.2022.105702","chicago":"Stouffer, Melissa A, R. Khalaf-Nazzal, C. Cifuentes-Diaz, G. Albertini, E. Bandet, G. Grannec, V. Lavilla, et al. “Doublecortin Mutation Leads to Persistent Defects in the Golgi Apparatus and Mitochondria in Adult Hippocampal Pyramidal Cells.” Neurobiology of Disease. Elsevier, 2022. https://doi.org/10.1016/j.nbd.2022.105702.","mla":"Stouffer, Melissa A., et al. “Doublecortin Mutation Leads to Persistent Defects in the Golgi Apparatus and Mitochondria in Adult Hippocampal Pyramidal Cells.” Neurobiology of Disease, vol. 168, 105702, Elsevier, 2022, doi:10.1016/j.nbd.2022.105702."},"article_number":"105702","external_id":{"pmid":["35339680"]},"oa":1,"intvolume":" 168","ddc":["570"],"has_accepted_license":"1","date_created":"2024-05-29T06:10:05Z","acknowledgement":"We thank Sylvie Dumont for initial aid with laser microdissection and G. Martinez-Lorenzana for experimental help with electron microscopy. We thank the animal experimentation facility and cellular and tissue imaging platforms at the Institut du Fer à Moulin, supported also by the Région Ile de France and the FRC Rotary. The Francis lab was associated with the BioPsy Labex project and the Ecole des Neurosciences de Paris Ile-de-France (ENP) network. Our salaries and lab were supported by Inserm, the Centre national de la recherche scientifique (CNRS) and Sorbonne University. The Francis group obtained the following funding contributing to this project: the European Union (EU- HEALTH-2013, DESIRE, N° 60253), the JTC 2015 Neurodevelopmental Disorders affiliated with the French Agence National de la Recherche (for \r\nNEURON8-Full- 815-006 STEM-MCD, to FF), E-Rare-3, the ERA-Net for Research on Rare Diseases affiliated with the French ANR (ERARE18-049), the European Cooperation on Science and Technology (COST Action CA16118).","type":"journal_article","volume":168,"publisher":"Elsevier","article_processing_charge":"Yes"},{"author":[{"full_name":"Navarrete, Fernando","first_name":"Fernando","last_name":"Navarrete"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","full_name":"Gallei, Michelle C","last_name":"Gallei"},{"last_name":"Kornienko","first_name":"Aleksandra E.","full_name":"Kornienko, Aleksandra E."},{"first_name":"Indira","full_name":"Saado, Indira","last_name":"Saado"},{"full_name":"Khan, Mamoona","first_name":"Mamoona","last_name":"Khan"},{"last_name":"Chia","first_name":"Khong-Sam","full_name":"Chia, Khong-Sam"},{"last_name":"Darino","full_name":"Darino, Martin A.","first_name":"Martin A."},{"last_name":"Bindics","full_name":"Bindics, Janos","first_name":"Janos"},{"last_name":"Djamei","first_name":"Armin","full_name":"Djamei, Armin"}],"quality_controlled":"1","article_type":"original","file":[{"file_size":3216686,"creator":"dernst","content_type":"application/pdf","file_id":"17393","date_created":"2024-08-05T10:26:29Z","relation":"main_file","checksum":"1eeb6ee65419e4aa34627fea6857f343","success":1,"date_updated":"2024-08-05T10:26:29Z","access_level":"open_access","file_name":"2022_PlantComm_Navarrete.pdf"}],"date_updated":"2024-08-05T10:27:03Z","_id":"17068","year":"2022","file_date_updated":"2024-08-05T10:26:29Z","scopus_import":"1","month":"03","publication":"Plant Communications","abstract":[{"lang":"eng","text":"In plants, the antagonism between growth and defense is hardwired by hormonal signaling. The perception of pathogen-associated molecular patterns (PAMPs) from invading microorganisms inhibits auxin signaling and plant growth. Conversely, pathogens manipulate auxin signaling to promote disease, but how this hormone inhibits immunity is not fully understood. Ustilago maydis is a maize pathogen that induces auxin signaling in its host. We characterized a U. maydis effector protein, Naked1 (Nkd1), that is translocated into the host nucleus. Through its native ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif, Nkd1 binds to the transcriptional co-repressors TOPLESS/TOPLESS-related (TPL/TPRs) and prevents the recruitment of a transcriptional repressor involved in hormonal signaling, leading to the de-repression of auxin and jasmonate signaling and thereby promoting susceptibility to (hemi)biotrophic pathogens. A moderate upregulation of auxin signaling inhibits the PAMP-triggered reactive oxygen species (ROS) burst, an early defense response. Thus, our findings establish a clear mechanism for auxin-induced pathogen susceptibility. Engineered Nkd1 variants with increased expression or increased EAR-mediated TPL/TPR binding trigger typical salicylic-acid-mediated defense reactions, leading to pathogen resistance. This implies that moderate binding of Nkd1 to TPL is a result of a balancing evolutionary selection process to enable TPL manipulation while avoiding host recognition."}],"department":[{"_id":"JiFr"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publication_identifier":{"issn":["2590-3462"]},"title":"TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1","date_published":"2022-03-14T00:00:00Z","doi":"10.1016/j.xplc.2021.100269","oa_version":"Published Version","issue":"2","day":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["580"],"intvolume":" 3","has_accepted_license":"1","date_created":"2024-05-29T06:10:22Z","volume":3,"article_processing_charge":"Yes","publisher":"Elsevier","type":"journal_article","acknowledgement":"The research leading to these results received funding from the European Research Council under the European Union Seventh Framework Programme ERC-2013-STG grant agreement \r\n335691; the Austrian Science Fund (FWF) P27818-B22,I 3033-B22; the Austrian Academy of Sciences (OEAW); and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2070-390732324.\r\nWe would like to thank the GMI/IMBA/IMP core facilities for excellent technical support, especially the BioOptics and Molecular Biology Services. We thank the Plant Sciences and Next Generation Sequencing Facilities at the Vienna BioCenter Core Facilities GmbH (VBCF). We are grateful to the Jirí Friml and Jürgen Kleine-Vehn laboratories for providing useful A. thaliana lines. We thank Mathias Madalinski for peptide synthesis and Dr. J. Matthew Watson for proofreading and valuable feedback on the manuscript. The authors declare no competing interests.","language":[{"iso":"eng"}],"pmid":1,"publication_status":"published","citation":{"ieee":"F. Navarrete et al., “TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1,” Plant Communications, vol. 3, no. 2. Elsevier, 2022.","ama":"Navarrete F, Gallei MC, Kornienko AE, et al. TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. Plant Communications. 2022;3(2). doi:10.1016/j.xplc.2021.100269","short":"F. Navarrete, M.C. Gallei, A.E. Kornienko, I. Saado, M. Khan, K.-S. Chia, M.A. Darino, J. Bindics, A. Djamei, Plant Communications 3 (2022).","mla":"Navarrete, Fernando, et al. “TOPLESS Promotes Plant Immunity by Repressing Auxin Signaling and Is Targeted by the Fungal Effector Naked1.” Plant Communications, vol. 3, no. 2, 100269, Elsevier, 2022, doi:10.1016/j.xplc.2021.100269.","apa":"Navarrete, F., Gallei, M. C., Kornienko, A. E., Saado, I., Khan, M., Chia, K.-S., … Djamei, A. (2022). TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2021.100269","chicago":"Navarrete, Fernando, Michelle C Gallei, Aleksandra E. Kornienko, Indira Saado, Mamoona Khan, Khong-Sam Chia, Martin A. Darino, Janos Bindics, and Armin Djamei. “TOPLESS Promotes Plant Immunity by Repressing Auxin Signaling and Is Targeted by the Fungal Effector Naked1.” Plant Communications. Elsevier, 2022. https://doi.org/10.1016/j.xplc.2021.100269.","ista":"Navarrete F, Gallei MC, Kornienko AE, Saado I, Khan M, Chia K-S, Darino MA, Bindics J, Djamei A. 2022. TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. Plant Communications. 3(2), 100269."},"oa":1,"external_id":{"pmid":["35529945"]},"article_number":"100269"},{"quality_controlled":"1","article_type":"original","author":[{"first_name":"Sheng","full_name":"Zhong, Sheng","last_name":"Zhong"},{"last_name":"Li","full_name":"Li, Ling","first_name":"Ling"},{"last_name":"Wang","first_name":"Zhijuan","full_name":"Wang, Zhijuan"},{"id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","first_name":"Zengxiang","full_name":"Ge, Zengxiang","last_name":"Ge","orcid":"0000-0001-9381-3577"},{"last_name":"Li","full_name":"Li, Qiyun","first_name":"Qiyun"},{"first_name":"Andrea","full_name":"Bleckmann, Andrea","last_name":"Bleckmann"},{"first_name":"Jizong","full_name":"Wang, Jizong","last_name":"Wang"},{"first_name":"Zihan","full_name":"Song, Zihan","last_name":"Song"},{"full_name":"Shi, Yihao","first_name":"Yihao","last_name":"Shi"},{"full_name":"Liu, Tianxu","first_name":"Tianxu","last_name":"Liu"},{"last_name":"Li","full_name":"Li, Luhan","first_name":"Luhan"},{"last_name":"Zhou","full_name":"Zhou, Huabin","first_name":"Huabin"},{"last_name":"Wang","full_name":"Wang, Yanyan","first_name":"Yanyan"},{"first_name":"Li","full_name":"Zhang, Li","last_name":"Zhang"},{"last_name":"Wu","full_name":"Wu, Hen-Ming","first_name":"Hen-Ming"},{"full_name":"Lai, Luhua","first_name":"Luhua","last_name":"Lai"},{"first_name":"Hongya","full_name":"Gu, Hongya","last_name":"Gu"},{"last_name":"Dong","full_name":"Dong, Juan","first_name":"Juan"},{"last_name":"Cheung","first_name":"Alice Y.","full_name":"Cheung, Alice Y."},{"full_name":"Dresselhaus, Thomas","first_name":"Thomas","last_name":"Dresselhaus"},{"full_name":"Qu, Li-Jia","first_name":"Li-Jia","last_name":"Qu"}],"date_updated":"2025-04-24T11:39:46Z","OA_place":"repository","_id":"17069","scopus_import":"1","year":"2022","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9040003"}],"abstract":[{"lang":"eng","text":"Fertilization of an egg by multiple sperm (polyspermy) leads to lethal genome imbalance and chromosome segregation defects. In Arabidopsis thaliana, the block to polyspermy is facilitated by a mechanism that prevents polytubey (the arrival of multiple pollen tubes to one ovule). We show here that FERONIA, ANJEA, and HERCULES RECEPTOR KINASE 1 receptor-like kinases located at the septum interact with pollen tube–specific RALF6, 7, 16, 36, and 37 peptide ligands to establish this polytubey block. The same combination of RALF (rapid alkalinization factor) peptides and receptor complexes controls pollen tube reception and rupture inside the targeted ovule. Pollen tube rupture releases the polytubey block at the septum, which allows the emergence of secondary pollen tubes upon fertilization failure. Thus, orchestrated steps in the fertilization process in Arabidopsis are coordinated by the same signaling components to guarantee and optimize reproductive success."}],"publication":"Science","month":"01","department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"title":"RALF peptide signaling controls the polytubey block in Arabidopsis","doi":"10.1126/science.abl4683","date_published":"2022-01-20T00:00:00Z","oa_version":"Submitted Version","issue":"6578","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"20","intvolume":" 375","date_created":"2024-05-29T06:11:10Z","acknowledgement":"We thank D. Ye for providing fer-4 and myb97 myb101 myb120 mutant seeds; L. Smith for sharing anj, herk1, anj herk1, and fer anj herk1 mutant seeds; J. F. Harper for providing aca9 mutant seeds; and C. Li and Q. Duan for sharing fer+/− mutant seeds.\r\nL.-J.Q. was funded by the National Natural Science Foundation of China (grant nos. 31991202, 31830004, 31620103903, and 31621001), S.Z. was supported by the Young Elite Scientists Sponsorship Program by the China Association of Science and Technology (2019QNRC001), Z.G. was supported by a NSFC Young Scientists Fund (31900161), A.Y.C. was funded by the US Natural Science Foundation (IOS-1645854, MCB-1715764, and MCB-0955910), J.D. was funded by the National Institute of Health (R01GM109080), and T.D. was supported by the German Research Foundation DFG (SFB924).","type":"journal_article","publisher":"American Association for the Advancement of Science","article_processing_charge":"No","volume":375,"language":[{"iso":"eng"}],"pmid":1,"publication_status":"published","citation":{"ama":"Zhong S, Li L, Wang Z, et al. RALF peptide signaling controls the polytubey block in Arabidopsis. Science. 2022;375(6578):290-296. doi:10.1126/science.abl4683","short":"S. Zhong, L. Li, Z. Wang, Z. Ge, Q. Li, A. Bleckmann, J. Wang, Z. Song, Y. Shi, T. Liu, L. Li, H. Zhou, Y. Wang, L. Zhang, H.-M. Wu, L. Lai, H. Gu, J. Dong, A.Y. Cheung, T. Dresselhaus, L.-J. Qu, Science 375 (2022) 290–296.","ieee":"S. Zhong et al., “RALF peptide signaling controls the polytubey block in Arabidopsis,” Science, vol. 375, no. 6578. American Association for the Advancement of Science, pp. 290–296, 2022.","chicago":"Zhong, Sheng, Ling Li, Zhijuan Wang, Zengxiang Ge, Qiyun Li, Andrea Bleckmann, Jizong Wang, et al. “RALF Peptide Signaling Controls the Polytubey Block in Arabidopsis.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abl4683.","mla":"Zhong, Sheng, et al. “RALF Peptide Signaling Controls the Polytubey Block in Arabidopsis.” Science, vol. 375, no. 6578, American Association for the Advancement of Science, 2022, pp. 290–96, doi:10.1126/science.abl4683.","apa":"Zhong, S., Li, L., Wang, Z., Ge, Z., Li, Q., Bleckmann, A., … Qu, L.-J. (2022). RALF peptide signaling controls the polytubey block in Arabidopsis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abl4683","ista":"Zhong S, Li L, Wang Z, Ge Z, Li Q, Bleckmann A, Wang J, Song Z, Shi Y, Liu T, Li L, Zhou H, Wang Y, Zhang L, Wu H-M, Lai L, Gu H, Dong J, Cheung AY, Dresselhaus T, Qu L-J. 2022. RALF peptide signaling controls the polytubey block in Arabidopsis. Science. 375(6578), 290–296."},"external_id":{"pmid":["35050671"]},"oa":1,"page":"290-296","OA_type":"green"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron","publication_identifier":{"issn":["1367-2630"]},"oa_version":"Published Version","doi":"10.1088/1367-2630/ac836c","date_published":"2022-09-08T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","issue":"8","date_updated":"2024-07-31T12:14:55Z","quality_controlled":"1","article_type":"original","file":[{"file_size":4201283,"creator":"dernst","content_type":"application/pdf","file_id":"17358","relation":"main_file","date_created":"2024-07-31T12:13:16Z","checksum":"85776a9d3abe163b33b322c8e346752a","success":1,"date_updated":"2024-07-31T12:13:16Z","access_level":"open_access","file_name":"2022_NewJournPhysics_Mistakidis.pdf"}],"author":[{"first_name":"S I","full_name":"Mistakidis, S I","last_name":"Mistakidis"},{"last_name":"Koutentakis","first_name":"Georgios","full_name":"Koutentakis, Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95"},{"first_name":"F","full_name":"Grusdt, F","last_name":"Grusdt"},{"full_name":"Schmelcher, P","first_name":"P","last_name":"Schmelcher"},{"last_name":"Sadeghpour","full_name":"Sadeghpour, H R","first_name":"H R"}],"file_date_updated":"2024-07-31T12:13:16Z","scopus_import":"1","year":"2022","_id":"17070","department":[{"_id":"MiLe"}],"abstract":[{"text":"We investigate the formation of magnetic Bose polaron, an impurity atom dressed by spin-wave excitations, in a one-dimensional spinor Bose gas. Within an effective potential model, the impurity is strongly confined by the host excitations which can even overcome the impurity-medium repulsion leading to a self-localized quasi-particle state. The phase diagram of the attractive and self-bound repulsive magnetic polaron, repulsive non-magnetic (Fröhlich-type) polaron and impurity-medium phase-separation regimes is explored with respect to the Rabi-coupling between the spin components, spin–spin interactions and impurity-medium coupling. The residue of such magnetic polarons decreases substantially in both strong attractive and repulsive branches with strong impurity-spin interactions, illustrating significant dressing of the impurity. The impurity can be used to probe and maneuver the spin polarization of the magnetic medium while suppressing ferromagnetic spin–spin correlations. It is shown that mean-field theory fails as the spinor gas approaches immiscibility since the generated spin-wave excitations are prominent. Our findings illustrate that impurities can be utilized to generate controllable spin–spin correlations and magnetic polaron states which can be realized with current cold atom setups.","lang":"eng"}],"publication":"New Journal of Physics","month":"09","publication_status":"published","language":[{"iso":"eng"}],"citation":{"ieee":"S. I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, and H. R. Sadeghpour, “Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron,” New Journal of Physics, vol. 24, no. 8. IOP Publishing, 2022.","ama":"Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. 2022;24(8). doi:10.1088/1367-2630/ac836c","short":"S.I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, H.R. Sadeghpour, New Journal of Physics 24 (2022).","mla":"Mistakidis, S. I., et al. “Inducing Spin-Order with an Impurity: Phase Diagram of the Magnetic Bose Polaron.” New Journal of Physics, vol. 24, no. 8, 083030, IOP Publishing, 2022, doi:10.1088/1367-2630/ac836c.","chicago":"Mistakidis, S I, Georgios Koutentakis, F Grusdt, P Schmelcher, and H R Sadeghpour. “Inducing Spin-Order with an Impurity: Phase Diagram of the Magnetic Bose Polaron.” New Journal of Physics. IOP Publishing, 2022. https://doi.org/10.1088/1367-2630/ac836c.","apa":"Mistakidis, S. I., Koutentakis, G., Grusdt, F., Schmelcher, P., & Sadeghpour, H. R. (2022). Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac836c","ista":"Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. 2022. Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron. New Journal of Physics. 24(8), 083030."},"arxiv":1,"article_number":"083030","external_id":{"arxiv":["2204.10960"]},"oa":1,"intvolume":" 24","ddc":["530"],"has_accepted_license":"1","date_created":"2024-05-29T06:11:35Z","type":"journal_article","publisher":"IOP Publishing","article_processing_charge":"Yes","volume":24},{"article_number":"abm9506","external_id":{"pmid":["35679397"]},"publication_status":"published","pmid":1,"language":[{"iso":"eng"}],"citation":{"mla":"Mosalaganti, Shyamal, et al. “AI-Based Structure Prediction Empowers Integrative Structural Analysis of Human Nuclear Pores.” Science, vol. 376, no. 6598, abm9506, American Association for the Advancement of Science, 2022, doi:10.1126/science.abm9506.","apa":"Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová, B., Zimmerli, C. E., … Beck, M. (2022). AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abm9506","chicago":"Mosalaganti, Shyamal, Agnieszka Obarska-Kosinska, Marc Siggel, Reiya Taniguchi, Beata Turoňová, Christian E. Zimmerli, Katarzyna Buczak, et al. “AI-Based Structure Prediction Empowers Integrative Structural Analysis of Human Nuclear Pores.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abm9506.","ista":"Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli CE, Buczak K, Schmidt F, Margiotta E, Mackmull M-T, Hagen WJH, Hummer G, Kosinski J, Beck M. 2022. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. 376(6598), abm9506.","ama":"Mosalaganti S, Obarska-Kosinska A, Siggel M, et al. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. 2022;376(6598). doi:10.1126/science.abm9506","short":"S. Mosalaganti, A. Obarska-Kosinska, M. Siggel, R. Taniguchi, B. Turoňová, C.E. Zimmerli, K. Buczak, F. Schmidt, E. Margiotta, M.-T. Mackmull, W.J.H. Hagen, G. Hummer, J. Kosinski, M. Beck, Science 376 (2022).","ieee":"S. Mosalaganti et al., “AI-based structure prediction empowers integrative structural analysis of human nuclear pores,” Science, vol. 376, no. 6598. American Association for the Advancement of Science, 2022."},"date_created":"2024-05-29T06:12:02Z","acknowledgement":"We acknowledge support from the Electron Microscopy Core Facility (EMCF) and IT services of European Molecular Biology Laboratory (EMBL) Heidelberg. We thank S. Welsch at the Central Electron Microscopy Facility of the Max Planck Institute of Biophysics for technical expertise. We thank T. Hoffman and R. Alves for help with the AlphaFold installation.\r\nFunding: M.B. acknowledges funding by EMBL, the Max Planck Society, and the European Research Council (ComplexAssembly 724349). J.K. acknowledges funding from the Federal Ministry of Education and Research of Germany (FKZ 031L0100). The work by M.S. and G.H. on computer simulations was supported by the Max Planck Society. M.S. was supported by the EMBL Interdisciplinary Postdoc Programme under Marie Curie COFUND actions. M.S. and G.H. were supported by the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) DynaMem program of the State of Hessen.","type":"journal_article","article_processing_charge":"No","volume":376,"publisher":"American Association for the Advancement of Science","intvolume":" 376","doi":"10.1126/science.abm9506","date_published":"2022-06-10T00:00:00Z","oa_version":"None","issue":"6598","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"title":"AI-based structure prediction empowers integrative structural analysis of human nuclear pores","_id":"17071","scopus_import":"1","year":"2022","abstract":[{"text":"The eukaryotic nucleus protects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa, the human NPC is one of the largest protein complexes. Its ~1000 proteins are taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs). They can be roughly categorized into two classes. Scaffold NUPs contain folded domains and form a cylindrical scaffold architecture around a central channel. Intrinsically disordered NUPs line the scaffold and extend into the central channel, where they interact with cargo complexes. The NPC architecture is highly dynamic. It responds to changes in nuclear envelope tension with conformational breathing that manifests in dilation and constriction movements. Elucidating the scaffold architecture, ultimately at atomic resolution, will be important for gaining a more precise understanding of NPC function and dynamics but imposes a substantial challenge for structural biologists.\r\nConsiderable progress has been made toward this goal by a joint effort in the field. A synergistic combination of complementary approaches has turned out to be critical. In situ structural biology techniques were used to reveal the overall layout of the NPC scaffold that defines the spatial reference for molecular modeling. High-resolution structures of many NUPs were determined in vitro. Proteomic analysis and extensive biochemical work unraveled the interaction network of NUPs. Integrative modeling has been used to combine the different types of data, resulting in a rough outline of the NPC scaffold. Previous structural models of the human NPC, however, were patchy and limited in accuracy owing to several challenges: (i) Many of the high-resolution structures of individual NUPs have been solved from distantly related species and, consequently, do not comprehensively cover their human counterparts. (ii) The scaffold is interconnected by a set of intrinsically disordered linker NUPs that are not straightforwardly accessible to common structural biology techniques. (iii) The NPC scaffold intimately embraces the fused inner and outer nuclear membranes in a distinctive topology and cannot be studied in isolation. (iv) The conformational dynamics of scaffold NUPs limits the resolution achievable in structure determination.\r\nIn this study, we used artificial intelligence (AI)–based prediction to generate an extensive repertoire of structural models of human NUPs and their subcomplexes. The resulting models cover various domains and interfaces that so far remained structurally uncharacterized. Benchmarking against previous and unpublished x-ray and cryo–electron microscopy structures revealed unprecedented accuracy. We obtained well-resolved cryo–electron tomographic maps of both the constricted and dilated conformational states of the human NPC. Using integrative modeling, we fitted the structural models of individual NUPs into the cryo–electron microscopy maps. We explicitly included several linker NUPs and traced their trajectory through the NPC scaffold. We elucidated in great detail how membrane-associated and transmembrane NUPs are distributed across the fusion topology of both nuclear membranes. The resulting architectural model increases the structural coverage of the human NPC scaffold by about twofold. We extensively validated our model against both earlier and new experimental data. The completeness of our model has enabled microsecond-long coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit membrane environment and solvent. These simulations reveal that the NPC scaffold prevents the constriction of the otherwise stable double-membrane fusion pore to small diameters in the absence of membrane tension\r\nOur 70-MDa atomically resolved model covers >90% of the human NPC scaffold. It captures conformational changes that occur during dilation and constriction. It also reveals the precise anchoring sites for intrinsically disordered NUPs, the identification of which is a prerequisite for a complete and dynamic model of the NPC. Our study exemplifies how AI-based structure prediction may accelerate the elucidation of subcellular architecture at atomic resolution.","lang":"eng"}],"publication":"Science","month":"06","department":[{"_id":"MaJö"}],"quality_controlled":"1","article_type":"original","author":[{"last_name":"Mosalaganti","full_name":"Mosalaganti, Shyamal","first_name":"Shyamal"},{"last_name":"Obarska-Kosinska","first_name":"Agnieszka","full_name":"Obarska-Kosinska, Agnieszka"},{"last_name":"Siggel","full_name":"Siggel, Marc","first_name":"Marc"},{"last_name":"Taniguchi","full_name":"Taniguchi, Reiya","first_name":"Reiya"},{"first_name":"Beata","full_name":"Turoňová, Beata","last_name":"Turoňová"},{"first_name":"Christian E.","full_name":"Zimmerli, Christian E.","last_name":"Zimmerli"},{"last_name":"Buczak","full_name":"Buczak, Katarzyna","first_name":"Katarzyna"},{"id":"A2EF226A-AF19-11E9-924C-0525E6697425","last_name":"Schmidt","first_name":"Florian","full_name":"Schmidt, Florian"},{"full_name":"Margiotta, Erica","first_name":"Erica","last_name":"Margiotta"},{"full_name":"Mackmull, Marie-Therese","first_name":"Marie-Therese","last_name":"Mackmull"},{"full_name":"Hagen, Wim J. H.","first_name":"Wim J. H.","last_name":"Hagen"},{"last_name":"Hummer","first_name":"Gerhard","full_name":"Hummer, Gerhard"},{"last_name":"Kosinski","full_name":"Kosinski, Jan","first_name":"Jan"},{"last_name":"Beck","full_name":"Beck, Martin","first_name":"Martin"}],"date_updated":"2024-07-31T12:10:32Z"}]