[{"scopus_import":"1","department":[{"_id":"JiFr"}],"volume":7,"citation":{"chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y.","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504.","ieee":"E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,” Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y.","apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-021-01011-y","ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y"},"doi":"10.1038/s41477-021-01011-y","_id":"10326","quality_controlled":"1","oa_version":"Submitted Version","day":"11","acknowledgement":"We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).","article_type":"original","publication_identifier":{"eissn":["2055-0278"]},"file_date_updated":"2025-01-21T12:41:43Z","OA_place":"repository","external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"author":[{"first_name":"Enjun","last_name":"Xu","full_name":"Xu, Enjun"},{"full_name":"Chai, Liang","last_name":"Chai","first_name":"Liang"},{"last_name":"Zhang","first_name":"Shiqi","full_name":"Zhang, Shiqi"},{"full_name":"Yu, Ruixue","last_name":"Yu","first_name":"Ruixue"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","orcid":"0000-0001-7048-4627","first_name":"Xixi"},{"last_name":"Xu","first_name":"Chongyi","full_name":"Xu, Chongyi"},{"first_name":"Yuxin","last_name":"Hu","full_name":"Hu, Yuxin"}],"title":"Catabolism of strigolactones by a carboxylesterase","date_updated":"2025-01-21T12:42:52Z","pmid":1,"has_accepted_license":"1","date_created":"2021-11-21T23:01:30Z","abstract":[{"text":"Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants.","lang":"eng"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"OA_type":"green","intvolume":" 7","status":"public","month":"11","ddc":["580"],"publication":"Nature Plants","page":"1495–1504 ","isi":1,"type":"journal_article","oa":1,"publication_status":"published","year":"2021","article_processing_charge":"No","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":41109943,"file_name":"Accepted version_Xu et al.,2021 Catabolism of strigolactones by a carboxylesterase.pdf","checksum":"d20231806bea67f0fd19e96a94a048f4","creator":"dernst","relation":"main_file","date_created":"2025-01-21T12:41:43Z","date_updated":"2025-01-21T12:41:43Z","file_id":"18864","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-11-11T00:00:00Z"},{"intvolume":" 220","language":[{"iso":"eng"}],"publisher":"Rockefeller University Press","date_created":"2021-11-25T15:21:30Z","pmid":1,"abstract":[{"lang":"eng","text":"The T cell receptor (TCR) pathway receives, processes, and amplifies the signal from pathogenic antigens to the activation of T cells. Although major components in this pathway have been identified, the knowledge on how individual components cooperate to effectively transduce signals remains limited. Phase separation emerges as a biophysical principle in organizing signaling molecules into liquid-like condensates. Here, we report that phospholipase Cγ1 (PLCγ1) promotes phase separation of LAT, a key adaptor protein in the TCR pathway. PLCγ1 directly cross-links LAT through its two SH2 domains. PLCγ1 also protects LAT from dephosphorylation by the phosphatase CD45 and promotes LAT-dependent ERK activation and SLP76 phosphorylation. Intriguingly, a nonmonotonic effect of PLCγ1 on LAT clustering was discovered. Computer simulations, based on patchy particles, revealed how the cluster size is regulated by protein compositions. Together, these results define a critical function of PLCγ1 in promoting phase separation of the LAT complex and TCR signal transduction."}],"publication":"Journal of Cell Biology","month":"04","status":"public","issue":"6","type":"journal_article","article_number":"e202009154","date_published":"2021-04-30T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["cell biology"],"article_processing_charge":"No","year":"2021","publication_status":"published","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"doi":"10.1083/jcb.202009154","citation":{"apa":"Zeng, L., Palaia, I., Šarić, A., & Su, X. (2021). PLCγ1 promotes phase separation of T cell signaling components. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202009154","ista":"Zeng L, Palaia I, Šarić A, Su X. 2021. PLCγ1 promotes phase separation of T cell signaling components. Journal of Cell Biology. 220(6), e202009154.","ama":"Zeng L, Palaia I, Šarić A, Su X. PLCγ1 promotes phase separation of T cell signaling components. Journal of Cell Biology. 2021;220(6). doi:10.1083/jcb.202009154","mla":"Zeng, Longhui, et al. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” Journal of Cell Biology, vol. 220, no. 6, e202009154, Rockefeller University Press, 2021, doi:10.1083/jcb.202009154.","ieee":"L. Zeng, I. Palaia, A. Šarić, and X. Su, “PLCγ1 promotes phase separation of T cell signaling components,” Journal of Cell Biology, vol. 220, no. 6. Rockefeller University Press, 2021.","short":"L. Zeng, I. Palaia, A. Šarić, X. Su, Journal of Cell Biology 220 (2021).","chicago":"Zeng, Longhui, Ivan Palaia, Anđela Šarić, and Xiaolei Su. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” Journal of Cell Biology. Rockefeller University Press, 2021. https://doi.org/10.1083/jcb.202009154."},"volume":220,"scopus_import":"1","oa_version":"None","quality_controlled":"1","extern":"1","_id":"10337","external_id":{"pmid":["33929486"]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","article_type":"original","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"acknowledgement":"Charles H. Hood Foundation (NO AWARD) ; Rally Foundation (NO AWARD)","day":"30","date_updated":"2021-11-25T15:33:08Z","title":"PLCγ1 promotes phase separation of T cell signaling components","author":[{"full_name":"Zeng, Longhui","last_name":"Zeng","first_name":"Longhui"},{"first_name":"Ivan","last_name":"Palaia","full_name":"Palaia, Ivan"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"full_name":"Su, Xiaolei","first_name":"Xiaolei","last_name":"Su"}]},{"language":[{"iso":"eng"}],"intvolume":" 120","date_created":"2021-11-25T15:36:36Z","pmid":1,"abstract":[{"lang":"eng","text":"In the nuclear pore complex, intrinsically disordered proteins (FG Nups), along with their interactions with more globular proteins called nuclear transport receptors (NTRs), are vital to the selectivity of transport into and out of the cell nucleus. Although such interactions can be modeled at different levels of coarse graining, in vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, in which the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and noncohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity in a minimal fashion and compare them with experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does play a role in determining equilibrium binding properties but is of much greater significance when it comes to unbinding and binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences."}],"publisher":"Elsevier","publication":"Biophysical Journal","status":"public","month":"02","issue":"9","type":"journal_article","oa":1,"page":"1565-1577","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-02-19T00:00:00Z","article_processing_charge":"No","keyword":["biophysics"],"year":"2021","publication_status":"published","doi":"10.1016/j.bpj.2021.01.039","citation":{"chicago":"Davis, Luke K., Anđela Šarić, Bart W. Hoogenboom, and Anton Zilman. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” Biophysical Journal. Elsevier, 2021. https://doi.org/10.1016/j.bpj.2021.01.039.","short":"L.K. Davis, A. Šarić, B.W. Hoogenboom, A. Zilman, Biophysical Journal 120 (2021) 1565–1577.","mla":"Davis, Luke K., et al. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” Biophysical Journal, vol. 120, no. 9, Elsevier, 2021, pp. 1565–77, doi:10.1016/j.bpj.2021.01.039.","ieee":"L. K. Davis, A. Šarić, B. W. Hoogenboom, and A. Zilman, “Physical modeling of multivalent interactions in the nuclear pore complex,” Biophysical Journal, vol. 120, no. 9. Elsevier, pp. 1565–1577, 2021.","ama":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. Physical modeling of multivalent interactions in the nuclear pore complex. Biophysical Journal. 2021;120(9):1565-1577. doi:10.1016/j.bpj.2021.01.039","apa":"Davis, L. K., Šarić, A., Hoogenboom, B. W., & Zilman, A. (2021). Physical modeling of multivalent interactions in the nuclear pore complex. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2021.01.039","ista":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. 2021. Physical modeling of multivalent interactions in the nuclear pore complex. Biophysical Journal. 120(9), 1565–1577."},"scopus_import":"1","volume":120,"extern":"1","_id":"10338","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.10.01.322156"}],"oa_version":"Preprint","quality_controlled":"1","external_id":{"pmid":["33617830"]},"article_type":"original","publication_identifier":{"issn":["0006-3495"]},"day":"19","date_updated":"2022-04-01T10:34:38Z","title":"Physical modeling of multivalent interactions in the nuclear pore complex","author":[{"last_name":"Davis","first_name":"Luke K.","full_name":"Davis, Luke K."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"last_name":"Hoogenboom","first_name":"Bart W.","full_name":"Hoogenboom, Bart W."},{"full_name":"Zilman, Anton","first_name":"Anton","last_name":"Zilman"}]},{"day":"16","article_type":"original","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"acknowledgement":"We acknowledge support from the Royal Society (C. V. C. and A. Sˇ.), the Medical Research Council (C. V. C. and A. Sˇ.), and the European Research Council (Starting grant ‘‘NEPA’’ 802960 to A. Sˇ.). We thank Johannes Krausser and Ivan Palaia for fruitful discussions.","related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.11.16.384602v2","relation":"earlier_version"}]},"OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc/3.0/","external_id":{"pmid":["33629089"]},"author":[{"full_name":"Vanhille-Campos, Christian","first_name":"Christian","last_name":"Vanhille-Campos"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"title":"Modelling the dynamics of vesicle reshaping and scission under osmotic shocks","date_updated":"2024-10-14T14:20:59Z","scopus_import":"1","volume":17,"citation":{"ista":"Vanhille-Campos C, Šarić A. 2021. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. 17(14), 3798–3806.","apa":"Vanhille-Campos, C., & Šarić, A. (2021). Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d0sm02012e","ama":"Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. 2021;17(14):3798-3806. doi:10.1039/d0sm02012e","ieee":"C. Vanhille-Campos and A. Šarić, “Modelling the dynamics of vesicle reshaping and scission under osmotic shocks,” Soft Matter, vol. 17, no. 14. Royal Society of Chemistry, pp. 3798–3806, 2021.","mla":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” Soft Matter, vol. 17, no. 14, Royal Society of Chemistry, 2021, pp. 3798–806, doi:10.1039/d0sm02012e.","short":"C. Vanhille-Campos, A. Šarić, Soft Matter 17 (2021) 3798–3806.","chicago":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” Soft Matter. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d0sm02012e."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png"},"doi":"10.1039/d0sm02012e","extern":"1","_id":"10339","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2021/sm/d0sm02012e","open_access":"1"}],"page":"3798-3806","type":"journal_article","oa":1,"publication_status":"published","year":"2021","article_processing_charge":"No","keyword":["condensed matter physics","general chemistry"],"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","date_published":"2021-02-16T00:00:00Z","abstract":[{"text":"We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation.","lang":"eng"}],"pmid":1,"date_created":"2021-11-25T16:06:42Z","publisher":"Royal Society of Chemistry","OA_type":"hybrid","language":[{"iso":"eng"}],"intvolume":" 17","issue":"14","month":"02","status":"public","publication":"Soft Matter"},{"author":[{"full_name":"Paraschiv, Alexandru","first_name":"Alexandru","last_name":"Paraschiv"},{"full_name":"Lagny, Thibaut J.","last_name":"Lagny","first_name":"Thibaut J."},{"last_name":"Campos","first_name":"Christian Vanhille","full_name":"Campos, Christian Vanhille"},{"first_name":"Evelyne","last_name":"Coudrier","full_name":"Coudrier, Evelyne"},{"full_name":"Bassereau, Patricia","last_name":"Bassereau","first_name":"Patricia"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"title":"Influence of membrane-cortex linkers on the extrusion of membrane tubes","date_updated":"2024-10-14T11:13:03Z","day":"16","acknowledgement":"We thank Ewa Paluch, Alba Diz-Muñoz, Guillaume Salbreux, Guillaume Charras, and Shiladitya Banerjee for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P., C.V.C., and A.Š.), the Royal Society (C.V.C. and A.Š.), and the European Research Council (Starting grant EP/R011818/1 to A.Š.; E.C. and P.B. are partners of the advanced grant, project 339847) and from Institut Curie (E.C. and P.B.) and Centre National de la Recherche Scientifique (CNRS) (E.C. and P.B.). The P.B. and E.C. groups belong to Labex CelTisPhyBio (ANR-11-LABX0038) and to Paris Sciences et Lettres (ANR-10-IDEX-0001-02). T.L. received a PhD grant from Paris Sciences et Lettres Research University and support from the Institut Curie.","article_type":"original","publication_identifier":{"issn":["0006-3495"]},"external_id":{"pmid":["33460596"]},"_id":"10340","extern":"1","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1101/2020.07.28.224741","open_access":"1"}],"scopus_import":"1","volume":120,"citation":{"short":"A. Paraschiv, T.J. Lagny, C.V. Campos, E. Coudrier, P. Bassereau, A. Šarić, Biophysical Journal 120 (2021) 598–606.","chicago":"Paraschiv, Alexandru, Thibaut J. Lagny, Christian Vanhille Campos, Evelyne Coudrier, Patricia Bassereau, and Anđela Šarić. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” Biophysical Journal. Cell Press, 2021. https://doi.org/10.1016/j.bpj.2020.12.028.","ama":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical Journal. 2021;120(4):598-606. doi:10.1016/j.bpj.2020.12.028","apa":"Paraschiv, A., Lagny, T. J., Campos, C. V., Coudrier, E., Bassereau, P., & Šarić, A. (2021). Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical Journal. Cell Press. https://doi.org/10.1016/j.bpj.2020.12.028","ista":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. 2021. Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical Journal. 120(4), 598–606.","mla":"Paraschiv, Alexandru, et al. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” Biophysical Journal, vol. 120, no. 4, Cell Press, 2021, pp. 598–606, doi:10.1016/j.bpj.2020.12.028.","ieee":"A. Paraschiv, T. J. Lagny, C. V. Campos, E. Coudrier, P. Bassereau, and A. Šarić, “Influence of membrane-cortex linkers on the extrusion of membrane tubes,” Biophysical Journal, vol. 120, no. 4. Cell Press, pp. 598–606, 2021."},"doi":"10.1016/j.bpj.2020.12.028","publication_status":"published","keyword":["biophysics"],"year":"2021","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-01-16T00:00:00Z","page":"598-606","type":"journal_article","oa":1,"issue":"4","month":"01","publication":"Biophysical Journal","status":"public","pmid":1,"date_created":"2021-11-25T16:18:23Z","abstract":[{"lang":"eng","text":"The cell membrane is an inhomogeneous system composed of phospholipids, sterols, carbohydrates, and proteins that can be directly attached to underlying cytoskeleton. The protein linkers between the membrane and the cytoskeleton are believed to have a profound effect on the mechanical properties of the cell membrane and its ability to reshape. Here, we investigate the role of membrane-cortex linkers on the extrusion of membrane tubes using computer simulations and experiments. In simulations, we find that the force for tube extrusion has a nonlinear dependence on the density of membrane-cortex attachments: at a range of low and intermediate linker densities, the force is not significantly influenced by the presence of the membrane-cortex attachments and resembles that of the bare membrane. For large concentrations of linkers, however, the force substantially increases compared with the bare membrane. In both cases, the linkers provided membrane tubes with increased stability against coalescence. We then pulled tubes from HEK cells using optical tweezers for varying expression levels of the membrane-cortex attachment protein Ezrin. In line with simulations, we observed that overexpression of Ezrin led to an increased extrusion force, while Ezrin depletion had a negligible effect on the force. Our results shed light on the importance of local protein rearrangements for membrane reshaping at nanoscopic scales."}],"publisher":"Cell Press","language":[{"iso":"eng"}],"intvolume":" 120"},{"day":"18","file_date_updated":"2023-10-11T09:31:43Z","acknowledgement":"S.G. acknowledges funding from FEDER Prostem Research Project no. 1510614 (Wallonia DG06), F.R.S.-FNRS Epiforce Research Project no. T.0092.21 and Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional, FEDER-ERDF). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme grant agreement 851288 (to E.H.), and by the Austrian Science Fund (FWF) (P 31639; to E.H.). L.R.M. acknowledges funding from the Agence National de la Recherche (ANR), as part of the ‘Investments d’Avenir’ Programme (I-SITE ULNE/ANR-16-IDEX-0004 ULNE). This work benefited from ANR-10-EQPX-04-01 and FEDER 12001407 grants to F.L. W.D.V. is supported by the Research Foundation Flanders (FWO 1516619N, FWO GOO5819N, FWO I003420N, FWO IRI I000321N) and is member of the Research Excellence Consortium µNEURO at the University of Antwerp. M.L. is financially supported by FRIA (F.R.S.-FNRS). M.S. is a Senior Research Associate of the Fund for Scientific Research (F.R.S.-FNRS) and acknowledges EOS grant no. 30650939 (PRECISION). Sketches in Figs. 1a and 5e and Extended Data Fig. 9 were drawn by C. Levicek.","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-cells-feel-curvature/","relation":"press_release","description":"News on IST Webpage"}]},"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"article_type":"original","external_id":{"isi":["000720204300004"]},"author":[{"full_name":"Luciano, Marine","last_name":"Luciano","first_name":"Marine"},{"last_name":"Xue","first_name":"Shi-lei","full_name":"Xue, Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Vos, Winnok H.","first_name":"Winnok H.","last_name":"De Vos"},{"last_name":"Redondo-Morata","first_name":"Lorena","full_name":"Redondo-Morata, Lorena"},{"last_name":"Surin","first_name":"Mathieu","full_name":"Surin, Mathieu"},{"full_name":"Lafont, Frank","first_name":"Frank","last_name":"Lafont"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gabriele, Sylvain","last_name":"Gabriele","first_name":"Sylvain"}],"title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","date_updated":"2025-04-14T07:52:26Z","department":[{"_id":"EdHa"}],"scopus_import":"1","volume":17,"project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics, vol. 17, no. 12, Springer Nature, 2021, pp. 1382–1390, doi:10.1038/s41567-021-01374-1.","ieee":"M. Luciano et al., “Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation,” Nature Physics, vol. 17, no. 12. Springer Nature, pp. 1382–1390, 2021.","ista":"Luciano M, Xue S, De Vos WH, Redondo-Morata L, Surin M, Lafont F, Hannezo EB, Gabriele S. 2021. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 17(12), 1382–1390.","apa":"Luciano, M., Xue, S., De Vos, W. H., Redondo-Morata, L., Surin, M., Lafont, F., … Gabriele, S. (2021). Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-021-01374-1","ama":"Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. Nature Physics. 2021;17(12):1382–1390. doi:10.1038/s41567-021-01374-1","chicago":"Luciano, Marine, Shi-lei Xue, Winnok H. De Vos, Lorena Redondo-Morata, Mathieu Surin, Frank Lafont, Edouard B Hannezo, and Sylvain Gabriele. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” Nature Physics. Springer Nature, 2021. https://doi.org/10.1038/s41567-021-01374-1.","short":"M. Luciano, S. Xue, W.H. De Vos, L. Redondo-Morata, M. Surin, F. Lafont, E.B. Hannezo, S. Gabriele, Nature Physics 17 (2021) 1382–1390."},"doi":"10.1038/s41567-021-01374-1","_id":"10365","oa_version":"Submitted Version","quality_controlled":"1","page":"1382–1390","type":"journal_article","isi":1,"ec_funded":1,"oa":1,"publication_status":"published","article_processing_charge":"No","year":"2021","file":[{"success":1,"file_id":"14420","date_updated":"2023-10-11T09:31:43Z","checksum":"5d6d76750a71d7cb632bb15417c38ef7","creator":"channezo","file_name":"50145_4_merged_1630498627.pdf","date_created":"2023-10-11T09:31:43Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":40285498}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-11-18T00:00:00Z","has_accepted_license":"1","abstract":[{"text":"The early development of many organisms involves the folding of cell monolayers, but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic causes and effects of local curvature remain unclear. Here we study epithelial cell monolayers on corrugated hydrogels engineered into wavy patterns, examining how concave and convex curvatures affect cellular and nuclear shape. We find that substrate curvature affects monolayer thickness, which is larger in valleys than crests. We show that this feature generically arises in a vertex model, leading to the hypothesis that cells may sense curvature by modifying the thickness of the tissue. We find that local curvature also affects nuclear morphology and positioning, which we explain by extending the vertex model to take into account membrane–nucleus interactions, encoding thickness modulation in changes to nuclear deformation and position. We propose that curvature governs the spatial distribution of yes-associated proteins via nuclear shape and density changes. We show that curvature also induces significant variations in lamins, chromatin condensation and cell proliferation rate in folded epithelial tissues. Together, this work identifies active cell mechanics and nuclear mechanoadaptation as the key players of the mechanistic regulation of epithelia to substrate curvature.","lang":"eng"}],"date_created":"2021-11-28T23:01:29Z","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":" 17","issue":"12","publication":"Nature Physics","corr_author":"1","status":"public","ddc":["530"],"month":"11"},{"publisher":"Elsevier","pmid":1,"date_created":"2021-11-28T23:01:30Z","intvolume":" 168","language":[{"iso":"eng"}],"issue":"12","corr_author":"1","status":"public","month":"11","ddc":["570"],"publication":"Cells and Development","oa":1,"isi":1,"type":"journal_article","year":"2021","article_processing_charge":"No","publication_status":"published","article_number":"203758","date_published":"2021-11-17T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":168,"scopus_import":"1","department":[{"_id":"CaHe"}],"doi":"10.1016/j.cdev.2021.203758","citation":{"ista":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.","ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. 2021;168(12). doi:10.1016/j.cdev.2021.203758","apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758","mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development, vol. 168, no. 12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758.","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” Cells and Development, vol. 168, no. 12. Elsevier, 2021.","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cdev.2021.203758"}],"oa_version":"Published Version","quality_controlled":"1","_id":"10366","article_type":"letter_note","publication_identifier":{"issn":["2667-2901"]},"day":"17","external_id":{"isi":["000974771600028"],"pmid":["34800748"]},"author":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"first_name":"Ana Maria","last_name":"Lennon","full_name":"Lennon, Ana Maria"},{"first_name":"Roberto","last_name":"Mayor","full_name":"Mayor, Roberto"},{"last_name":"Salbreux","first_name":"Guillaume","full_name":"Salbreux, Guillaume"}],"date_updated":"2026-06-18T08:37:21Z","title":"Special rebranding issue: “Quantitative cell and developmental biology”"},{"year":"2021","article_processing_charge":"No","publication_status":"published","file":[{"relation":"main_file","date_created":"2021-11-29T08:41:00Z","creator":"cchlebak","file_name":"2021_ACL_Ilharco.pdf","checksum":"b14052a025a6ecf675bdfe51db98c0d7","file_size":1227703,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"10368","date_updated":"2021-11-29T08:41:00Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2021-08-01T00:00:00Z","page":"29-30","type":"conference","oa":1,"month":"08","publication":"59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts","ddc":["000"],"status":"public","date_created":"2021-11-28T23:01:30Z","abstract":[{"lang":"eng","text":"How information is created, shared and consumed has changed rapidly in recent decades, in part thanks to new social platforms and technologies on the web. With ever-larger amounts of unstructured and limited labels, organizing and reconciling information from different sources and modalities is a central challenge in machine learning. This cutting-edge tutorial aims to introduce the multimodal entailment task, which can be useful for detecting semantic alignments when a single modality alone does not suffice for a whole content understanding. Starting with a brief overview of natural language processing, computer vision, structured data and neural graph learning, we lay the foundations for the multimodal sections to follow. We then discuss recent multimodal learning literature covering visual, audio and language streams, and explore case studies focusing on tasks which require fine-grained understanding of visual and linguistic semantics question answering, veracity and hatred classification. Finally, we introduce a new dataset for recognizing multimodal entailment, exploring it in a hands-on collaborative section. Overall, this tutorial gives an overview of multimodal learning, introduces a multimodal entailment dataset, and encourages future research in the topic."}],"has_accepted_license":"1","publisher":"Association for Computational Linguistics","language":[{"iso":"eng"}],"author":[{"last_name":"Ilharco","first_name":"Cesar","full_name":"Ilharco, Cesar"},{"full_name":"Shirazi, Afsaneh","last_name":"Shirazi","first_name":"Afsaneh"},{"full_name":"Gopalan, Arjun","first_name":"Arjun","last_name":"Gopalan"},{"full_name":"Nagrani, Arsha","last_name":"Nagrani","first_name":"Arsha"},{"full_name":"Bratanič, Blaž","last_name":"Bratanič","first_name":"Blaž"},{"full_name":"Bregler, Chris","last_name":"Bregler","first_name":"Chris"},{"last_name":"Liu","first_name":"Christina","full_name":"Liu, Christina"},{"full_name":"Ferreira, Felipe","last_name":"Ferreira","first_name":"Felipe"},{"first_name":"Gabriek","last_name":"Barcik","full_name":"Barcik, Gabriek"},{"last_name":"Ilharco","first_name":"Gabriel","full_name":"Ilharco, Gabriel"},{"full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","last_name":"Osang"},{"first_name":"Jannis","last_name":"Bulian","full_name":"Bulian, Jannis"},{"full_name":"Frank, Jared","first_name":"Jared","last_name":"Frank"},{"full_name":"Smaira, Lucas","first_name":"Lucas","last_name":"Smaira"},{"full_name":"Cao, Qin","first_name":"Qin","last_name":"Cao"},{"first_name":"Ricardo","last_name":"Marino","full_name":"Marino, Ricardo"},{"first_name":"Roma","last_name":"Patel","full_name":"Patel, Roma"},{"full_name":"Leung, Thomas","first_name":"Thomas","last_name":"Leung"},{"full_name":"Imbrasaite, Vaiva","last_name":"Imbrasaite","first_name":"Vaiva"}],"date_updated":"2022-01-26T14:26:36Z","title":"Recognizing multimodal entailment","acknowledgement":"We would like to thank Abby Schantz, Abe Ittycheriah, Aliaksei Severyn, Allan Heydon, Aly\r\nGrealish, Andrey Vlasov, Arkaitz Zubiaga, Ashwin Kakarla, Chen Sun, Clayton Williams, Cong\r\nYu, Cordelia Schmid, Da-Cheng Juan, Dan Finnie, Dani Valevski, Daniel Rocha, David Price, David Sklar, Devi Krishna, Elena Kochkina, Enrique Alfonseca, Franc¸oise Beaufays, Isabelle Augenstein, Jialu Liu, John Cantwell, John Palowitch, Jordan Boyd-Graber, Lei Shi, Luis Valente, Maria Voitovich, Mehmet Aktuna, Mogan Brown, Mor Naaman, Natalia P, Nidhi Hebbar, Pete Aykroyd, Rahul Sukthankar, Richa Dixit, Steve Pucci, Tania Bedrax-Weiss, Tobias Kaufmann, Tom Boulos, Tu Tsao, Vladimir Chtchetkine, Yair Kurzion, Yifan Xu and Zach Hynes.","publication_identifier":{"isbn":["9-781-9540-8557-2"]},"file_date_updated":"2021-11-29T08:41:00Z","day":"01","conference":{"end_date":"2021-08-06","name":"ACL: Association for Computational Linguistics ; IJCNLP: International Joint Conference on Natural Language Processing","location":"Bangkok, Thailand","start_date":"2021-08-01"},"_id":"10367","main_file_link":[{"open_access":"1","url":"https://aclanthology.org/2021.acl-tutorials.6/"}],"oa_version":"Published Version","quality_controlled":"1","scopus_import":"1","department":[{"_id":"HeEd"}],"doi":"10.18653/v1/2021.acl-tutorials.6","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Ilharco, Cesar, Afsaneh Shirazi, Arjun Gopalan, Arsha Nagrani, Blaž Bratanič, Chris Bregler, Christina Liu, et al. “Recognizing Multimodal Entailment.” In 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts, 29–30. Association for Computational Linguistics, 2021. https://doi.org/10.18653/v1/2021.acl-tutorials.6.","short":"C. Ilharco, A. Shirazi, A. Gopalan, A. Nagrani, B. Bratanič, C. Bregler, C. Liu, F. Ferreira, G. Barcik, G. Ilharco, G.F. Osang, J. Bulian, J. Frank, L. Smaira, Q. Cao, R. Marino, R. Patel, T. Leung, V. Imbrasaite, in:, 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts, Association for Computational Linguistics, 2021, pp. 29–30.","ieee":"C. Ilharco et al., “Recognizing multimodal entailment,” in 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts, Bangkok, Thailand, 2021, pp. 29–30.","mla":"Ilharco, Cesar, et al. “Recognizing Multimodal Entailment.” 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts, Association for Computational Linguistics, 2021, pp. 29–30, doi:10.18653/v1/2021.acl-tutorials.6.","apa":"Ilharco, C., Shirazi, A., Gopalan, A., Nagrani, A., Bratanič, B., Bregler, C., … Imbrasaite, V. (2021). Recognizing multimodal entailment. In 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts (pp. 29–30). Bangkok, Thailand: Association for Computational Linguistics. https://doi.org/10.18653/v1/2021.acl-tutorials.6","ista":"Ilharco C, Shirazi A, Gopalan A, Nagrani A, Bratanič B, Bregler C, Liu C, Ferreira F, Barcik G, Ilharco G, Osang GF, Bulian J, Frank J, Smaira L, Cao Q, Marino R, Patel R, Leung T, Imbrasaite V. 2021. Recognizing multimodal entailment. 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts. ACL: Association for Computational Linguistics ; IJCNLP: International Joint Conference on Natural Language Processing, 29–30.","ama":"Ilharco C, Shirazi A, Gopalan A, et al. Recognizing multimodal entailment. In: 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts. Association for Computational Linguistics; 2021:29-30. doi:10.18653/v1/2021.acl-tutorials.6"}},{"status":"public","ddc":["530"],"month":"11","publication":"Communications Physics","issue":"1","intvolume":" 4","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_created":"2021-12-05T23:01:39Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Theoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect."}],"article_number":"252","date_published":"2021-11-26T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_updated":"2021-12-06T14:53:41Z","success":1,"file_id":"10420","content_type":"application/pdf","access_level":"open_access","file_size":1068984,"checksum":"9097319952cb9a3d96e7fd3aa9813a03","creator":"alisjak","file_name":"2021_NatComm_Barfknecht.pdf","relation":"main_file","date_created":"2021-12-06T14:53:41Z"}],"year":"2021","article_processing_charge":"No","publication_status":"published","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","quality_controlled":"1","oa_version":"Published Version","_id":"10401","doi":"10.1038/s42005-021-00753-7","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7","ama":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 2021;4(1). doi:10.1038/s42005-021-00753-7","ista":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 4(1), 252.","ieee":"R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation of spin currents by a temperature gradient in a two-terminal device,” Communications Physics, vol. 4, no. 1. Springer Nature, 2021.","mla":"Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no. 1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7.","short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021).","chicago":"Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7."},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"volume":4,"scopus_import":"1","department":[{"_id":"MiLe"}],"date_updated":"2026-04-02T14:05:00Z","title":"Generation of spin currents by a temperature gradient in a two-terminal device","author":[{"full_name":"Barfknecht, Rafael E.","last_name":"Barfknecht","first_name":"Rafael E."},{"first_name":"Angela","last_name":"Foerster","full_name":"Foerster, Angela"},{"first_name":"Nikolaj T.","last_name":"Zinner","full_name":"Zinner, Nikolaj T."},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525"}],"external_id":{"isi":["000722867600002"],"arxiv":["2101.02020"]},"arxiv":1,"acknowledgement":"The authors acknowledge support from the European QuantERA ERA-NET Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under the Jens Christian Skou fellowship program (N.T.Z).","article_type":"original","file_date_updated":"2021-12-06T14:53:41Z","publication_identifier":{"eissn":["2399-3650"]},"day":"26"},{"status":"public","publication":"Nature Communications","month":"11","ddc":["573"],"language":[{"iso":"eng"}],"intvolume":" 12","date_created":"2021-12-05T23:01:40Z","pmid":1,"abstract":[{"text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales.","lang":"eng"}],"has_accepted_license":"1","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"6830","date_published":"2021-11-24T00:00:00Z","publication_status":"published","year":"2021","article_processing_charge":"No","file":[{"file_name":"2021_NatComm_Ucar.pdf","checksum":"63c56ec75314a71e63e7dd2920b3c5b5","creator":"cchlebak","date_created":"2021-12-10T08:54:09Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":2303405,"file_id":"10529","success":1,"date_updated":"2021-12-10T08:54:09Z"}],"type":"journal_article","isi":1,"ec_funded":1,"oa":1,"_id":"10402","oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"citation":{"chicago":"Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature, 2021, doi:10.1038/s41467-021-27135-5.","ieee":"M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021.","apa":"Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5","ista":"Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830.","ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-021-27135-5","department":[{"_id":"EdHa"}],"scopus_import":"1","volume":12,"title":"Theory of branching morphogenesis by local interactions and global guidance","date_updated":"2025-04-14T07:43:47Z","author":[{"first_name":"Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"first_name":"Dmitrii","last_name":"Kamenev","full_name":"Kamenev, Dmitrii"},{"full_name":"Sunadome, Kazunori","last_name":"Sunadome","first_name":"Kazunori"},{"full_name":"Fachet, Dominik C","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","last_name":"Fachet","first_name":"Dominik C"},{"first_name":"Francois","last_name":"Lallemend","full_name":"Lallemend, Francois"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"},{"full_name":"Hadjab, Saida","first_name":"Saida","last_name":"Hadjab"},{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["34819507"],"isi":["000722322900020"]},"day":"24","related_material":{"record":[{"relation":"research_data","id":"13058","status":"public"}]},"article_type":"original","acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","file_date_updated":"2021-12-10T08:54:09Z","publication_identifier":{"eissn":["2041-1723"]}},{"intvolume":" 10","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","pmid":1,"abstract":[{"text":"Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits.","lang":"eng"}],"date_created":"2021-12-05T23:01:40Z","has_accepted_license":"1","publication":"eLife","status":"public","month":"11","ddc":["570"],"oa":1,"isi":1,"type":"journal_article","date_published":"2021-11-03T00:00:00Z","article_number":"e65954","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","date_created":"2021-12-10T08:31:41Z","checksum":"c7c33c3319428d56e332e22349c50ed3","creator":"cchlebak","file_name":"2021_eLife_Biane.pdf","file_size":13131322,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"10528","date_updated":"2021-12-10T08:31:41Z"}],"publication_status":"published","year":"2021","article_processing_charge":"No","doi":"10.7554/eLife.65954","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).","chicago":"Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.65954.","ista":"Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954.","ama":"Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10. doi:10.7554/eLife.65954","apa":"Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.65954","mla":"Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife Sciences Publications, 2021, doi:10.7554/eLife.65954.","ieee":"C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences Publications, 2021."},"volume":10,"department":[{"_id":"RySh"}],"scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","_id":"10403","external_id":{"isi":["000715789500001"],"pmid":["34730085"]},"day":"03","acknowledgement":"This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript.","file_date_updated":"2021-12-10T08:31:41Z","publication_identifier":{"eissn":["2050-084X"]},"article_type":"original","title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","date_updated":"2025-03-07T08:12:39Z","author":[{"full_name":"Biane, Celia","first_name":"Celia","last_name":"Biane"},{"full_name":"Rückerl, Florian","last_name":"Rückerl","first_name":"Florian"},{"last_name":"Abrahamsson","first_name":"Therese","full_name":"Abrahamsson, Therese"},{"first_name":"Cécile","last_name":"Saint-Cloment","full_name":"Saint-Cloment, Cécile"},{"last_name":"Mariani","first_name":"Jean","full_name":"Mariani, Jean"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"last_name":"Digregorio","first_name":"David A.","full_name":"Digregorio, David A."},{"full_name":"Sherrard, Rachel M.","first_name":"Rachel M.","last_name":"Sherrard"},{"full_name":"Cathala, Laurence","first_name":"Laurence","last_name":"Cathala"}]},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.07667"}],"oa_version":"Preprint","quality_controlled":"1","_id":"10404","doi":"10.1111/cgf.14418","citation":{"chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.14418.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418.","ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021). Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14418"},"project":[{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"volume":40,"scopus_import":"1","department":[{"_id":"ToHe"}],"date_updated":"2025-04-15T06:25:55Z","title":"Interactive analysis of CNN robustness","author":[{"first_name":"Stefan","last_name":"Sietzen","full_name":"Sietzen, Stefan"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias"},{"last_name":"Borowski","first_name":"Judy","full_name":"Borowski, Judy"},{"full_name":"Hasani, Ramin","first_name":"Ramin","last_name":"Hasani"},{"full_name":"Waldner, Manuela","first_name":"Manuela","last_name":"Waldner"}],"external_id":{"isi":["000722952000024"],"arxiv":["2110.07667"]},"arxiv":1,"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"article_type":"original","acknowledgement":"We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n","day":"27","publication":"Computer Graphics Forum","month":"11","status":"public","issue":"7","intvolume":" 40","language":[{"iso":"eng"}],"publisher":"Wiley","date_created":"2021-12-05T23:01:40Z","abstract":[{"lang":"eng","text":"While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models."}],"date_published":"2021-11-27T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","year":"2021","publication_status":"published","oa":1,"type":"journal_article","isi":1,"page":"253-264"},{"status":"public","month":"08","ddc":["570"],"corr_author":"1","publication":"Annual Review of Genetics","publisher":"Annual Reviews","date_created":"2021-12-05T23:01:41Z","abstract":[{"text":"Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future.","lang":"eng"}],"pmid":1,"intvolume":" 55","OA_type":"free access","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2021","keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"publication_status":"published","date_published":"2021-08-30T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"209-233","oa":1,"ec_funded":1,"isi":1,"type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1146/annurev-genet-071819-103748","open_access":"1"}],"oa_version":"Published Version","quality_controlled":"1","_id":"10406","volume":55,"scopus_import":"1","department":[{"_id":"CaHe"}],"citation":{"chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748.","short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.","mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748.","ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” Annual Review of Genetics, vol. 55. Annual Reviews, pp. 209–233, 2021.","ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233.","apa":"Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-071819-103748","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748"},"doi":"10.1146/annurev-genet-071819-103748","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","full_name":"Mishra, Nikhil","first_name":"Nikhil","orcid":"0000-0002-6425-5788","last_name":"Mishra"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-06-18T08:39:48Z","title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","acknowledgement":"The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action).","publication_identifier":{"eissn":["1545-2948"],"issn":["0066-4197"]},"article_type":"original","day":"30","external_id":{"pmid":["34460295"],"isi":["000747220900010"]},"OA_place":"publisher"},{"month":"11","status":"public","publisher":"Springer Nature","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification F one has more sophisticated circuits F⋄ manufactured (where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to F . Those solutions impose a significant overhead as F⋄ is much more complex than F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where F has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of F need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound."}],"date_created":"2021-12-05T23:01:42Z","intvolume":" 13043","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2021","publication_status":"published","date_published":"2021-11-04T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"397-428","oa":1,"isi":1,"ec_funded":1,"type":"conference","main_file_link":[{"url":"https://eprint.iacr.org/2021/1224","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","_id":"10407","volume":13043,"department":[{"_id":"KrPi"}],"scopus_import":"1","doi":"10.1007/978-3-030-90453-1_14","citation":{"ista":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.","ama":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14","apa":"Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., & Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14","mla":"Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14.","ieee":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.","short":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428.","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14."},"project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"author":[{"last_name":"Chakraborty","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","full_name":"Chakraborty, Suvradip"},{"last_name":"Dziembowski","first_name":"Stefan","full_name":"Dziembowski, Stefan"},{"full_name":"Gałązka, Małgorzata","first_name":"Małgorzata","last_name":"Gałązka"},{"last_name":"Lizurej","first_name":"Tomasz","full_name":"Lizurej, Tomasz"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","orcid":"0009-0001-3676-4809","last_name":"Yeo","first_name":"Michelle X"}],"date_updated":"2025-04-14T07:22:05Z","title":"Trojan-resilience without cryptography","publication_identifier":{"issn":["0302-9743"],"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"]},"day":"04","external_id":{"isi":["000728364000014"]},"conference":{"end_date":"2021-11-11","start_date":"2021-11-08","location":"Raleigh, NC, United States","name":"TCC: Theory of Cryptography Conference"}},{"related_material":{"record":[{"id":"18088","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-030-90456-2"],"isbn":["9-783-0309-0455-5"]},"day":"04","conference":{"start_date":"2021-11-08","location":"Raleigh, NC, United States","name":"TCC: Theory of Cryptography","end_date":"2021-11-11"},"external_id":{"isi":["000728363700008"]},"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F"},{"first_name":"Benedikt","last_name":"Auerbach","orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425"},{"full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad","last_name":"Baig"},{"first_name":"Miguel","orcid":"0000-0002-2505-4246","last_name":"Cueto Noval","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","full_name":"Cueto Noval, Miguel"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen","first_name":"Karen","last_name":"Klein"},{"first_name":"Guillermo","last_name":"Pascual Perez","orcid":"0000-0001-8630-415X","full_name":"Pascual Perez, Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","last_name":"Walter","first_name":"Michael"}],"date_updated":"2026-04-07T13:01:26Z","title":"Grafting key trees: Efficient key management for overlapping groups","department":[{"_id":"KrPi"}],"scopus_import":"1","volume":13044,"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"doi":"10.1007/978-3-030-90456-2_8","citation":{"ieee":"J. F. Alwen et al., “Grafting key trees: Efficient key management for overlapping groups,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253.","mla":"Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” 19th International Conference, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:10.1007/978-3-030-90456-2_8.","apa":"Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for overlapping groups. In 19th International Conference (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90456-2_8","ama":"Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: 19th International Conference. Vol 13044. Springer Nature; 2021:222-253. doi:10.1007/978-3-030-90456-2_8","ista":"Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13044, 222–253.","chicago":"Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In 19th International Conference, 13044:222–53. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90456-2_8.","short":"J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 222–253."},"_id":"10408","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1158"}],"oa_version":"Preprint","quality_controlled":"1","page":"222-253","isi":1,"ec_funded":1,"type":"conference","oa":1,"article_processing_charge":"No","year":"2021","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-11-04T00:00:00Z","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Key trees are often the best solution in terms of transmission cost and storage requirements for managing keys in a setting where a group needs to share a secret key, while being able to efficiently rotate the key material of users (in order to recover from a potential compromise, or to add or remove users). Applications include multicast encryption protocols like LKH (Logical Key Hierarchies) or group messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced) binary tree, where each node is identified with a key: leaf nodes hold users’ secret keys while the root is the shared group key. For a group of size N, each user just holds log(N) keys (the keys on the path from its leaf to the root) and its entire key material can be rotated by broadcasting 2log(N) ciphertexts (encrypting each fresh key on the path under the keys of its parents). In this work we consider the natural setting where we have many groups with partially overlapping sets of users, and ask if we can find solutions where the cost of rotating a key is better than in the trivial one where we have a separate key tree for each group. We show that in an asymptotic setting (where the number m of groups is fixed while the number N of users grows) there exist more general key graphs whose cost converges to the cost of a single group, thus saving a factor linear in the number of groups over the trivial solution. As our asymptotic “solution” converges very slowly and performs poorly on concrete examples, we propose an algorithm that uses a natural heuristic to compute a key graph for any given group structure. Our algorithm combines two greedy algorithms, and is thus very efficient: it first converts the group structure into a “lattice graph”, which is then turned into a key graph by repeatedly applying the algorithm for constructing a Huffman code. To better understand how far our proposal is from an optimal solution, we prove lower bounds on the update cost of continuous group-key agreement and multicast encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom generators, and secret sharing as building blocks."}],"date_created":"2021-12-05T23:01:42Z","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":" 13044","status":"public","month":"11","publication":"19th International Conference"},{"alternative_title":["LNCS"],"date_created":"2021-12-05T23:01:45Z","abstract":[{"text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in LexRSM not existing even for simple terminating programs. Our contributions are twofold: First, we introduce a generalization of LexRSMs which allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs.","lang":"eng"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":" 13047","month":"11","publication":"24th International Symposium on Formal Methods","status":"public","page":"619-639","type":"conference","isi":1,"ec_funded":1,"oa":1,"year":"2021","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-11-10T00:00:00Z","scopus_import":"1","department":[{"_id":"KrCh"}],"volume":13047,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.1007/978-3-030-90870-6_33","citation":{"short":"K. Chatterjee, E. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:, 24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.","chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” In 24th International Symposium on Formal Methods, 13047:619–39. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90870-6_33.","apa":"Chatterjee, K., Goharshady, E., Novotný, P., Zárevúcky, J., & Zikelic, D. (2021). On lexicographic proof rules for probabilistic termination. In 24th International Symposium on Formal Methods (Vol. 13047, pp. 619–639). Virtual: Springer Nature. https://doi.org/10.1007/978-3-030-90870-6_33","ista":"Chatterjee K, Goharshady E, Novotný P, Zárevúcky J, Zikelic D. 2021. On lexicographic proof rules for probabilistic termination. 24th International Symposium on Formal Methods. FM: Formal Methods, LNCS, vol. 13047, 619–639.","ama":"Chatterjee K, Goharshady E, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. In: 24th International Symposium on Formal Methods. Vol 13047. Springer Nature; 2021:619-639. doi:10.1007/978-3-030-90870-6_33","ieee":"K. Chatterjee, E. Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” in 24th International Symposium on Formal Methods, Virtual, 2021, vol. 13047, pp. 619–639.","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” 24th International Symposium on Formal Methods, vol. 13047, Springer Nature, 2021, pp. 619–39, doi:10.1007/978-3-030-90870-6_33."},"_id":"10414","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.02188"}],"oa_version":"Preprint","quality_controlled":"1","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the Czech Science Foundation grant No. GJ19-15134Y, and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","related_material":{"record":[{"relation":"later_version","id":"14778","status":"public"},{"status":"public","relation":"dissertation_contains","id":"14539"}]},"publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-030-90870-6"],"isbn":["9-783-0309-0869-0"],"eissn":["1611-3349"]},"day":"10","arxiv":1,"conference":{"name":"FM: Formal Methods","location":"Virtual","start_date":"2021-11-20","end_date":"2021-11-26"},"external_id":{"arxiv":["2108.02188"],"isi":["000758218600033"]},"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0002-8595-0587","last_name":"Kafshdar Goharshadi","first_name":"Ehsan","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","full_name":"Kafshdar Goharshadi, Ehsan"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr","first_name":"Petr","last_name":"Novotný"},{"full_name":"Zárevúcky, Jiří","first_name":"Jiří","last_name":"Zárevúcky"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699"}],"date_updated":"2026-04-07T13:27:55Z","title":"On lexicographic proof rules for probabilistic termination"},{"language":[{"iso":"eng"}],"intvolume":" 343","citation":{"chicago":"Browning, Timothy D. Cubic Forms and the Circle Method. Vol. 343. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-86872-7.","short":"T.D. Browning, Cubic Forms and the Circle Method, Springer Nature, Cham, 2021.","ieee":"T. D. Browning, Cubic Forms and the Circle Method, vol. 343. Cham: Springer Nature, 2021.","mla":"Browning, Timothy D. Cubic Forms and the Circle Method. Vol. 343, Springer Nature, 2021, doi:10.1007/978-3-030-86872-7.","ama":"Browning TD. Cubic Forms and the Circle Method. Vol 343. Cham: Springer Nature; 2021. doi:10.1007/978-3-030-86872-7","ista":"Browning TD. 2021. Cubic Forms and the Circle Method, Cham: Springer Nature, XIV, 166p.","apa":"Browning, T. D. (2021). Cubic Forms and the Circle Method (Vol. 343). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-86872-7"},"doi":"10.1007/978-3-030-86872-7","date_created":"2021-12-05T23:01:46Z","department":[{"_id":"TiBr"}],"abstract":[{"lang":"eng","text":"The Hardy–Littlewood circle method was invented over a century ago to study integer solutions to special Diophantine equations, but it has since proven to be one of the most successful all-purpose tools available to number theorists. Not only is it capable of handling remarkably general systems of polynomial equations defined over arbitrary global fields, but it can also shed light on the space of rational curves that lie on algebraic varieties. This book, in which the arithmetic of cubic polynomials takes centre stage, is aimed at bringing beginning graduate students into contact with some of the many facets of the circle method, both classical and modern. This monograph is the winner of the 2021 Ferran Sunyer i Balaguer Prize, a prestigious award for books of expository nature presenting the latest developments in an active area of research in mathematics."}],"scopus_import":"1","alternative_title":["Progress in Mathematics"],"publisher":"Springer Nature","volume":343,"_id":"10415","month":"12","corr_author":"1","quality_controlled":"1","oa_version":"None","status":"public","type":"book","day":"01","publication_identifier":{"eisbn":["978-3-030-86872-7"],"isbn":["978-3-030-86871-0"],"issn":["0743-1643"],"eissn":["2296-505X"]},"page":"XIV, 166","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"Cham","title":"Cubic Forms and the Circle Method","date_updated":"2024-10-09T21:01:16Z","date_published":"2021-12-01T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2021","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D"}]},{"oa_version":"Published Version","_id":"10422","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"citation":{"ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:10.15479/at:ista:10422","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","apa":"Piankov, A. (2021). Towards designer materials using customizable particle shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","mla":"Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422."},"doi":"10.15479/at:ista:10422","author":[{"id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","full_name":"Piankov, Anton","last_name":"Piankov","first_name":"Anton"}],"date_updated":"2026-04-08T06:58:55Z","title":"Towards designer materials using customizable particle shape","file_date_updated":"2022-03-10T12:10:25Z","publication_identifier":{"issn":["2791-4585"]},"day":"07","OA_place":"publisher","degree_awarded":"MS","status":"public","ddc":["530"],"corr_author":"1","month":"12","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Master's Thesis"],"abstract":[{"lang":"eng","text":"Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems."}],"has_accepted_license":"1","date_created":"2021-12-07T10:48:06Z","language":[{"iso":"eng"}],"supervisor":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","first_name":"Carl Peter"}],"file":[{"file_id":"10424","date_updated":"2022-03-10T12:10:25Z","relation":"source_file","date_created":"2021-12-07T11:13:52Z","creator":"cchlebak","file_name":"Thesis.zip","checksum":"114e8f4b2c002c6c352416c12de2c695","file_size":394018,"content_type":"application/x-zip-compressed","access_level":"closed"},{"date_updated":"2022-03-10T12:10:25Z","file_id":"10425","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":47638,"file_name":"Preliminary_pages_Piankov.docx","checksum":"cd15ae991ced352a9959815f794e657c","creator":"cchlebak","relation":"source_file","date_created":"2021-12-07T11:14:01Z"},{"date_created":"2021-12-07T11:20:35Z","relation":"main_file","creator":"cchlebak","file_name":"2021_Piankov_combined.pdf","checksum":"e6899c798b75ba42fab9822bce309050","file_size":484965,"access_level":"open_access","content_type":"application/pdf","file_id":"10426","success":1,"date_updated":"2021-12-07T11:20:35Z"}],"article_processing_charge":"No","year":"2021","publication_status":"published","date_published":"2021-12-07T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"type":"dissertation"},{"date_published":"2021-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","article_processing_charge":"No","publication_status":"published","oa":1,"ec_funded":1,"type":"conference","publication":"35th Conference on Neural Information Processing Systems","status":"public","month":"12","ddc":["000"],"language":[{"iso":"eng"}],"publisher":"Neural Information Processing Systems Foundation","abstract":[{"text":"Decentralized optimization is emerging as a viable alternative for scalable distributed machine learning, but also introduces new challenges in terms of synchronization costs. To this end, several communication-reduction techniques, such as non-blocking communication, quantization, and local steps, have been explored in the decentralized setting. Due to the complexity of analyzing optimization in such a relaxed setting, this line of work often assumes \\emph{global} communication rounds, which require additional synchronization. In this paper, we consider decentralized optimization in the simpler, but harder to analyze, \\emph{asynchronous gossip} model, in which communication occurs in discrete, randomly chosen pairings among nodes. Perhaps surprisingly, we show that a variant of SGD called \\emph{SwarmSGD} still converges in this setting, even if \\emph{non-blocking communication}, \\emph{quantization}, and \\emph{local steps} are all applied \\emph{in conjunction}, and even if the node data distributions and underlying graph topology are both \\emph{heterogenous}. Our analysis is based on a new connection with multi-dimensional load-balancing processes. We implement this algorithm and deploy it in a super-computing environment, showing that it can outperform previous decentralized methods in terms of end-to-end training time, and that it can even rival carefully-tuned large-batch SGD for certain tasks.","lang":"eng"}],"date_created":"2021-12-09T10:59:12Z","date_updated":"2026-06-18T08:41:40Z","title":"Asynchronous decentralized SGD with quantized and local updates","author":[{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","full_name":"Nadiradze, Giorgi","first_name":"Giorgi","orcid":"0000-0001-5634-0731","last_name":"Nadiradze"},{"full_name":"Sabour, Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","last_name":"Sabour","first_name":"Amirmojtaba"},{"first_name":"Peter","last_name":"Davies","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425"},{"full_name":"Li, Shigang","first_name":"Shigang","last_name":"Li"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"external_id":{"arxiv":["1910.12308"]},"conference":{"end_date":"2021-12-14","start_date":"2021-12-06","name":"NeurIPS: Neural Information Processing Systems","location":"Sydney, Australia"},"arxiv":1,"related_material":{"record":[{"status":"public","id":"10429","relation":"dissertation_contains"}]},"acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). PD partly conducted this work while at IST Austria and was supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n","day":"01","main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html"}],"oa_version":"Published Version","quality_controlled":"1","_id":"10435","citation":{"ama":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized SGD with quantized and local updates. In: 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation; 2021.","ista":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized SGD with quantized and local updates. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","apa":"Nadiradze, G., Sabour, A., Davies, P., Li, S., & Alistarh, D.-A. (2021). Asynchronous decentralized SGD with quantized and local updates. In 35th Conference on Neural Information Processing Systems. Sydney, Australia: Neural Information Processing Systems Foundation.","ieee":"G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous decentralized SGD with quantized and local updates,” in 35th Conference on Neural Information Processing Systems, Sydney, Australia, 2021.","mla":"Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and Local Updates.” 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","short":"G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","chicago":"Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation, 2021."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"department":[{"_id":"DaAl"}]},{"external_id":{"arxiv":["2109.00011"],"isi":["000923819400004"]},"arxiv":1,"day":"09","acknowledgement":"We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/"}]},"article_type":"original","title":"Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene","date_updated":"2025-04-14T07:43:47Z","author":[{"first_name":"Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"first_name":"Tobias","last_name":"Holder","full_name":"Holder, Tobias"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","first_name":"Maksym"},{"first_name":"Erez","last_name":"Berg","full_name":"Berg, Erez"}],"doi":"10.1103/physrevlett.127.247001","citation":{"short":"A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021).","chicago":"Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.247001.","ista":"Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001.","apa":"Ghazaryan, A., Holder, T., Serbyn, M., & Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.247001","ama":"Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 2021;127(24). doi:10.1103/physrevlett.127.247001","mla":"Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:10.1103/physrevlett.127.247001.","ieee":"A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” Physical Review Letters, vol. 127, no. 24. American Physical Society, 2021."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"volume":127,"scopus_import":"1","department":[{"_id":"MaSe"}],"oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2109.00011"}],"_id":"10527","oa":1,"isi":1,"type":"journal_article","ec_funded":1,"article_number":"247001","date_published":"2021-12-09T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","keyword":["general physics and astronomy"],"article_processing_charge":"No","year":"2021","intvolume":" 127","language":[{"iso":"eng"}],"publisher":"American Physical Society","abstract":[{"lang":"eng","text":"We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase."}],"date_created":"2021-12-10T07:51:33Z","month":"12","publication":"Physical Review Letters","status":"public","issue":"24"}]