[{"oa":1,"year":"2021","alternative_title":["LNCS"],"date_updated":"2023-08-14T12:59:26Z","publication":"25th International Conference on Financial Cryptography and Data Security","page":"3-36","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ElKo"}],"date_created":"2021-11-21T23:01:29Z","scopus_import":"1","external_id":{"isi":["000712016200001"]},"date_published":"2021-10-23T00:00:00Z","publisher":"Springer Nature","main_file_link":[{"url":"https://eprint.iacr.org/2019/1128","open_access":"1"}],"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"_id":"10325","title":"SoK: Communication across distributed ledgers","author":[{"first_name":"Alexei","last_name":"Zamyatin","full_name":"Zamyatin, Alexei"},{"first_name":"Mustafa","last_name":"Al-Bassam","full_name":"Al-Bassam, Mustafa"},{"full_name":"Zindros, Dionysis","last_name":"Zindros","first_name":"Dionysis"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"first_name":"Pedro","last_name":"Moreno-Sanchez","full_name":"Moreno-Sanchez, Pedro"},{"first_name":"Aggelos","full_name":"Kiayias, Aggelos","last_name":"Kiayias"},{"last_name":"Knottenbelt","full_name":"Knottenbelt, William J.","first_name":"William J."}],"doi":"10.1007/978-3-662-64331-0_1","abstract":[{"lang":"eng","text":"Since the inception of Bitcoin, a plethora of distributed ledgers differing in design and purpose has been created. While by design, blockchains provide no means to securely communicate with external systems, numerous attempts towards trustless cross-chain communication have been proposed over the years. Today, cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges, scalability efforts via sharding, extension of existing systems through sidechains, and bootstrapping of new blockchains. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence in their correctness and composability. We provide the first systematic exposition of cross-chain communication protocols. We formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. With this result in mind, we develop a framework to design new and evaluate existing CCC protocols, focusing on the inherent trust assumptions thereof, and derive a classification covering the field of cross-chain communication to date. We conclude by discussing open challenges for CCC research and the implications of interoperability on the security and privacy of blockchains."}],"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-662-64331-0"],"isbn":["9-783-6626-4330-3"]},"status":"public","publication_status":"published","acknowledgement":"We would like express our gratitude to Georgia Avarikioti, Daniel Perez and Dominik Harz for helpful comments and feedback on earlier versions of this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler, Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages of this research. We also wish to thank the anonymous reviewers for their valuable comments that helped improve the presentation of our results. This research was funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian Doppler Laboratory for Security and Quality Improvement in the Production System Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs through the project SLN: Scalability for the Lightning Network; and by the Austrian Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted the early stages of this work during his time at SBA Research, and was supported by a Binance Research Fellowship.","month":"10","citation":{"chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” In <i>25th International Conference on Financial Cryptography and Data Security</i>, 12675:3–36. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-662-64331-0_1\">https://doi.org/10.1007/978-3-662-64331-0_1</a>.","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” <i>25th International Conference on Financial Cryptography and Data Security</i>, vol. 12675, Springer Nature, 2021, pp. 3–36, doi:<a href=\"https://doi.org/10.1007/978-3-662-64331-0_1\">10.1007/978-3-662-64331-0_1</a>.","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 3–36.","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. In: <i>25th International Conference on Financial Cryptography and Data Security</i>. Vol 12675. Springer Nature; 2021:3-36. doi:<a href=\"https://doi.org/10.1007/978-3-662-64331-0_1\">10.1007/978-3-662-64331-0_1</a>","ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. 2021. SoK: Communication across distributed ledgers. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 3–36.","ieee":"A. Zamyatin <i>et al.</i>, “SoK: Communication across distributed ledgers,” in <i>25th International Conference on Financial Cryptography and Data Security</i>, Virtual, 2021, vol. 12675, pp. 3–36.","apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., &#38; Knottenbelt, W. J. (2021). SoK: Communication across distributed ledgers. In <i>25th International Conference on Financial Cryptography and Data Security</i> (Vol. 12675, pp. 3–36). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-64331-0_1\">https://doi.org/10.1007/978-3-662-64331-0_1</a>"},"day":"23","oa_version":"Preprint","conference":{"name":"FC: Financial Cryptography","start_date":"2021-03-01","location":"Virtual","end_date":"2021-03-05"},"volume":"12675 ","article_processing_charge":"No"},{"publication_identifier":{"eissn":["2055-0278"]},"publication_status":"published","acknowledgement":"We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).","status":"public","title":"Catabolism of strigolactones by a carboxylesterase","author":[{"first_name":"Enjun","last_name":"Xu","full_name":"Xu, Enjun"},{"full_name":"Chai, Liang","last_name":"Chai","first_name":"Liang"},{"last_name":"Zhang","full_name":"Zhang, Shiqi","first_name":"Shiqi"},{"first_name":"Ruixue","full_name":"Yu, Ruixue","last_name":"Yu"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","full_name":"Zhang, Xixi","last_name":"Zhang","orcid":"0000-0001-7048-4627"},{"first_name":"Chongyi","full_name":"Xu, Chongyi","last_name":"Xu"},{"first_name":"Yuxin","last_name":"Hu","full_name":"Hu, Yuxin"}],"_id":"10326","abstract":[{"lang":"eng","text":"Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants."}],"doi":"10.1038/s41477-021-01011-y","volume":7,"article_processing_charge":"No","citation":{"ieee":"E. Xu <i>et al.</i>, “Catabolism of strigolactones by a carboxylesterase,” <i>Nature Plants</i>, vol. 7. Springer Nature, pp. 1495–1504, 2021.","apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., &#38; Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-021-01011-y\">https://doi.org/10.1038/s41477-021-01011-y</a>","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504.","ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. <i>Nature Plants</i>. 2021;7:1495–1504. doi:<a href=\"https://doi.org/10.1038/s41477-021-01011-y\">10.1038/s41477-021-01011-y</a>","ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” <i>Nature Plants</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41477-021-01011-y\">https://doi.org/10.1038/s41477-021-01011-y</a>.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” <i>Nature Plants</i>, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:<a href=\"https://doi.org/10.1038/s41477-021-01011-y\">10.1038/s41477-021-01011-y</a>."},"day":"11","month":"11","pmid":1,"oa_version":"None","publication":"Nature Plants","date_updated":"2023-08-14T11:54:02Z","page":"1495–1504 ","article_type":"original","year":"2021","publisher":"Springer Nature","intvolume":"         7","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-11-11T00:00:00Z","external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"date_created":"2021-11-21T23:01:30Z","scopus_import":"1"},{"publisher":"American Chemical Society ","intvolume":"        13","main_file_link":[{"url":"https://upcommons.upc.edu/bitstream/2117/363528/1/Pb%20mengyao.pdf","open_access":"1"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"}],"date_created":"2021-11-21T23:01:30Z","scopus_import":"1","date_published":"2021-10-19T00:00:00Z","external_id":{"pmid":["34665616"],"isi":["000715852100070"]},"date_updated":"2023-10-03T09:55:33Z","publication":"ACS Applied Materials and Interfaces","page":"51373–51382","article_type":"original","oa":1,"keyword":["CuxS","PbS","energy conversion","nanocomposite","nanoparticle","solution synthesis","thermoelectric"],"year":"2021","article_processing_charge":"No","volume":13,"pmid":1,"month":"10","citation":{"ama":"Li M, Liu Y, Zhang Y, et al. PbS–Pb–CuxS composites for thermoelectric application. <i>ACS Applied Materials and Interfaces</i>. 2021;13(43):51373–51382. doi:<a href=\"https://doi.org/10.1021/acsami.1c15609\">10.1021/acsami.1c15609</a>","short":"M. Li, Y. Liu, Y. Zhang, X. Han, K. Xiao, M. Nabahat, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 13 (2021) 51373–51382.","ista":"Li M, Liu Y, Zhang Y, Han X, Xiao K, Nabahat M, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2021. PbS–Pb–CuxS composites for thermoelectric application. ACS Applied Materials and Interfaces. 13(43), 51373–51382.","ieee":"M. Li <i>et al.</i>, “PbS–Pb–CuxS composites for thermoelectric application,” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 43. American Chemical Society , pp. 51373–51382, 2021.","apa":"Li, M., Liu, Y., Zhang, Y., Han, X., Xiao, K., Nabahat, M., … Cabot, A. (2021). PbS–Pb–CuxS composites for thermoelectric application. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society . <a href=\"https://doi.org/10.1021/acsami.1c15609\">https://doi.org/10.1021/acsami.1c15609</a>","chicago":"Li, Mengyao, Yu Liu, Yu Zhang, Xu Han, Ke Xiao, Mehran Nabahat, Jordi Arbiol, Jordi Llorca, Maria Ibáñez, and Andreu Cabot. “PbS–Pb–CuxS Composites for Thermoelectric Application.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society , 2021. <a href=\"https://doi.org/10.1021/acsami.1c15609\">https://doi.org/10.1021/acsami.1c15609</a>.","mla":"Li, Mengyao, et al. “PbS–Pb–CuxS Composites for Thermoelectric Application.” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 43, American Chemical Society , 2021, pp. 51373–51382, doi:<a href=\"https://doi.org/10.1021/acsami.1c15609\">10.1021/acsami.1c15609</a>."},"day":"19","oa_version":"Submitted Version","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"ec_funded":1,"status":"public","acknowledgement":"This work was supported by the European Regional Development Funds. M.L., Y.Z., X.H., and K.X. thank the China Scholarship Council for scholarship support. M. I. has been financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. J.L. is a Serra Húnter fellow and is grateful to ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project NANOGEN (PID2020-116093RB-C43). ICN2 was supported by the Severo Ochoa program from Spanish MINECO (grant no. SEV-2017-0706) and was funded by the CERCA Programme/Generalitat de Catalunya. X.H. thanks China Scholarship Council for scholarship support (201804910551). Part of the present work was performed in the framework of Universitat Autònoma de Barcelona Materials Science Ph.D. program.","publication_status":"published","_id":"10327","title":"PbS–Pb–CuxS composites for thermoelectric application","author":[{"last_name":"Li","full_name":"Li, Mengyao","first_name":"Mengyao"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","full_name":"Liu, Yu","last_name":"Liu","orcid":"0000-0001-7313-6740"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"last_name":"Han","full_name":"Han, Xu","first_name":"Xu"},{"first_name":"Ke","last_name":"Xiao","full_name":"Xiao, Ke"},{"first_name":"Mehran","last_name":"Nabahat","full_name":"Nabahat, Mehran"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Jordi","full_name":"Llorca, Jordi","last_name":"Llorca"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"doi":"10.1021/acsami.1c15609","abstract":[{"text":"Composite materials offer numerous advantages in a wide range of applications, including thermoelectrics. Here, semiconductor–metal composites are produced by just blending nanoparticles of a sulfide semiconductor obtained in aqueous solution and at room temperature with a metallic Cu powder. The obtained blend is annealed in a reducing atmosphere and afterward consolidated into dense polycrystalline pellets through spark plasma sintering (SPS). We observe that, during the annealing process, the presence of metallic copper activates a partial reduction of the PbS, resulting in the formation of PbS–Pb–CuxS composites. The presence of metallic lead during the SPS process habilitates the liquid-phase sintering of the composite. Besides, by comparing the transport properties of PbS, the PbS–Pb–CuxS composites, and PbS–CuxS composites obtained by blending PbS and CuxS nanoparticles, we demonstrate that the presence of metallic lead decisively contributes to a strong increase of the charge carrier concentration through spillover of charge carriers enabled by the low work function of lead. The increase in charge carrier concentration translates into much higher electrical conductivities and moderately lower Seebeck coefficients. These properties translate into power factors up to 2.1 mW m–1 K–2 at ambient temperature, well above those of PbS and PbS + CuxS. Additionally, the presence of multiple phases in the final composite results in a notable decrease in the lattice thermal conductivity. Overall, the introduction of metallic copper in the initial blend results in a significant improvement of the thermoelectric performance of PbS, reaching a dimensionless thermoelectric figure of merit ZT = 1.1 at 750 K, which represents about a 400% increase over bare PbS. Besides, an average ZTave = 0.72 in the temperature range 320–773 K is demonstrated.","lang":"eng"}],"issue":"43"},{"oa":1,"year":"2021","date_updated":"2023-08-14T13:01:38Z","publication":"Protein Engineering, Design and Selection","article_number":"gzab025","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CaGu"}],"date_created":"2021-11-28T23:01:28Z","scopus_import":"1","date_published":"2021-11-01T00:00:00Z","external_id":{"isi":["000746596900001"],"pmid":["34725710"]},"publisher":"Oxford University Press","intvolume":"        34","main_file_link":[{"url":"https://doi.org/10.1093/protein/gzab025","open_access":"1"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"_id":"10363","title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","author":[{"full_name":"Lee, Jungmin","last_name":"Lee","first_name":"Jungmin"},{"full_name":"Vernet, Andyna","last_name":"Vernet","first_name":"Andyna"},{"full_name":"Gruber, Nathalie","last_name":"Gruber","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425","first_name":"Nathalie"},{"first_name":"Kasia M.","last_name":"Kready","full_name":"Kready, Kasia M."},{"last_name":"Burrill","full_name":"Burrill, Devin R.","first_name":"Devin R."},{"last_name":"Way","full_name":"Way, Jeffrey C.","first_name":"Jeffrey C."},{"last_name":"Silver","full_name":"Silver, Pamela A.","first_name":"Pamela A."}],"doi":"10.1093/protein/gzab025","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."}],"publication_identifier":{"issn":["1741-0126"],"eissn":["1741-0134"]},"publication_status":"published","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.","status":"public","pmid":1,"month":"11","citation":{"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>.","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).","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.","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>","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>","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."},"day":"01","oa_version":"Published Version","article_processing_charge":"No","volume":34},{"oa_version":"Submitted Version","day":"18","citation":{"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.","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.","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>","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>","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.","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>.","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>."},"file_date_updated":"2023-10-11T09:31:43Z","month":"11","ddc":["530"],"has_accepted_license":"1","article_processing_charge":"No","volume":17,"file":[{"file_id":"14420","date_created":"2023-10-11T09:31:43Z","file_name":"50145_4_merged_1630498627.pdf","file_size":40285498,"relation":"main_file","creator":"channezo","access_level":"open_access","checksum":"5d6d76750a71d7cb632bb15417c38ef7","content_type":"application/pdf","success":1,"date_updated":"2023-10-11T09:31:43Z"}],"issue":"12","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."}],"doi":"10.1038/s41567-021-01374-1","author":[{"full_name":"Luciano, Marine","last_name":"Luciano","first_name":"Marine"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","full_name":"Xue, Shi-lei","last_name":"Xue"},{"last_name":"De Vos","full_name":"De Vos, Winnok H.","first_name":"Winnok H."},{"full_name":"Redondo-Morata, Lorena","last_name":"Redondo-Morata","first_name":"Lorena"},{"first_name":"Mathieu","last_name":"Surin","full_name":"Surin, Mathieu"},{"first_name":"Frank","full_name":"Lafont, Frank","last_name":"Lafont"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvain","last_name":"Gabriele","full_name":"Gabriele, Sylvain"}],"title":"Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation","_id":"10365","publication_status":"published","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.","status":"public","ec_funded":1,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton"}],"date_published":"2021-11-18T00:00:00Z","external_id":{"isi":["000720204300004"]},"scopus_import":"1","date_created":"2021-11-28T23:01:29Z","department":[{"_id":"EdHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":"        17","publisher":"Springer Nature","year":"2021","oa":1,"related_material":{"link":[{"description":"News on IST Webpage","url":"https://ist.ac.at/en/news/how-cells-feel-curvature/","relation":"press_release"}]},"article_type":"original","page":"1382–1390","publication":"Nature Physics","date_updated":"2023-10-16T06:31:54Z"},{"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":"       168","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cdev.2021.203758"}],"publisher":"Elsevier","external_id":{"pmid":["34800748"],"isi":["000974771600028"]},"date_published":"2021-11-17T00:00:00Z","scopus_import":"1","date_created":"2021-11-28T23:01:30Z","department":[{"_id":"CaHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"letter_note","article_number":"203758","publication":"Cells and Development","date_updated":"2023-08-14T13:02:40Z","year":"2021","oa":1,"article_processing_charge":"No","volume":168,"oa_version":"Published Version","day":"17","citation":{"short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","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>","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.","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>","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>.","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>."},"pmid":1,"month":"11","publication_status":"published","status":"public","publication_identifier":{"issn":["2667-2901"]},"issue":"12","doi":"10.1016/j.cdev.2021.203758","author":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Ana Maria","last_name":"Lennon","full_name":"Lennon, Ana Maria"},{"last_name":"Mayor","full_name":"Mayor, Roberto","first_name":"Roberto"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"}],"title":"Special rebranding issue: “Quantitative cell and developmental biology”","_id":"10366"},{"page":"29-30","publication":"59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, Tutorial Abstracts","date_updated":"2022-01-26T14:26:36Z","year":"2021","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","main_file_link":[{"open_access":"1","url":"https://aclanthology.org/2021.acl-tutorials.6/"}],"publisher":"Association for Computational Linguistics","date_published":"2021-08-01T00:00:00Z","scopus_import":"1","date_created":"2021-11-28T23:01:30Z","department":[{"_id":"HeEd"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"We would like to thank Abby Schantz, Abe Ittycheriah, Aliaksei Severyn, Allan Heydon, Aly\r\nGrealish, Andrey Vlasov, Arkaitz Zubiaga, Ashwin Kakarla, Chen Sun, Clayton Williams, Cong\r\nYu, Cordelia Schmid, Da-Cheng Juan, Dan Finnie, Dani Valevski, Daniel Rocha, David Price, David Sklar, Devi Krishna, Elena Kochkina, Enrique Alfonseca, Franc¸oise Beaufays, Isabelle Augenstein, Jialu Liu, John Cantwell, John Palowitch, Jordan Boyd-Graber, Lei Shi, Luis Valente, Maria Voitovich, Mehmet Aktuna, Mogan Brown, Mor Naaman, Natalia P, Nidhi Hebbar, Pete Aykroyd, Rahul Sukthankar, Richa Dixit, Steve Pucci, Tania Bedrax-Weiss, Tobias Kaufmann, Tom Boulos, Tu Tsao, Vladimir Chtchetkine, Yair Kurzion, Yifan Xu and Zach Hynes.","publication_status":"published","status":"public","publication_identifier":{"isbn":["9-781-9540-8557-2"]},"abstract":[{"lang":"eng","text":"How information is created, shared and consumed has changed rapidly in recent decades, in part thanks to new social platforms and technologies on the web. With ever-larger amounts of unstructured and limited labels, organizing and reconciling information from different sources and modalities is a central challenge in machine learning. This cutting-edge tutorial aims to introduce the multimodal entailment task, which can be useful for detecting semantic alignments when a single modality alone does not suffice for a whole content understanding. Starting with a brief overview of natural language processing, computer vision, structured data and neural graph learning, we lay the foundations for the multimodal sections to follow. We then discuss recent multimodal learning literature covering visual, audio and language streams, and explore case studies focusing on tasks which require fine-grained understanding of visual and linguistic semantics question answering, veracity and hatred classification. Finally, we introduce a new dataset for recognizing multimodal entailment, exploring it in a hands-on collaborative section. Overall, this tutorial gives an overview of multimodal learning, introduces a multimodal entailment dataset, and encourages future research in the topic."}],"doi":"10.18653/v1/2021.acl-tutorials.6","author":[{"full_name":"Ilharco, Cesar","last_name":"Ilharco","first_name":"Cesar"},{"first_name":"Afsaneh","last_name":"Shirazi","full_name":"Shirazi, Afsaneh"},{"first_name":"Arjun","full_name":"Gopalan, Arjun","last_name":"Gopalan"},{"first_name":"Arsha","last_name":"Nagrani","full_name":"Nagrani, Arsha"},{"full_name":"Bratanič, Blaž","last_name":"Bratanič","first_name":"Blaž"},{"first_name":"Chris","last_name":"Bregler","full_name":"Bregler, Chris"},{"first_name":"Christina","full_name":"Liu, Christina","last_name":"Liu"},{"last_name":"Ferreira","full_name":"Ferreira, Felipe","first_name":"Felipe"},{"first_name":"Gabriek","full_name":"Barcik, Gabriek","last_name":"Barcik"},{"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"},{"last_name":"Bulian","full_name":"Bulian, Jannis","first_name":"Jannis"},{"full_name":"Frank, Jared","last_name":"Frank","first_name":"Jared"},{"first_name":"Lucas","full_name":"Smaira, Lucas","last_name":"Smaira"},{"first_name":"Qin","last_name":"Cao","full_name":"Cao, Qin"},{"full_name":"Marino, Ricardo","last_name":"Marino","first_name":"Ricardo"},{"full_name":"Patel, Roma","last_name":"Patel","first_name":"Roma"},{"full_name":"Leung, Thomas","last_name":"Leung","first_name":"Thomas"},{"last_name":"Imbrasaite","full_name":"Imbrasaite, Vaiva","first_name":"Vaiva"}],"title":"Recognizing multimodal entailment","_id":"10367","has_accepted_license":"1","article_processing_charge":"No","file":[{"date_created":"2021-11-29T08:41:00Z","file_id":"10368","relation":"main_file","file_size":1227703,"creator":"cchlebak","file_name":"2021_ACL_Ilharco.pdf","date_updated":"2021-11-29T08:41:00Z","success":1,"checksum":"b14052a025a6ecf675bdfe51db98c0d7","content_type":"application/pdf","access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"conference":{"end_date":"2021-08-06","location":"Bangkok, Thailand","start_date":"2021-08-01","name":"ACL: Association for Computational Linguistics ; IJCNLP: International Joint Conference on Natural Language Processing"},"oa_version":"Published Version","day":"01","citation":{"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.","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>","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.","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>","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.","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>.","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>."},"ddc":["000"],"month":"08","file_date_updated":"2021-11-29T08:41:00Z"},{"_id":"10401","title":"Generation of spin currents by a temperature gradient in a two-terminal device","author":[{"first_name":"Rafael E.","full_name":"Barfknecht, Rafael E.","last_name":"Barfknecht"},{"last_name":"Foerster","full_name":"Foerster, Angela","first_name":"Angela"},{"full_name":"Zinner, Nikolaj T.","last_name":"Zinner","first_name":"Nikolaj T."},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem","last_name":"Volosniev"}],"doi":"10.1038/s42005-021-00753-7","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."}],"issue":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["23993650"]},"ec_funded":1,"status":"public","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).","publication_status":"published","month":"11","ddc":["530"],"file_date_updated":"2021-12-06T14:53:41Z","citation":{"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.","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.","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>","short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021).","chicago":"Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” <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>.","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>."},"day":"26","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","checksum":"9097319952cb9a3d96e7fd3aa9813a03","content_type":"application/pdf","success":1,"date_updated":"2021-12-06T14:53:41Z","file_name":"2021_NatComm_Barfknecht.pdf","file_size":1068984,"relation":"main_file","creator":"alisjak","file_id":"10420","date_created":"2021-12-06T14:53:41Z"}],"arxiv":1,"article_processing_charge":"No","volume":4,"has_accepted_license":"1","oa":1,"year":"2021","date_updated":"2023-08-14T13:04:34Z","publication":"Communications Physics","article_number":"252","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"date_created":"2021-12-05T23:01:39Z","scopus_import":"1","date_published":"2021-11-26T00:00:00Z","external_id":{"isi":["10.1038/s42005-021-00753-7"],"arxiv":["2101.02020"]},"publisher":"Springer Nature","intvolume":"         4","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article"},{"publication_identifier":{"eissn":["2041-1723"]},"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","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.).","status":"public","ec_funded":1,"title":"Theory of branching morphogenesis by local interactions and global guidance","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","full_name":"Ucar, Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217"},{"full_name":"Kamenev, Dmitrii","last_name":"Kamenev","first_name":"Dmitrii"},{"last_name":"Sunadome","full_name":"Sunadome, Kazunori","first_name":"Kazunori"},{"id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","first_name":"Dominik C","full_name":"Fachet, Dominik C","last_name":"Fachet"},{"full_name":"Lallemend, Francois","last_name":"Lallemend","first_name":"Francois"},{"first_name":"Igor","full_name":"Adameyko, Igor","last_name":"Adameyko"},{"last_name":"Hadjab","full_name":"Hadjab, Saida","first_name":"Saida"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"}],"_id":"10402","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."}],"doi":"10.1038/s41467-021-27135-5","file":[{"file_name":"2021_NatComm_Ucar.pdf","creator":"cchlebak","file_size":2303405,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"63c56ec75314a71e63e7dd2920b3c5b5","success":1,"date_updated":"2021-12-10T08:54:09Z","file_id":"10529","date_created":"2021-12-10T08:54:09Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":12,"citation":{"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.","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>","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>","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","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>.","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>."},"day":"24","file_date_updated":"2021-12-10T08:54:09Z","ddc":["573"],"month":"11","pmid":1,"oa_version":"Published Version","publication":"Nature Communications","date_updated":"2023-08-14T13:18:46Z","related_material":{"record":[{"id":"13058","status":"public","relation":"research_data"}]},"article_number":"6830","article_type":"original","oa":1,"year":"2021","publisher":"Springer Nature","intvolume":"        12","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"EdHa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-11-24T00:00:00Z","external_id":{"isi":["000722322900020"],"pmid":["34819507"]},"date_created":"2021-12-05T23:01:40Z","scopus_import":"1"},{"year":"2021","oa":1,"article_type":"original","article_number":"e65954","date_updated":"2023-08-14T13:12:07Z","publication":"eLife","scopus_import":"1","date_created":"2021-12-05T23:01:40Z","date_published":"2021-11-03T00:00:00Z","external_id":{"isi":["000715789500001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"RySh"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":"        10","publisher":"eLife Sciences Publications","doi":"10.7554/eLife.65954","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"}],"_id":"10403","author":[{"first_name":"Celia","last_name":"Biane","full_name":"Biane, Celia"},{"last_name":"Rückerl","full_name":"Rückerl, Florian","first_name":"Florian"},{"full_name":"Abrahamsson, Therese","last_name":"Abrahamsson","first_name":"Therese"},{"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"},{"first_name":"David A.","full_name":"Digregorio, David A.","last_name":"Digregorio"},{"last_name":"Sherrard","full_name":"Sherrard, Rachel M.","first_name":"Rachel M."},{"first_name":"Laurence","full_name":"Cathala, Laurence","last_name":"Cathala"}],"title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","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.","status":"public","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"oa_version":"Published Version","month":"11","file_date_updated":"2021-12-10T08:31:41Z","ddc":["570"],"day":"03","citation":{"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>.","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>.","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.","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).","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>","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.","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>"},"article_processing_charge":"No","volume":10,"has_accepted_license":"1","file":[{"file_id":"10528","date_created":"2021-12-10T08:31:41Z","file_name":"2021_eLife_Biane.pdf","relation":"main_file","creator":"cchlebak","file_size":13131322,"access_level":"open_access","checksum":"c7c33c3319428d56e332e22349c50ed3","content_type":"application/pdf","success":1,"date_updated":"2021-12-10T08:31:41Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"volume":40,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","month":"11","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.","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>","ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. <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>","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","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>.","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>."},"day":"27","publication_status":"published","status":"public","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","project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"doi":"10.1111/cgf.14418","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"}],"issue":"7","_id":"10404","title":"Interactive analysis of CNN robustness","author":[{"full_name":"Sietzen, Stefan","last_name":"Sietzen","first_name":"Stefan"},{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Judy","last_name":"Borowski","full_name":"Borowski, Judy"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"first_name":"Manuela","full_name":"Waldner, Manuela","last_name":"Waldner"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publisher":"Wiley","intvolume":"        40","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.07667"}],"date_created":"2021-12-05T23:01:40Z","scopus_import":"1","external_id":{"arxiv":["2110.07667"],"isi":["000722952000024"]},"date_published":"2021-11-27T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToHe"}],"page":"253-264","article_type":"original","date_updated":"2023-08-14T13:11:42Z","publication":"Computer Graphics Forum","year":"2021","oa":1},{"oa_version":"None","citation":{"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>.","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>.","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.","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>","ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233.","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>","short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233."},"day":"30","pmid":1,"month":"08","article_processing_charge":"No","volume":55,"abstract":[{"lang":"eng","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."}],"doi":"10.1146/annurev-genet-071819-103748","title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","author":[{"orcid":"0000-0002-6425-5788","id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","first_name":"Nikhil","full_name":"Mishra, Nikhil","last_name":"Mishra"},{"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"}],"_id":"10406","status":"public","publication_status":"published","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).","ec_funded":1,"publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"date_published":"2021-08-30T00:00:00Z","external_id":{"pmid":["34460295"],"isi":["000747220900010"]},"date_created":"2021-12-05T23:01:41Z","scopus_import":"1","department":[{"_id":"CaHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Annual Reviews","intvolume":"        55","year":"2021","keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"page":"209-233","article_type":"original","publication":"Annual Review of Genetics","date_updated":"2023-08-14T13:05:13Z"},{"department":[{"_id":"KrPi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-11-04T00:00:00Z","external_id":{"isi":["000728364000014"]},"date_created":"2021-12-05T23:01:42Z","scopus_import":"1","publisher":"Springer Nature","intvolume":"     13043","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1224"}],"isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","oa":1,"alternative_title":["LNCS"],"year":"2021","date_updated":"2023-08-14T13:07:46Z","page":"397-428","citation":{"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>","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.","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>","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.","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>.","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>."},"day":"04","month":"11","oa_version":"Preprint","conference":{"name":"TCC: Theory of Cryptography Conference","start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11"},"article_processing_charge":"No","volume":13043,"title":"Trojan-resilience without cryptography","author":[{"full_name":"Chakraborty, Suvradip","last_name":"Chakraborty","id":"B9CD0494-D033-11E9-B219-A439E6697425","first_name":"Suvradip"},{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"last_name":"Gałązka","full_name":"Gałązka, Małgorzata","first_name":"Małgorzata"},{"first_name":"Tomasz","full_name":"Lizurej, Tomasz","last_name":"Lizurej"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"full_name":"Yeo, Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"_id":"10407","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"}],"doi":"10.1007/978-3-030-90453-1_14","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9-783-0309-0452-4"]},"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"status":"public","publication_status":"published","ec_funded":1},{"oa_version":"Preprint","conference":{"start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11","name":"TCC: Theory of Cryptography"},"citation":{"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.","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>","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.","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>.","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>."},"day":"04","month":"11","article_processing_charge":"No","volume":13044,"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."}],"doi":"10.1007/978-3-030-90456-2_8","title":"Grafting key trees: Efficient key management for overlapping groups","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","first_name":"Benedikt","full_name":"Auerbach, Benedikt","last_name":"Auerbach","orcid":"0000-0002-7553-6606"},{"first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","last_name":"Baig","full_name":"Baig, Mirza Ahad"},{"first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel"},{"full_name":"Klein, Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"orcid":"0000-0001-8630-415X","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","last_name":"Pascual Perez","full_name":"Pascual Perez, Guillermo"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"},{"orcid":"0000-0003-3186-2482","first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","full_name":"Walter, Michael"}],"_id":"10408","publication_status":"published","status":"public","acknowledgement":"B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","ec_funded":1,"publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0309-0455-5"],"eisbn":["978-3-030-90456-2"],"issn":["0302-9743"]},"project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"date_published":"2021-11-04T00:00:00Z","external_id":{"isi":["000728363700008"]},"date_created":"2021-12-05T23:01:42Z","scopus_import":"1","department":[{"_id":"KrPi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1158"}],"intvolume":"     13044","alternative_title":["LNCS"],"year":"2021","oa":1,"page":"222-253","publication":"19th International Conference","date_updated":"2023-08-14T13:19:39Z"},{"title":"On treewidth, separators and Yao’s garbling","author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"_id":"10409","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"}],"doi":"10.1007/978-3-030-90453-1_17","publication_identifier":{"issn":["0302-9743"],"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"]},"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"status":"public","publication_status":"published","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.","ec_funded":1,"citation":{"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>","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.","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.","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>","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>.","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>."},"day":"04","month":"11","oa_version":"Preprint","conference":{"name":"TCC: Theory of Cryptography","start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11"},"article_processing_charge":"No","volume":"13043 ","oa":1,"year":"2021","alternative_title":["LNCS"],"publication":"19th International Conference","date_updated":"2023-08-17T06:21:38Z","related_material":{"record":[{"id":"10044","status":"public","relation":"earlier_version"}]},"page":"486-517","department":[{"_id":"KrPi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000728364000017"]},"date_published":"2021-11-04T00:00:00Z","date_created":"2021-12-05T23:01:43Z","scopus_import":"1","publisher":"Springer Nature","main_file_link":[{"url":"https://eprint.iacr.org/2021/926","open_access":"1"}],"isi":1,"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1"},{"date_created":"2021-12-05T23:01:43Z","scopus_import":"1","external_id":{"isi":["000728364000019"]},"date_published":"2021-11-04T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"KrPi"}],"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Springer Nature","intvolume":"     13043","main_file_link":[{"url":"https://ia.cr/2021/059","open_access":"1"}],"year":"2021","alternative_title":["LNCS"],"oa":1,"page":"550-581","related_material":{"record":[{"id":"10048","relation":"earlier_version","status":"public"}]},"date_updated":"2023-10-17T09:24:07Z","publication":"19th International Conference","oa_version":"Preprint","conference":{"name":"TCC: Theory of Cryptography","start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11"},"month":"11","citation":{"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>","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.","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>","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.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 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>.","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>."},"day":"04","volume":13043,"article_processing_charge":"No","doi":"10.1007/978-3-030-90453-1_19","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"}],"_id":"10410","title":"The cost of adaptivity in security games on graphs","author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"ec_funded":1,"status":"public","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).","publication_status":"published","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"],"issn":["0302-9743"]}},{"year":"2021","alternative_title":["LNCS"],"oa":1,"page":"619-639","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14539"},{"status":"public","relation":"later_version","id":"14778"}]},"date_updated":"2025-07-14T09:10:11Z","publication":"24th International Symposium on Formal Methods","scopus_import":"1","date_created":"2021-12-05T23:01:45Z","date_published":"2021-11-10T00:00:00Z","external_id":{"isi":["000758218600033"],"arxiv":["2108.02188"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/2108.02188","open_access":"1"}],"intvolume":"     13047","publisher":"Springer Nature","doi":"10.1007/978-3-030-90870-6_33","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"}],"_id":"10414","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady","first_name":"Ehsan Kafshdar"},{"full_name":"Novotný, Petr","last_name":"Novotný","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"last_name":"Zárevúcky","full_name":"Zárevúcky, Jiří","first_name":"Jiří"},{"orcid":"0000-0002-4681-1699","last_name":"Zikelic","full_name":"Zikelic, Dorde","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"title":"On lexicographic proof rules for probabilistic termination","ec_funded":1,"publication_status":"published","status":"public","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.","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"publication_identifier":{"eisbn":["978-3-030-90870-6"],"issn":["0302-9743"],"isbn":["9-783-0309-0869-0"],"eissn":["1611-3349"]},"conference":{"name":"FM: Formal Methods","start_date":"2021-11-20","location":"Virtual","end_date":"2021-11-26"},"oa_version":"Preprint","month":"11","day":"10","citation":{"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>.","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>","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.","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.","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.","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>"},"volume":13047,"article_processing_charge":"No","arxiv":1},{"_id":"10415","title":"Cubic Forms and the Circle Method","author":[{"orcid":"0000-0002-8314-0177","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","full_name":"Browning, Timothy D"}],"doi":"10.1007/978-3-030-86872-7","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."}],"year":"2021","alternative_title":["Progress in Mathematics"],"date_updated":"2022-06-03T07:38:33Z","publication_identifier":{"eisbn":["978-3-030-86872-7"],"issn":["0743-1643"],"isbn":["978-3-030-86871-0"],"eissn":["2296-505X"]},"place":"Cham","page":"XIV, 166","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","citation":{"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>","ieee":"T. D. Browning, <i>Cubic Forms and the Circle Method</i>, vol. 343. Cham: Springer Nature, 2021.","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>","short":"T.D. Browning, Cubic Forms and the Circle Method, Springer Nature, Cham, 2021.","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>.","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>."},"day":"01","department":[{"_id":"TiBr"}],"oa_version":"None","date_created":"2021-12-05T23:01:46Z","scopus_import":"1","date_published":"2021-12-01T00:00:00Z","publisher":"Springer Nature","intvolume":"       343","article_processing_charge":"No","volume":343,"type":"book","quality_controlled":"1","language":[{"iso":"eng"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2022-03-10T12:10:25Z","ddc":["530"],"month":"12","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"day":"07","citation":{"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>.","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","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>","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","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>"},"date_created":"2021-12-07T10:48:06Z","oa_version":"Published Version","date_published":"2021-12-07T00:00:00Z","file":[{"date_updated":"2022-03-10T12:10:25Z","access_level":"closed","checksum":"114e8f4b2c002c6c352416c12de2c695","content_type":"application/x-zip-compressed","file_name":"Thesis.zip","creator":"cchlebak","file_size":394018,"relation":"source_file","file_id":"10424","date_created":"2021-12-07T11:13:52Z"},{"file_id":"10425","date_created":"2021-12-07T11:14:01Z","file_name":"Preliminary_pages_Piankov.docx","relation":"source_file","file_size":47638,"creator":"cchlebak","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"cd15ae991ced352a9959815f794e657c","date_updated":"2022-03-10T12:10:25Z"},{"date_created":"2021-12-07T11:20:35Z","file_id":"10426","content_type":"application/pdf","checksum":"e6899c798b75ba42fab9822bce309050","access_level":"open_access","date_updated":"2021-12-07T11:20:35Z","success":1,"file_size":484965,"creator":"cchlebak","relation":"main_file","file_name":"2021_Piankov_combined.pdf"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"MS","language":[{"iso":"eng"}],"type":"dissertation","article_processing_charge":"No","has_accepted_license":"1","_id":"10422","author":[{"first_name":"Anton","id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","last_name":"Piankov","full_name":"Piankov, Anton"}],"oa":1,"supervisor":[{"orcid":"0000-0002-1307-5074","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"title":"Towards designer materials using customizable particle shape","doi":"10.15479/at:ista:10422","year":"2021","alternative_title":["ISTA Master's Thesis"],"abstract":[{"lang":"eng","text":"Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems."}],"date_updated":"2023-09-07T13:34:12Z","publication_identifier":{"issn":["2791-4585"]},"publication_status":"published","status":"public"},{"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"status":"public","publication_status":"published","_id":"10429","author":[{"orcid":"0000-0001-5634-0731","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"title":"On achieving scalability through relaxation","doi":"10.15479/at:ista:10429","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"}],"file":[{"file_name":"Thesis_Final_09_12_2021.pdf","creator":"gnadirad","file_size":2370859,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"6bf14e9a523387328f016c0689f5e10e","success":1,"date_updated":"2021-12-09T17:47:49Z","file_id":"10436","date_created":"2021-12-09T17:47:49Z"},{"file_size":2596924,"relation":"source_file","creator":"gnadirad","file_name":"Thesis_Final_09_12_2021.zip","content_type":"application/zip","checksum":"914d6c5ca86bd0add471971a8f4c4341","access_level":"closed","date_updated":"2022-03-28T12:55:12Z","date_created":"2021-12-09T17:47:49Z","file_id":"10437"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","ddc":["000"],"month":"12","file_date_updated":"2022-03-28T12:55:12Z","day":"09","citation":{"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>.","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>","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021.","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>","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria."},"oa_version":"Published Version","date_updated":"2023-10-17T11:48:55Z","page":"132","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10432"},{"id":"6673","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"5965"},{"status":"public","relation":"part_of_dissertation","id":"10435"}]},"oa":1,"year":"2021","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"date_created":"2021-12-08T21:52:28Z","date_published":"2021-12-09T00:00:00Z"}]