[{"oa":1,"intvolume":"        17","issue":"14","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.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2021/sm/d0sm02012e","open_access":"1"}],"related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2020.11.16.384602v2"}]},"volume":17,"license":"https://creativecommons.org/licenses/by-nc/3.0/","extern":"1","scopus_import":"1","article_processing_charge":"No","keyword":["condensed matter physics","general chemistry"],"date_published":"2021-02-16T00:00:00Z","title":"Modelling the dynamics of vesicle reshaping and scission under osmotic shocks","date_updated":"2021-11-30T08:20:09Z","month":"02","_id":"10339","external_id":{"pmid":["33629089"]},"date_created":"2021-11-25T16:06:42Z","publication":"Soft Matter","page":"3798-3806","quality_controlled":"1","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"}],"publication_status":"published","pmid":1,"status":"public","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","citation":{"short":"C. Vanhille-Campos, A. Šarić, Soft Matter 17 (2021) 3798–3806.","apa":"Vanhille-Campos, C., &#38; Šarić, A. (2021). Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>","ieee":"C. Vanhille-Campos and A. Šarić, “Modelling the dynamics of vesicle reshaping and scission under osmotic shocks,” <i>Soft Matter</i>, vol. 17, no. 14. Royal Society of Chemistry, pp. 3798–3806, 2021.","ama":"Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. 2021;17(14):3798-3806. doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>","chicago":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” <i>Soft Matter</i>. Royal Society of Chemistry, 2021. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>.","ista":"Vanhille-Campos C, Šarić A. 2021. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. 17(14), 3798–3806.","mla":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” <i>Soft Matter</i>, vol. 17, no. 14, Royal Society of Chemistry, 2021, pp. 3798–806, doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>."},"year":"2021","author":[{"first_name":"Christian","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian"},{"last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"tmp":{"short":"CC BY-NC (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","image":"/images/cc_by_nc.png"},"publisher":"Royal Society of Chemistry","day":"16","doi":"10.1039/d0sm02012e","oa_version":"Published Version"},{"article_type":"original","type":"journal_article","citation":{"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.” <i>Biophysical Journal</i>, vol. 120, no. 4, Cell Press, 2021, pp. 598–606, doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>.","ama":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. 2021;120(4):598-606. doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>","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.” <i>Biophysical Journal</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>.","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,” <i>Biophysical Journal</i>, vol. 120, no. 4. Cell Press, pp. 598–606, 2021.","apa":"Paraschiv, A., Lagny, T. J., Campos, C. V., Coudrier, E., Bassereau, P., &#38; Šarić, A. (2021). Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>","short":"A. Paraschiv, T.J. Lagny, C.V. Campos, E. Coudrier, P. Bassereau, A. Šarić, Biophysical Journal 120 (2021) 598–606."},"quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"publication_status":"published","status":"public","pmid":1,"language":[{"iso":"eng"}],"publisher":"Cell Press","day":"16","doi":"10.1016/j.bpj.2020.12.028","oa_version":"Preprint","year":"2021","author":[{"last_name":"Paraschiv","full_name":"Paraschiv, Alexandru","first_name":"Alexandru"},{"first_name":"Thibaut J.","last_name":"Lagny","full_name":"Lagny, Thibaut J."},{"last_name":"Campos","full_name":"Campos, Christian Vanhille","first_name":"Christian Vanhille"},{"full_name":"Coudrier, Evelyne","last_name":"Coudrier","first_name":"Evelyne"},{"first_name":"Patricia","full_name":"Bassereau, Patricia","last_name":"Bassereau"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"}],"publication_identifier":{"issn":["0006-3495"]},"extern":"1","scopus_import":"1","oa":1,"intvolume":"       120","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.07.28.224741"}],"volume":120,"_id":"10340","external_id":{"pmid":["33460596"]},"date_created":"2021-11-25T16:18:23Z","publication":"Biophysical Journal","page":"598-606","keyword":["biophysics"],"article_processing_charge":"No","date_published":"2021-01-16T00:00:00Z","title":"Influence of membrane-cortex linkers on the extrusion of membrane tubes","date_updated":"2022-04-01T10:38:01Z","month":"01"},{"status":"public","pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia."}],"quality_controlled":"1","citation":{"apa":"Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., &#38; Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. <i>Protein Engineering, Design and Selection</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/protein/gzab025\">https://doi.org/10.1093/protein/gzab025</a>","short":"J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021).","ieee":"J. Lee <i>et al.</i>, “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” <i>Protein Engineering, Design and Selection</i>, vol. 34. Oxford University Press, 2021.","ama":"Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. <i>Protein Engineering, Design and Selection</i>. 2021;34. doi:<a href=\"https://doi.org/10.1093/protein/gzab025\">10.1093/protein/gzab025</a>","chicago":"Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” <i>Protein Engineering, Design and Selection</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/protein/gzab025\">https://doi.org/10.1093/protein/gzab025</a>.","mla":"Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” <i>Protein Engineering, Design and Selection</i>, vol. 34, gzab025, Oxford University Press, 2021, doi:<a href=\"https://doi.org/10.1093/protein/gzab025\">10.1093/protein/gzab025</a>.","ista":"Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025."},"type":"journal_article","article_type":"original","publication_identifier":{"eissn":["1741-0134"],"issn":["1741-0126"]},"department":[{"_id":"CaGu"}],"year":"2021","isi":1,"author":[{"full_name":"Lee, Jungmin","last_name":"Lee","first_name":"Jungmin"},{"first_name":"Andyna","full_name":"Vernet, Andyna","last_name":"Vernet"},{"id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425","first_name":"Nathalie","full_name":"Gruber, Nathalie","last_name":"Gruber"},{"last_name":"Kready","full_name":"Kready, Kasia M.","first_name":"Kasia M."},{"first_name":"Devin R.","full_name":"Burrill, Devin R.","last_name":"Burrill"},{"last_name":"Way","full_name":"Way, Jeffrey C.","first_name":"Jeffrey C."},{"full_name":"Silver, Pamela A.","last_name":"Silver","first_name":"Pamela A."}],"oa_version":"Published Version","doi":"10.1093/protein/gzab025","day":"01","publisher":"Oxford University Press","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/protein/gzab025"}],"volume":34,"intvolume":"        34","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support.","article_number":"gzab025","scopus_import":"1","month":"11","date_updated":"2023-08-14T13:01:38Z","title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","article_processing_charge":"No","date_published":"2021-11-01T00:00:00Z","publication":"Protein Engineering, Design and Selection","external_id":{"pmid":["34725710"],"isi":["000746596900001"]},"date_created":"2021-11-28T23:01:28Z","_id":"10363"},{"scopus_import":"1","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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"12","intvolume":"        17","oa":1,"volume":17,"related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/how-cells-feel-curvature/"}]},"date_created":"2021-11-28T23:01:29Z","external_id":{"isi":["000720204300004"]},"project":[{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton"}],"_id":"10365","page":"1382–1390","file_date_updated":"2023-10-11T09:31:43Z","publication":"Nature Physics","ec_funded":1,"date_published":"2021-11-18T00:00:00Z","article_processing_charge":"No","month":"11","title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","date_updated":"2023-10-16T06:31:54Z","article_type":"original","ddc":["530"],"citation":{"ama":"Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation. <i>Nature Physics</i>. 2021;17(12):1382–1390. doi:<a href=\"https://doi.org/10.1038/s41567-021-01374-1\">10.1038/s41567-021-01374-1</a>","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.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-021-01374-1\">https://doi.org/10.1038/s41567-021-01374-1</a>.","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.","mla":"Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.” <i>Nature Physics</i>, vol. 17, no. 12, Springer Nature, 2021, pp. 1382–1390, doi:<a href=\"https://doi.org/10.1038/s41567-021-01374-1\">10.1038/s41567-021-01374-1</a>.","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. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-021-01374-1\">https://doi.org/10.1038/s41567-021-01374-1</a>","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.","ieee":"M. Luciano <i>et al.</i>, “Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation,” <i>Nature Physics</i>, vol. 17, no. 12. Springer Nature, pp. 1382–1390, 2021."},"type":"journal_article","file":[{"checksum":"5d6d76750a71d7cb632bb15417c38ef7","relation":"main_file","date_updated":"2023-10-11T09:31:43Z","content_type":"application/pdf","file_size":40285498,"file_name":"50145_4_merged_1630498627.pdf","success":1,"access_level":"open_access","file_id":"14420","date_created":"2023-10-11T09:31:43Z","creator":"channezo"}],"quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","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."}],"publication_status":"published","day":"18","publisher":"Springer Nature","oa_version":"Submitted Version","doi":"10.1038/s41567-021-01374-1","author":[{"full_name":"Luciano, Marine","last_name":"Luciano","first_name":"Marine"},{"last_name":"Xue","full_name":"Xue, Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei"},{"first_name":"Winnok H.","full_name":"De Vos, Winnok H.","last_name":"De Vos"},{"first_name":"Lorena","last_name":"Redondo-Morata","full_name":"Redondo-Morata, Lorena"},{"first_name":"Mathieu","last_name":"Surin","full_name":"Surin, Mathieu"},{"full_name":"Lafont, Frank","last_name":"Lafont","first_name":"Frank"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Gabriele","full_name":"Gabriele, Sylvain","first_name":"Sylvain"}],"isi":1,"year":"2021","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"department":[{"_id":"EdHa"}]},{"type":"journal_article","citation":{"mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” <i>Cells and Development</i>, vol. 168, no. 12, 203758, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">10.1016/j.cdev.2021.203758</a>.","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.","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” <i>Cells and Development</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">https://doi.org/10.1016/j.cdev.2021.203758</a>.","ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” <i>Cells and Development</i>. 2021;168(12). doi:<a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">10.1016/j.cdev.2021.203758</a>","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” <i>Cells and Development</i>, vol. 168, no. 12. Elsevier, 2021.","apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., &#38; Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” <i>Cells and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cdev.2021.203758\">https://doi.org/10.1016/j.cdev.2021.203758</a>","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021)."},"article_type":"letter_note","publication_status":"published","language":[{"iso":"eng"}],"status":"public","pmid":1,"quality_controlled":"1","doi":"10.1016/j.cdev.2021.203758","oa_version":"Published Version","publisher":"Elsevier","day":"17","department":[{"_id":"CaHe"}],"publication_identifier":{"issn":["2667-2901"]},"author":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"last_name":"Lennon","full_name":"Lennon, Ana Maria","first_name":"Ana Maria"},{"first_name":"Roberto","full_name":"Mayor, Roberto","last_name":"Mayor"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"}],"isi":1,"year":"2021","scopus_import":"1","volume":168,"main_file_link":[{"url":"https://doi.org/10.1016/j.cdev.2021.203758","open_access":"1"}],"article_number":"203758","issue":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"intvolume":"       168","publication":"Cells and Development","_id":"10366","date_created":"2021-11-28T23:01:30Z","external_id":{"pmid":["34800748"],"isi":["000974771600028"]},"date_updated":"2023-08-14T13:02:40Z","title":"Special rebranding issue: “Quantitative cell and developmental biology”","month":"11","date_published":"2021-11-17T00:00:00Z","article_processing_charge":"No"},{"_id":"10367","date_created":"2021-11-28T23:01:30Z","publication":"59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts","file_date_updated":"2021-11-29T08:41:00Z","page":"29-30","article_processing_charge":"No","date_published":"2021-08-01T00:00:00Z","title":"Recognizing multimodal entailment","date_updated":"2022-01-26T14:26:36Z","month":"08","scopus_import":"1","oa":1,"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.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://aclanthology.org/2021.acl-tutorials.6/","open_access":"1"}],"publisher":"Association for Computational Linguistics","day":"01","doi":"10.18653/v1/2021.acl-tutorials.6","oa_version":"Published Version","year":"2021","conference":{"name":"ACL: Association for Computational Linguistics ; IJCNLP: International Joint Conference on Natural Language Processing","end_date":"2021-08-06","location":"Bangkok, Thailand","start_date":"2021-08-01"},"author":[{"first_name":"Cesar","last_name":"Ilharco","full_name":"Ilharco, Cesar"},{"first_name":"Afsaneh","last_name":"Shirazi","full_name":"Shirazi, Afsaneh"},{"first_name":"Arjun","last_name":"Gopalan","full_name":"Gopalan, Arjun"},{"full_name":"Nagrani, Arsha","last_name":"Nagrani","first_name":"Arsha"},{"first_name":"Blaž","last_name":"Bratanič","full_name":"Bratanič, Blaž"},{"first_name":"Chris","full_name":"Bregler, Chris","last_name":"Bregler"},{"first_name":"Christina","last_name":"Liu","full_name":"Liu, Christina"},{"first_name":"Felipe","last_name":"Ferreira","full_name":"Ferreira, Felipe"},{"full_name":"Barcik, Gabriek","last_name":"Barcik","first_name":"Gabriek"},{"full_name":"Ilharco, Gabriel","last_name":"Ilharco","first_name":"Gabriel"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","full_name":"Osang, Georg F","last_name":"Osang"},{"first_name":"Jannis","full_name":"Bulian, Jannis","last_name":"Bulian"},{"full_name":"Frank, Jared","last_name":"Frank","first_name":"Jared"},{"first_name":"Lucas","full_name":"Smaira, Lucas","last_name":"Smaira"},{"full_name":"Cao, Qin","last_name":"Cao","first_name":"Qin"},{"last_name":"Marino","full_name":"Marino, Ricardo","first_name":"Ricardo"},{"first_name":"Roma","full_name":"Patel, Roma","last_name":"Patel"},{"first_name":"Thomas","full_name":"Leung, Thomas","last_name":"Leung"},{"first_name":"Vaiva","last_name":"Imbrasaite","full_name":"Imbrasaite, Vaiva"}],"publication_identifier":{"isbn":["9-781-9540-8557-2"]},"department":[{"_id":"HeEd"}],"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"},"ddc":["000"],"file":[{"file_id":"10368","creator":"cchlebak","date_created":"2021-11-29T08:41:00Z","relation":"main_file","checksum":"b14052a025a6ecf675bdfe51db98c0d7","date_updated":"2021-11-29T08:41:00Z","content_type":"application/pdf","file_size":1227703,"file_name":"2021_ACL_Ilharco.pdf","success":1,"access_level":"open_access"}],"type":"conference","citation":{"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.","mla":"Ilharco, Cesar, et al. “Recognizing Multimodal Entailment.” <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i>, Association for Computational Linguistics, 2021, pp. 29–30, doi:<a href=\"https://doi.org/10.18653/v1/2021.acl-tutorials.6\">10.18653/v1/2021.acl-tutorials.6</a>.","chicago":"Ilharco, Cesar, Afsaneh Shirazi, Arjun Gopalan, Arsha Nagrani, Blaž Bratanič, Chris Bregler, Christina Liu, et al. “Recognizing Multimodal Entailment.” In <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i>, 29–30. Association for Computational Linguistics, 2021. <a href=\"https://doi.org/10.18653/v1/2021.acl-tutorials.6\">https://doi.org/10.18653/v1/2021.acl-tutorials.6</a>.","ama":"Ilharco C, Shirazi A, Gopalan A, et al. Recognizing multimodal entailment. In: <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i>. Association for Computational Linguistics; 2021:29-30. doi:<a href=\"https://doi.org/10.18653/v1/2021.acl-tutorials.6\">10.18653/v1/2021.acl-tutorials.6</a>","ieee":"C. Ilharco <i>et al.</i>, “Recognizing multimodal entailment,” in <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i>, Bangkok, Thailand, 2021, pp. 29–30.","apa":"Ilharco, C., Shirazi, A., Gopalan, A., Nagrani, A., Bratanič, B., Bregler, C., … Imbrasaite, V. (2021). Recognizing multimodal entailment. In <i>59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts</i> (pp. 29–30). Bangkok, Thailand: Association for Computational Linguistics. <a href=\"https://doi.org/10.18653/v1/2021.acl-tutorials.6\">https://doi.org/10.18653/v1/2021.acl-tutorials.6</a>","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."},"quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"publication_status":"published","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}]},{"month":"11","title":"Generation of spin currents by a temperature gradient in a two-terminal device","date_updated":"2023-08-14T13:04:34Z","ec_funded":1,"article_processing_charge":"No","date_published":"2021-11-26T00:00:00Z","publication":"Communications Physics","file_date_updated":"2021-12-06T14:53:41Z","external_id":{"isi":["10.1038/s42005-021-00753-7"],"arxiv":["2101.02020"]},"date_created":"2021-12-05T23:01:39Z","_id":"10401","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"volume":4,"oa":1,"intvolume":"         4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"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_number":"252","scopus_import":"1","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"},"department":[{"_id":"MiLe"}],"publication_identifier":{"eissn":["23993650"]},"year":"2021","author":[{"first_name":"Rafael E.","last_name":"Barfknecht","full_name":"Barfknecht, Rafael E."},{"first_name":"Angela","full_name":"Foerster, Angela","last_name":"Foerster"},{"full_name":"Zinner, Nikolaj T.","last_name":"Zinner","first_name":"Nikolaj T."},{"last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"arxiv":1,"oa_version":"Published Version","doi":"10.1038/s42005-021-00753-7","day":"26","publisher":"Springer Nature","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"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."}],"publication_status":"published","quality_controlled":"1","citation":{"short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021).","apa":"Barfknecht, R. E., Foerster, A., Zinner, N. T., &#38; Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-021-00753-7\">https://doi.org/10.1038/s42005-021-00753-7</a>","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,” <i>Communications Physics</i>, vol. 4, no. 1. Springer Nature, 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.” <i>Communications Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s42005-021-00753-7\">https://doi.org/10.1038/s42005-021-00753-7</a>.","ama":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. <i>Communications Physics</i>. 2021;4(1). doi:<a href=\"https://doi.org/10.1038/s42005-021-00753-7\">10.1038/s42005-021-00753-7</a>","mla":"Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” <i>Communications Physics</i>, vol. 4, no. 1, 252, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s42005-021-00753-7\">10.1038/s42005-021-00753-7</a>.","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."},"type":"journal_article","file":[{"file_size":1068984,"content_type":"application/pdf","date_updated":"2021-12-06T14:53:41Z","relation":"main_file","checksum":"9097319952cb9a3d96e7fd3aa9813a03","access_level":"open_access","success":1,"file_name":"2021_NatComm_Barfknecht.pdf","file_id":"10420","date_created":"2021-12-06T14:53:41Z","creator":"alisjak"}],"article_type":"original","ddc":["530"]},{"date_created":"2021-12-05T23:01:40Z","external_id":{"isi":["000722322900020"],"pmid":["34819507"]},"_id":"10402","project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"file_date_updated":"2021-12-10T08:54:09Z","publication":"Nature Communications","ec_funded":1,"date_published":"2021-11-24T00:00:00Z","article_processing_charge":"No","month":"11","date_updated":"2023-08-14T13:18:46Z","title":"Theory of branching morphogenesis by local interactions and global guidance","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.).","intvolume":"        12","oa":1,"article_number":"6830","volume":12,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13058"}]},"day":"24","publisher":"Springer Nature","oa_version":"Published Version","doi":"10.1038/s41467-021-27135-5","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar"},{"full_name":"Kamenev, Dmitrii","last_name":"Kamenev","first_name":"Dmitrii"},{"first_name":"Kazunori","full_name":"Sunadome, Kazunori","last_name":"Sunadome"},{"first_name":"Dominik C","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","last_name":"Fachet","full_name":"Fachet, Dominik C"},{"full_name":"Lallemend, Francois","last_name":"Lallemend","first_name":"Francois"},{"last_name":"Adameyko","full_name":"Adameyko, Igor","first_name":"Igor"},{"first_name":"Saida","last_name":"Hadjab","full_name":"Hadjab, Saida"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"year":"2021","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"},"publication_identifier":{"eissn":["2041-1723"]},"department":[{"_id":"EdHa"}],"article_type":"original","ddc":["573"],"type":"journal_article","citation":{"ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-27135-5\">10.1038/s41467-021-27135-5</a>","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.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-27135-5\">https://doi.org/10.1038/s41467-021-27135-5</a>.","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.","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” <i>Nature Communications</i>, vol. 12, 6830, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-27135-5\">10.1038/s41467-021-27135-5</a>.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-27135-5\">https://doi.org/10.1038/s41467-021-27135-5</a>","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","ieee":"M. C. Ucar <i>et al.</i>, “Theory of branching morphogenesis by local interactions and global guidance,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021."},"file":[{"file_id":"10529","date_created":"2021-12-10T08:54:09Z","creator":"cchlebak","relation":"main_file","checksum":"63c56ec75314a71e63e7dd2920b3c5b5","content_type":"application/pdf","date_updated":"2021-12-10T08:54:09Z","file_size":2303405,"file_name":"2021_NatComm_Ucar.pdf","success":1,"access_level":"open_access"}],"quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","pmid":1,"publication_status":"published","abstract":[{"lang":"eng","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."}]},{"volume":10,"oa":1,"intvolume":"        10","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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e65954","scopus_import":"1","month":"11","date_updated":"2023-08-14T13:12:07Z","title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","article_processing_charge":"No","date_published":"2021-11-03T00:00:00Z","publication":"eLife","file_date_updated":"2021-12-10T08:31:41Z","external_id":{"isi":["000715789500001"]},"date_created":"2021-12-05T23:01:40Z","_id":"10403","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_status":"published","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"}],"quality_controlled":"1","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).","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. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.65954\">https://doi.org/10.7554/eLife.65954</a>","ieee":"C. Biane <i>et al.</i>, “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ama":"Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.65954\">10.7554/eLife.65954</a>","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.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.65954\">https://doi.org/10.7554/eLife.65954</a>.","mla":"Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” <i>ELife</i>, vol. 10, e65954, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.65954\">10.7554/eLife.65954</a>.","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."},"type":"journal_article","file":[{"creator":"cchlebak","date_created":"2021-12-10T08:31:41Z","file_id":"10528","access_level":"open_access","success":1,"file_name":"2021_eLife_Biane.pdf","file_size":13131322,"date_updated":"2021-12-10T08:31:41Z","content_type":"application/pdf","checksum":"c7c33c3319428d56e332e22349c50ed3","relation":"main_file"}],"article_type":"original","ddc":["570"],"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"},"publication_identifier":{"eissn":["2050-084X"]},"department":[{"_id":"RySh"}],"year":"2021","author":[{"first_name":"Celia","full_name":"Biane, Celia","last_name":"Biane"},{"first_name":"Florian","full_name":"Rückerl, Florian","last_name":"Rückerl"},{"first_name":"Therese","full_name":"Abrahamsson, Therese","last_name":"Abrahamsson"},{"full_name":"Saint-Cloment, Cécile","last_name":"Saint-Cloment","first_name":"Cécile"},{"first_name":"Jean","full_name":"Mariani, Jean","last_name":"Mariani"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"full_name":"Digregorio, David A.","last_name":"Digregorio","first_name":"David A."},{"full_name":"Sherrard, Rachel M.","last_name":"Sherrard","first_name":"Rachel M."},{"first_name":"Laurence","last_name":"Cathala","full_name":"Cathala, Laurence"}],"isi":1,"oa_version":"Published Version","doi":"10.7554/eLife.65954","day":"03","publisher":"eLife Sciences Publications"},{"publication_status":"published","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","type":"journal_article","citation":{"ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” <i>Computer Graphics Forum</i>, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., &#38; Waldner, M. (2021). Interactive analysis of CNN robustness. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14418\">https://doi.org/10.1111/cgf.14418</a>","mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” <i>Computer Graphics Forum</i>, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:<a href=\"https://doi.org/10.1111/cgf.14418\">10.1111/cgf.14418</a>.","ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” <i>Computer Graphics Forum</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/cgf.14418\">https://doi.org/10.1111/cgf.14418</a>.","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. <i>Computer Graphics Forum</i>. 2021;40(7):253-264. doi:<a href=\"https://doi.org/10.1111/cgf.14418\">10.1111/cgf.14418</a>"},"article_type":"original","department":[{"_id":"ToHe"}],"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"author":[{"first_name":"Stefan","last_name":"Sietzen","full_name":"Sietzen, Stefan"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","full_name":"Lechner, Mathias","last_name":"Lechner"},{"last_name":"Borowski","full_name":"Borowski, Judy","first_name":"Judy"},{"first_name":"Ramin","full_name":"Hasani, Ramin","last_name":"Hasani"},{"first_name":"Manuela","last_name":"Waldner","full_name":"Waldner, Manuela"}],"isi":1,"year":"2021","doi":"10.1111/cgf.14418","oa_version":"Preprint","arxiv":1,"publisher":"Wiley","day":"27","volume":40,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.07667"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7","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","oa":1,"intvolume":"        40","scopus_import":"1","title":"Interactive analysis of CNN robustness","date_updated":"2023-08-14T13:11:42Z","month":"11","date_published":"2021-11-27T00:00:00Z","article_processing_charge":"No","publication":"Computer Graphics Forum","page":"253-264","_id":"10404","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"date_created":"2021-12-05T23:01:40Z","external_id":{"arxiv":["2110.07667"],"isi":["000722952000024"]}},{"doi":"10.1146/annurev-genet-071819-103748","oa_version":"None","publisher":"Annual Reviews","day":"30","publication_identifier":{"eissn":["1545-2948"],"issn":["0066-4197"]},"department":[{"_id":"CaHe"}],"author":[{"first_name":"Nikhil","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","last_name":"Mishra","orcid":"0000-0002-6425-5788","full_name":"Mishra, Nikhil"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"year":"2021","type":"journal_article","citation":{"short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.","apa":"Mishra, N., &#38; Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. <i>Annual Review of Genetics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">https://doi.org/10.1146/annurev-genet-071819-103748</a>","ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” <i>Annual Review of Genetics</i>, vol. 55. Annual Reviews, pp. 209–233, 2021.","chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” <i>Annual Review of Genetics</i>. Annual Reviews, 2021. <a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">https://doi.org/10.1146/annurev-genet-071819-103748</a>.","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. <i>Annual Review of Genetics</i>. 2021;55:209-233. doi:<a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">10.1146/annurev-genet-071819-103748</a>","mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” <i>Annual Review of Genetics</i>, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:<a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">10.1146/annurev-genet-071819-103748</a>.","ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233."},"article_type":"original","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"}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","pmid":1,"quality_controlled":"1","publication":"Annual Review of Genetics","page":"209-233","_id":"10406","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_created":"2021-12-05T23:01:41Z","external_id":{"pmid":["34460295"],"isi":["000747220900010"]},"title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","date_updated":"2023-08-14T13:05:13Z","month":"08","date_published":"2021-08-30T00:00:00Z","article_processing_charge":"No","keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"ec_funded":1,"scopus_import":"1","volume":55,"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).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        55"},{"publication_status":"published","abstract":[{"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.","lang":"eng"}],"status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","citation":{"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.","apa":"Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_14\">https://doi.org/10.1007/978-3-030-90453-1_14</a>","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.","mla":"Chakraborty, Suvradip, et al. <i>Trojan-Resilience without Cryptography</i>. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_14\">10.1007/978-3-030-90453-1_14</a>.","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:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_14\">10.1007/978-3-030-90453-1_14</a>","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. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_14\">https://doi.org/10.1007/978-3-030-90453-1_14</a>."},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"]},"department":[{"_id":"KrPi"}],"conference":{"end_date":"2021-11-11","location":"Raleigh, NC, United States","start_date":"2021-11-08","name":"TCC: Theory of Cryptography Conference"},"year":"2021","isi":1,"author":[{"last_name":"Chakraborty","full_name":"Chakraborty, Suvradip","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"first_name":"Stefan","last_name":"Dziembowski","full_name":"Dziembowski, Stefan"},{"full_name":"Gałązka, Małgorzata","last_name":"Gałązka","first_name":"Małgorzata"},{"full_name":"Lizurej, Tomasz","last_name":"Lizurej","first_name":"Tomasz"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"},{"last_name":"Yeo","full_name":"Yeo, Michelle X","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1007/978-3-030-90453-1_14","oa_version":"Preprint","publisher":"Springer Nature","day":"04","main_file_link":[{"url":"https://eprint.iacr.org/2021/1224","open_access":"1"}],"alternative_title":["LNCS"],"volume":13043,"intvolume":"     13043","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","date_updated":"2023-08-14T13:07:46Z","title":"Trojan-resilience without cryptography","month":"11","article_processing_charge":"No","date_published":"2021-11-04T00:00:00Z","ec_funded":1,"page":"397-428","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"_id":"10407","external_id":{"isi":["000728364000014"]},"date_created":"2021-12-05T23:01:42Z"},{"scopus_import":"1","oa":1,"intvolume":"     13044","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).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1158"}],"volume":13044,"alternative_title":["LNCS"],"external_id":{"isi":["000728363700008"]},"date_created":"2021-12-05T23:01:42Z","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"_id":"10408","page":"222-253","publication":"19th International Conference","ec_funded":1,"article_processing_charge":"No","date_published":"2021-11-04T00:00:00Z","month":"11","date_updated":"2023-08-14T13:19:39Z","title":"Grafting key trees: Efficient key management for overlapping groups","type":"conference","citation":{"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 <i>19th International Conference</i>, 13044:222–53. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">https://doi.org/10.1007/978-3-030-90456-2_8</a>.","ama":"Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: <i>19th International Conference</i>. Vol 13044. Springer Nature; 2021:222-253. doi:<a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">10.1007/978-3-030-90456-2_8</a>","mla":"Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” <i>19th International Conference</i>, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:<a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">10.1007/978-3-030-90456-2_8</a>.","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.","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.","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 <i>19th International Conference</i> (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">https://doi.org/10.1007/978-3-030-90456-2_8</a>","ieee":"J. F. Alwen <i>et al.</i>, “Grafting key trees: Efficient key management for overlapping groups,” in <i>19th International Conference</i>, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253."},"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"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."}],"publication_status":"published","day":"04","publisher":"Springer Nature","oa_version":"Preprint","doi":"10.1007/978-3-030-90456-2_8","year":"2021","conference":{"location":"Raleigh, NC, United States","start_date":"2021-11-08","end_date":"2021-11-11","name":"TCC: Theory of Cryptography"},"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F"},{"id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","first_name":"Benedikt","orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt","last_name":"Auerbach"},{"last_name":"Baig","full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad"},{"last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel","first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc"},{"first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","full_name":"Klein, Karen"},{"full_name":"Pascual Perez, Guillermo","orcid":"0000-0001-8630-415X","last_name":"Pascual Perez","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"},{"id":"488F98B0-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","last_name":"Walter"}],"isi":1,"department":[{"_id":"KrPi"}],"publication_identifier":{"isbn":["9-783-0309-0455-5"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-030-90456-2"]}},{"acknowledgement":"We are grateful to Daniel Wichs for helpful discussions on the landscape of adaptive security of Yao’s garbling. We would also like to thank Crypto 2021 and TCC 2021 reviewers for their detailed review and suggestions, which helped improve presentation considerably.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":"13043 ","alternative_title":["LNCS"],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10044"}]},"main_file_link":[{"url":"https://eprint.iacr.org/2021/926","open_access":"1"}],"scopus_import":"1","date_published":"2021-11-04T00:00:00Z","article_processing_charge":"No","ec_funded":1,"date_updated":"2023-08-17T06:21:38Z","title":"On treewidth, separators and Yao’s garbling","month":"11","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"_id":"10409","date_created":"2021-12-05T23:01:43Z","external_id":{"isi":["000728364000017"]},"publication":"19th International Conference","page":"486-517","quality_controlled":"1","abstract":[{"text":"We show that Yao’s garbling scheme is adaptively indistinguishable for the class of Boolean circuits of size   S  and treewidth   w  with only a   SO(w)  loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly   O(δwlog(S)) ,   δ  being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity.  with only a   SO(w)  loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly   O(δwlog(S)) ,   δ  being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","citation":{"ieee":"C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “On treewidth, separators and Yao’s garbling,” in <i>19th International Conference</i>, Raleigh, NC, United States, 2021, vol. 13043, pp. 486–517.","apa":"Kamath Hosdurg, C., Klein, K., &#38; Pietrzak, K. Z. (2021). On treewidth, separators and Yao’s garbling. In <i>19th International Conference</i> (Vol. 13043, pp. 486–517). Raleigh, NC, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_17\">https://doi.org/10.1007/978-3-030-90453-1_17</a>","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th International Conference, Springer Nature, 2021, pp. 486–517.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ. 2021. On treewidth, separators and Yao’s garbling. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 486–517.","mla":"Kamath Hosdurg, Chethan, et al. “On Treewidth, Separators and Yao’s Garbling.” <i>19th International Conference</i>, vol. 13043, Springer Nature, 2021, pp. 486–517, doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_17\">10.1007/978-3-030-90453-1_17</a>.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ. On treewidth, separators and Yao’s garbling. In: <i>19th International Conference</i>. Vol 13043. Springer Nature; 2021:486-517. doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_17\">10.1007/978-3-030-90453-1_17</a>","chicago":"Kamath Hosdurg, Chethan, Karen Klein, and Krzysztof Z Pietrzak. “On Treewidth, Separators and Yao’s Garbling.” In <i>19th International Conference</i>, 13043:486–517. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_17\">https://doi.org/10.1007/978-3-030-90453-1_17</a>."},"type":"conference","isi":1,"author":[{"full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein","full_name":"Klein, Karen"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"conference":{"start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11","name":"TCC: Theory of Cryptography"},"year":"2021","department":[{"_id":"KrPi"}],"publication_identifier":{"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publisher":"Springer Nature","day":"04","doi":"10.1007/978-3-030-90453-1_17","oa_version":"Preprint"},{"year":"2021","conference":{"end_date":"2021-11-11","start_date":"2021-11-08","location":"Raleigh, NC, United States","name":"TCC: Theory of Cryptography"},"author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"full_name":"Klein, Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","full_name":"Walter, Michael","orcid":"0000-0003-3186-2482"}],"isi":1,"department":[{"_id":"KrPi"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"]},"day":"04","publisher":"Springer Nature","oa_version":"Preprint","doi":"10.1007/978-3-030-90453-1_19","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"text":"The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical framework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower bounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and broadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques.","lang":"eng"}],"citation":{"ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity in security games on graphs,” in <i>19th International Conference</i>, Raleigh, NC, United States, 2021, vol. 13043, pp. 550–581.","apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., &#38; Walter, M. (2021). The cost of adaptivity in security games on graphs. In <i>19th International Conference</i> (Vol. 13043, pp. 550–581). Raleigh, NC, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_19\">https://doi.org/10.1007/978-3-030-90453-1_19</a>","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 550–581.","mla":"Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on Graphs.” <i>19th International Conference</i>, vol. 13043, Springer Nature, 2021, pp. 550–81, doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_19\">10.1007/978-3-030-90453-1_19</a>.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity in security games on graphs. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 550–581.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “The Cost of Adaptivity in Security Games on Graphs.” In <i>19th International Conference</i>, 13043:550–81. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_19\">https://doi.org/10.1007/978-3-030-90453-1_19</a>.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in security games on graphs. In: <i>19th International Conference</i>. Vol 13043. Springer Nature; 2021:550-581. doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_19\">10.1007/978-3-030-90453-1_19</a>"},"type":"conference","ec_funded":1,"article_processing_charge":"No","date_published":"2021-11-04T00:00:00Z","month":"11","title":"The cost of adaptivity in security games on graphs","date_updated":"2023-10-17T09:24:07Z","external_id":{"isi":["000728364000019"]},"date_created":"2021-12-05T23:01:43Z","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"_id":"10410","page":"550-581","publication":"19th International Conference","oa":1,"intvolume":"     13043","acknowledgement":"C. Kamath—Supported by Azrieli International Postdoctoral Fellowship. Most of the work was done while the author was at Northeastern University and Charles University, funded by the IARPA grant IARPA/2019-19-020700009 and project PRIMUS/17/SCI/9, respectively. K. Klein—Supported in part by ERC CoG grant 724307. Most of the work was done while the author was at IST Austria funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT). K. Pietrzak—Funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10048"}]},"main_file_link":[{"url":"https://ia.cr/2021/059","open_access":"1"}],"alternative_title":["LNCS"],"volume":13043,"scopus_import":"1"},{"volume":13047,"alternative_title":["LNCS"],"related_material":{"record":[{"id":"14539","status":"public","relation":"dissertation_contains"},{"id":"14778","relation":"later_version","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.02188"}],"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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"     13047","oa":1,"scopus_import":"1","month":"11","title":"On lexicographic proof rules for probabilistic termination","date_updated":"2025-07-14T09:10:11Z","ec_funded":1,"date_published":"2021-11-10T00:00:00Z","article_processing_charge":"No","page":"619-639","publication":"24th International Symposium on Formal Methods","date_created":"2021-12-05T23:01:45Z","external_id":{"isi":["000758218600033"],"arxiv":["2108.02188"]},"_id":"10414","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"language":[{"iso":"eng"}],"status":"public","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"}],"publication_status":"published","quality_controlled":"1","type":"conference","citation":{"apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., Zárevúcky, J., &#38; Zikelic, D. (2021). On lexicographic proof rules for probabilistic termination. In <i>24th International Symposium on Formal Methods</i> (Vol. 13047, pp. 619–639). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90870-6_33\">https://doi.org/10.1007/978-3-030-90870-6_33</a>","short":"K. Chatterjee, E.K. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:, 24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” in <i>24th International Symposium on Formal Methods</i>, Virtual, 2021, vol. 13047, pp. 619–639.","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” In <i>24th International Symposium on Formal Methods</i>, 13047:619–39. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90870-6_33\">https://doi.org/10.1007/978-3-030-90870-6_33</a>.","ama":"Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. In: <i>24th International Symposium on Formal Methods</i>. Vol 13047. Springer Nature; 2021:619-639. doi:<a href=\"https://doi.org/10.1007/978-3-030-90870-6_33\">10.1007/978-3-030-90870-6_33</a>","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” <i>24th International Symposium on Formal Methods</i>, vol. 13047, Springer Nature, 2021, pp. 619–39, doi:<a href=\"https://doi.org/10.1007/978-3-030-90870-6_33\">10.1007/978-3-030-90870-6_33</a>.","ista":"Chatterjee K, Goharshady EK, 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."},"department":[{"_id":"KrCh"}],"publication_identifier":{"eisbn":["978-3-030-90870-6"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-0309-0869-0"]},"isi":1,"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady","first_name":"Ehsan Kafshdar"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný","full_name":"Novotný, Petr"},{"full_name":"Zárevúcky, Jiří","last_name":"Zárevúcky","first_name":"Jiří"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"}],"year":"2021","conference":{"start_date":"2021-11-20","location":"Virtual","end_date":"2021-11-26","name":"FM: Formal Methods"},"arxiv":1,"oa_version":"Preprint","doi":"10.1007/978-3-030-90870-6_33","day":"10","publisher":"Springer Nature"},{"language":[{"iso":"eng"}],"status":"public","alternative_title":["Progress in Mathematics"],"publication_status":"published","volume":343,"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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       343","place":"Cham","quality_controlled":"1","citation":{"ieee":"T. D. Browning, <i>Cubic Forms and the Circle Method</i>, vol. 343. Cham: Springer Nature, 2021.","short":"T.D. Browning, Cubic Forms and the Circle Method, Springer Nature, Cham, 2021.","apa":"Browning, T. D. (2021). <i>Cubic Forms and the Circle Method</i> (Vol. 343). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-86872-7\">https://doi.org/10.1007/978-3-030-86872-7</a>","ista":"Browning TD. 2021. Cubic Forms and the Circle Method, Cham: Springer Nature, XIV, 166p.","mla":"Browning, Timothy D. <i>Cubic Forms and the Circle Method</i>. Vol. 343, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/978-3-030-86872-7\">10.1007/978-3-030-86872-7</a>.","ama":"Browning TD. <i>Cubic Forms and the Circle Method</i>. Vol 343. Cham: Springer Nature; 2021. doi:<a href=\"https://doi.org/10.1007/978-3-030-86872-7\">10.1007/978-3-030-86872-7</a>","chicago":"Browning, Timothy D. <i>Cubic Forms and the Circle Method</i>. Vol. 343. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-86872-7\">https://doi.org/10.1007/978-3-030-86872-7</a>."},"type":"book","scopus_import":"1","month":"12","title":"Cubic Forms and the Circle Method","date_updated":"2022-06-03T07:38:33Z","publication_identifier":{"eisbn":["978-3-030-86872-7"],"issn":["0743-1643"],"eissn":["2296-505X"],"isbn":["978-3-030-86871-0"]},"department":[{"_id":"TiBr"}],"author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"}],"date_published":"2021-12-01T00:00:00Z","year":"2021","article_processing_charge":"No","oa_version":"None","page":"XIV, 166","doi":"10.1007/978-3-030-86872-7","date_created":"2021-12-05T23:01:46Z","day":"01","publisher":"Springer Nature","_id":"10415"},{"month":"12","date_updated":"2023-09-07T13:34:12Z","degree_awarded":"MS","title":"Towards designer materials using customizable particle shape","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"publication_identifier":{"issn":["2791-4585"]},"author":[{"first_name":"Anton","id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","full_name":"Piankov, Anton","last_name":"Piankov"}],"date_published":"2021-12-07T00:00:00Z","article_processing_charge":"No","year":"2021","oa_version":"Published Version","file_date_updated":"2022-03-10T12:10:25Z","supervisor":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074"}],"doi":"10.15479/at:ista:10422","date_created":"2021-12-07T10:48:06Z","day":"07","_id":"10422","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publication_status":"published","alternative_title":["ISTA Master's Thesis"],"abstract":[{"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.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"citation":{"ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10422\">10.15479/at:ista:10422</a>","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10422\">https://doi.org/10.15479/at:ista:10422</a>.","mla":"Piankov, Anton. <i>Towards Designer Materials Using Customizable Particle Shape</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10422\">10.15479/at:ista:10422</a>.","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","apa":"Piankov, A. (2021). <i>Towards designer materials using customizable particle shape</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10422\">https://doi.org/10.15479/at:ista:10422</a>","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021."},"type":"dissertation","file":[{"access_level":"closed","file_name":"Thesis.zip","file_size":394018,"content_type":"application/x-zip-compressed","date_updated":"2022-03-10T12:10:25Z","relation":"source_file","checksum":"114e8f4b2c002c6c352416c12de2c695","creator":"cchlebak","date_created":"2021-12-07T11:13:52Z","file_id":"10424"},{"file_size":47638,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2022-03-10T12:10:25Z","relation":"source_file","checksum":"cd15ae991ced352a9959815f794e657c","access_level":"closed","file_name":"Preliminary_pages_Piankov.docx","file_id":"10425","date_created":"2021-12-07T11:14:01Z","creator":"cchlebak"},{"date_updated":"2021-12-07T11:20:35Z","content_type":"application/pdf","file_size":484965,"checksum":"e6899c798b75ba42fab9822bce309050","relation":"main_file","success":1,"access_level":"open_access","file_name":"2021_Piankov_combined.pdf","file_id":"10426","date_created":"2021-12-07T11:20:35Z","creator":"cchlebak"}],"ddc":["530"]},{"file":[{"file_id":"10436","date_created":"2021-12-09T17:47:49Z","creator":"gnadirad","date_updated":"2021-12-09T17:47:49Z","content_type":"application/pdf","file_size":2370859,"relation":"main_file","checksum":"6bf14e9a523387328f016c0689f5e10e","success":1,"access_level":"open_access","file_name":"Thesis_Final_09_12_2021.pdf"},{"file_size":2596924,"date_updated":"2022-03-28T12:55:12Z","content_type":"application/zip","relation":"source_file","checksum":"914d6c5ca86bd0add471971a8f4c4341","access_level":"closed","file_name":"Thesis_Final_09_12_2021.zip","file_id":"10437","date_created":"2021-12-09T17:47:49Z","creator":"gnadirad"}],"type":"dissertation","citation":{"ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10429\">10.15479/at:ista:10429</a>","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10429\">https://doi.org/10.15479/at:ista:10429</a>.","mla":"Nadiradze, Giorgi. <i>On Achieving Scalability through Relaxation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10429\">10.15479/at:ista:10429</a>.","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","apa":"Nadiradze, G. (2021). <i>On achieving scalability through relaxation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10429\">https://doi.org/10.15479/at:ista:10429</a>","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021."},"ddc":["000"],"abstract":[{"text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently  creates a race condition. This bottleneck  can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the  stochastic gradient descent (SGD) algorithm, which distribute computation  among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be  relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","doi":"10.15479/at:ista:10429","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","day":"09","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze"}],"year":"2021","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"10432","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6673"},{"relation":"part_of_dissertation","status":"public","id":"5965"},{"status":"public","relation":"part_of_dissertation","id":"10435"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"file_date_updated":"2022-03-28T12:55:12Z","supervisor":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"page":"132","project":[{"call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning"}],"_id":"10429","date_created":"2021-12-08T21:52:28Z","date_updated":"2023-10-17T11:48:55Z","title":"On achieving scalability through relaxation","month":"12","date_published":"2021-12-09T00:00:00Z","article_processing_charge":"No","ec_funded":1},{"date_created":"2021-12-09T09:21:35Z","external_id":{"arxiv":["2001.05918"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning"}],"_id":"10432","page":"9037-9045","publication":"Proceedings of the AAAI Conference on Artificial Intelligence","ec_funded":1,"date_published":"2021-05-18T00:00:00Z","article_processing_charge":"No","month":"05","title":"Elastic consistency: A practical consistency model for distributed stochastic gradient descent","date_updated":"2023-09-07T13:31:39Z","acknowledgement":"We would like to thank Christopher De Sa for his feedback on an earlier draft of this paper, as well as the anonymous AAAI reviewers for their useful comments. This project has received\r\nfunding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Bapi\r\nChatterjee was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754411 (ISTPlus).","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"10","oa":1,"intvolume":"        35","volume":35,"main_file_link":[{"open_access":"1","url":"https://ojs.aaai.org/index.php/AAAI/article/view/17092"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10429"}]},"day":"18","oa_version":"Published Version","arxiv":1,"author":[{"orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi"},{"last_name":"Markov","full_name":"Markov, Ilia","first_name":"Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425"},{"id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi","last_name":"Chatterjee","full_name":"Chatterjee, Bapi","orcid":"0000-0002-2742-4028"},{"full_name":"Kungurtsev, Vyacheslav ","last_name":"Kungurtsev","first_name":"Vyacheslav "},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"conference":{"end_date":"2021-02-09","start_date":"2021-02-02","location":"Virtual","name":"AAAI: Association for the Advancement of Artificial Intelligence"},"year":"2021","department":[{"_id":"DaAl"}],"type":"conference","citation":{"ieee":"G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, and D.-A. Alistarh, “Elastic consistency: A practical consistency model for distributed stochastic gradient descent,” in <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, Virtual, 2021, vol. 35, no. 10, pp. 9037–9045.","short":"G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, D.-A. Alistarh, in:, Proceedings of the AAAI Conference on Artificial Intelligence, 2021, pp. 9037–9045.","apa":"Nadiradze, G., Markov, I., Chatterjee, B., Kungurtsev, V., &#38; Alistarh, D.-A. (2021). Elastic consistency: A practical consistency model for distributed stochastic gradient descent. In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i> (Vol. 35, pp. 9037–9045). Virtual.","ista":"Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. 2021. Elastic consistency: A practical consistency model for distributed stochastic gradient descent. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI: Association for the Advancement of Artificial Intelligence vol. 35, 9037–9045.","mla":"Nadiradze, Giorgi, et al. “Elastic Consistency: A Practical Consistency Model for Distributed Stochastic Gradient Descent.” <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, vol. 35, no. 10, 2021, pp. 9037–45.","chicago":"Nadiradze, Giorgi, Ilia Markov, Bapi Chatterjee, Vyacheslav  Kungurtsev, and Dan-Adrian Alistarh. “Elastic Consistency: A Practical Consistency Model for Distributed Stochastic Gradient Descent.” In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, 35:9037–45, 2021.","ama":"Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. Elastic consistency: A practical consistency model for distributed stochastic gradient descent. In: <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>. Vol 35. ; 2021:9037-9045."},"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"One key element behind the recent progress of machine learning has been the ability to train machine learning models in large-scale distributed shared-memory and message-passing environments. Most of these models are trained employing variants of stochastic gradient descent (SGD) based optimization, but most methods involve some type of consistency relaxation relative to sequential SGD, to mitigate its large communication or synchronization costs at scale. In this paper, we introduce a general consistency condition covering communication-reduced and asynchronous distributed SGD implementations. Our framework, called elastic consistency, decouples the system-specific aspects of the implementation from the SGD convergence requirements, giving a general way to obtain convergence bounds for a wide variety of distributed SGD methods used in practice. Elastic consistency can be used to re-derive or improve several previous convergence bounds in message-passing and shared-memory settings, but also to analyze new models and distribution schemes. As a direct application, we propose and analyze a new synchronization-avoiding scheduling scheme for distributed SGD, and show that it can be used to efficiently train deep convolutional models for image classification."}]}]