[{"ec_funded":1,"volume":15,"publication":"PLoS Computational Biology","date_published":"2019-11-01T00:00:00Z","intvolume":"        15","article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics.","lang":"eng"}],"publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1007268","quality_controlled":"1","has_accepted_license":"1","publication_identifier":{"issn":["1553-7358"]},"oa_version":"Published Version","ddc":["570","000"],"article_type":"original","year":"2019","file_date_updated":"2020-07-14T12:47:49Z","scopus_import":"1","_id":"7103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"11","day":"01","article_number":"e1007268","isi":1,"title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"oa":1,"citation":{"ama":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. <i>PLoS Computational Biology</i>. 2019;15(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">10.1371/journal.pcbi.1007268</a>","chicago":"Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">https://doi.org/10.1371/journal.pcbi.1007268</a>.","apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., &#38; Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">https://doi.org/10.1371/journal.pcbi.1007268</a>","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” <i>PLoS Computational Biology</i>, vol. 15, no. 11. Public Library of Science, 2019.","mla":"Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” <i>PLoS Computational Biology</i>, vol. 15, no. 11, e1007268, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">10.1371/journal.pcbi.1007268</a>.","short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).","ista":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268."},"date_updated":"2025-04-14T07:44:06Z","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"type":"journal_article","month":"11","file":[{"file_name":"2019_PLOSComBio_Wang.pdf","date_created":"2019-11-25T08:24:01Z","date_updated":"2020-07-14T12:47:49Z","access_level":"open_access","relation":"main_file","file_size":3982516,"content_type":"application/pdf","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","file_id":"7104","creator":"dernst"}],"publication_status":"published","author":[{"full_name":"Wang, Jilin W. J. L.","last_name":"Wang","first_name":"Jilin W. J. L."},{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"last_name":"Zhang","first_name":"Xiyun","full_name":"Zhang, Xiyun"},{"full_name":"Anaclet, Christelle","first_name":"Christelle","last_name":"Anaclet"},{"full_name":"Ivanov, Plamen Ch.","first_name":"Plamen Ch.","last_name":"Ivanov"}],"pmid":1,"department":[{"_id":"GaTk"}],"date_created":"2019-11-25T08:20:47Z","external_id":{"pmid":["31725712"],"isi":["000500976100014"]}},{"year":"2019","oa_version":"Submitted Version","article_type":"original","publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"quality_controlled":"1","doi":"10.1038/s41556-019-0411-5","abstract":[{"text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"article_processing_charge":"No","publication":"Nature Cell Biology","date_published":"2019-11-01T00:00:00Z","volume":21,"intvolume":"        21","department":[{"_id":"MiSi"}],"external_id":{"isi":["000495888300009"],"pmid":["31685997"]},"date_created":"2019-11-25T08:55:00Z","publication_status":"published","author":[{"full_name":"Yolland, Lawrence","first_name":"Lawrence","last_name":"Yolland"},{"full_name":"Burki, Mubarik","first_name":"Mubarik","last_name":"Burki"},{"full_name":"Marcotti, Stefania","last_name":"Marcotti","first_name":"Stefania"},{"full_name":"Luchici, Andrei","last_name":"Luchici","first_name":"Andrei"},{"first_name":"Fiona N.","last_name":"Kenny","full_name":"Kenny, Fiona N."},{"first_name":"John Robert","last_name":"Davis","full_name":"Davis, John Robert"},{"full_name":"Serna-Morales, Eduardo","first_name":"Eduardo","last_name":"Serna-Morales"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","last_name":"Müller","first_name":"Jan","full_name":"Müller, Jan"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"last_name":"Davidson","first_name":"Andrew","full_name":"Davidson, Andrew"},{"full_name":"Wood, Will","last_name":"Wood","first_name":"Will"},{"full_name":"Schumacher, Linus J.","first_name":"Linus J.","last_name":"Schumacher"},{"first_name":"Robert G.","last_name":"Endres","full_name":"Endres, Robert G."},{"first_name":"Mark","last_name":"Miodownik","full_name":"Miodownik, Mark"},{"full_name":"Stramer, Brian M.","last_name":"Stramer","first_name":"Brian M."}],"pmid":1,"page":"1370-1381","type":"journal_article","month":"11","status":"public","citation":{"mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” <i>Nature Cell Biology</i>, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:<a href=\"https://doi.org/10.1038/s41556-019-0411-5\">10.1038/s41556-019-0411-5</a>.","ieee":"L. Yolland <i>et al.</i>, “Persistent and polarized global actin flow is essential for directionality during cell migration,” <i>Nature Cell Biology</i>, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. <i>Nature Cell Biology</i>. 2019;21(11):1370-1381. doi:<a href=\"https://doi.org/10.1038/s41556-019-0411-5\">10.1038/s41556-019-0411-5</a>","chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” <i>Nature Cell Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41556-019-0411-5\">https://doi.org/10.1038/s41556-019-0411-5</a>.","apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-019-0411-5\">https://doi.org/10.1038/s41556-019-0411-5</a>"},"oa":1,"date_updated":"2023-09-06T11:08:52Z","isi":1,"title":"Persistent and polarized global actin flow is essential for directionality during cell migration","issue":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","scopus_import":"1","_id":"7105"},{"quality_controlled":"1","doi":"10.1038/s41477-019-0542-5","has_accepted_license":"1","publication_identifier":{"issn":["2055-0278"]},"ddc":["580"],"oa_version":"Submitted Version","article_type":"original","year":"2019","date_published":"2019-11-01T00:00:00Z","publication":"Nature Plants","volume":5,"ec_funded":1,"intvolume":"         5","language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes."}],"publisher":"Springer Nature","status":"public","file":[{"content_type":"application/pdf","file_size":1980851,"success":1,"file_id":"8660","checksum":"94e0426856aad9a9bd0135d5436efbf1","creator":"dernst","date_updated":"2020-10-14T08:54:49Z","date_created":"2020-10-14T08:54:49Z","file_name":"2019_NaturePlants_Skokan_accepted.pdf","relation":"main_file","access_level":"open_access"}],"page":"1114-1119","month":"11","type":"journal_article","publication_status":"published","author":[{"first_name":"Roman","last_name":"Skokan","full_name":"Skokan, Roman"},{"last_name":"Medvecká","first_name":"Eva","full_name":"Medvecká, Eva"},{"last_name":"Viaene","first_name":"Tom","full_name":"Viaene, Tom"},{"full_name":"Vosolsobě, Stanislav","first_name":"Stanislav","last_name":"Vosolsobě"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"full_name":"Müller, Karel","first_name":"Karel","last_name":"Müller"},{"last_name":"Skůpa","first_name":"Petr","full_name":"Skůpa, Petr"},{"full_name":"Karady, Michal","first_name":"Michal","last_name":"Karady"},{"last_name":"Zhang","first_name":"Yuzhou","full_name":"Zhang, Yuzhou"},{"full_name":"Janacek, Dorina P.","first_name":"Dorina P.","last_name":"Janacek"},{"last_name":"Hammes","first_name":"Ulrich Z.","full_name":"Hammes, Ulrich Z."},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"pmid":1,"department":[{"_id":"JiFr"}],"external_id":{"pmid":["31712756"],"isi":["000496526100010"]},"date_created":"2019-11-25T09:08:04Z","file_date_updated":"2020-10-14T08:54:49Z","scopus_import":"1","_id":"7106","issue":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","isi":1,"title":"PIN-driven auxin transport emerged early in streptophyte evolution","oa":1,"citation":{"apa":"Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-019-0542-5\">https://doi.org/10.1038/s41477-019-0542-5</a>","chicago":"Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” <i>Nature Plants</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41477-019-0542-5\">https://doi.org/10.1038/s41477-019-0542-5</a>.","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. <i>Nature Plants</i>. 2019;5(11):1114-1119. doi:<a href=\"https://doi.org/10.1038/s41477-019-0542-5\">10.1038/s41477-019-0542-5</a>","ista":"Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119.","short":"R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.","ieee":"R. Skokan <i>et al.</i>, “PIN-driven auxin transport emerged early in streptophyte evolution,” <i>Nature Plants</i>, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019.","mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” <i>Nature Plants</i>, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:<a href=\"https://doi.org/10.1038/s41477-019-0542-5\">10.1038/s41477-019-0542-5</a>."},"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-04-14T07:45:04Z"},{"doi":"10.1145/3314024","quality_controlled":"1","publication_identifier":{"issn":["0004-5411"]},"oa_version":"Preprint","article_type":"original","year":"2019","volume":66,"date_published":"2019-06-01T00:00:00Z","publication":"Journal of the ACM","intvolume":"        66","article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable."}],"main_file_link":[{"url":"https://arxiv.org/abs/1711.08436","open_access":"1"}],"publisher":"ACM","status":"public","type":"journal_article","month":"06","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","id":"184","status":"public"}]},"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"full_name":"Patak, Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83","first_name":"Pavel","last_name":"Patak"},{"full_name":"Patakova, Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683","first_name":"Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"department":[{"_id":"UlWa"}],"date_created":"2019-11-26T10:13:59Z","external_id":{"arxiv":["1711.08436"],"isi":["000495406300007"]},"scopus_import":"1","_id":"7108","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","day":"01","article_number":"21","arxiv":1,"isi":1,"title":"Shellability is NP-complete","oa":1,"citation":{"apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2019). Shellability is NP-complete. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3314024\">https://doi.org/10.1145/3314024</a>","ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. <i>Journal of the ACM</i>. 2019;66(3). doi:<a href=\"https://doi.org/10.1145/3314024\">10.1145/3314024</a>","chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” <i>Journal of the ACM</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3314024\">https://doi.org/10.1145/3314024</a>.","ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019).","mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” <i>Journal of the ACM</i>, vol. 66, no. 3, 21, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3314024\">10.1145/3314024</a>.","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” <i>Journal of the ACM</i>, vol. 66, no. 3. ACM, 2019."},"date_updated":"2025-06-04T07:49:03Z"},{"year":"2019","oa_version":"None","article_type":"original","publication_identifier":{"issn":["0004-5411"]},"doi":"10.1145/3286976","quality_controlled":"1","abstract":[{"text":"We show how to construct temporal testers for the logic MITL, a prominent linear-time logic for real-time systems. A temporal tester is a transducer that inputs a signal holding the Boolean value of atomic propositions and outputs the truth value of a formula along time. Here we consider testers over continuous-time Boolean signals that use clock variables to enforce duration constraints, as in timed automata. We first rewrite the MITL formula into a “simple” formula using a limited set of temporal modalities. We then build testers for these specific modalities and show how to compose testers for simple formulae into complex ones. Temporal testers can be turned into acceptors, yielding a compositional translation from MITL to timed automata. This construction is much simpler than previously known and remains asymptotically optimal. It supports both past and future operators and can easily be extended.","lang":"eng"}],"publisher":"ACM","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":66,"date_published":"2019-05-01T00:00:00Z","publication":"Journal of the ACM","intvolume":"        66","department":[{"_id":"ToHe"}],"external_id":{"isi":["000495406300005"]},"date_created":"2019-11-26T10:22:32Z","publication_status":"published","author":[{"full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere"},{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"},{"last_name":"Ničković","first_name":"Dejan","full_name":"Ničković, Dejan"},{"full_name":"Pnueli, Amir","last_name":"Pnueli","first_name":"Amir"}],"type":"journal_article","month":"05","status":"public","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"citation":{"apa":"Ferrere, T., Maler, O., Ničković, D., &#38; Pnueli, A. (2019). From real-time logic to timed automata. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3286976\">https://doi.org/10.1145/3286976</a>","ama":"Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata. <i>Journal of the ACM</i>. 2019;66(3). doi:<a href=\"https://doi.org/10.1145/3286976\">10.1145/3286976</a>","chicago":"Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time Logic to Timed Automata.” <i>Journal of the ACM</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3286976\">https://doi.org/10.1145/3286976</a>.","short":"T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).","ista":"Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed automata. Journal of the ACM. 66(3), 19.","ieee":"T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to timed automata,” <i>Journal of the ACM</i>, vol. 66, no. 3. ACM, 2019.","mla":"Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” <i>Journal of the ACM</i>, vol. 66, no. 3, 19, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3286976\">10.1145/3286976</a>."},"date_updated":"2025-04-15T06:26:06Z","isi":1,"title":"From real-time logic to timed automata","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"3","day":"01","article_number":"19","scopus_import":"1","_id":"7109"},{"publication_identifier":{"isbn":["9781538613955"],"issn":["0743-1546"]},"month":"01","type":"conference","quality_controlled":"1","doi":"10.1109/cdc.2018.8619625","conference":{"name":"CDC: Conference on Decision and Control","end_date":"2018-12-19","start_date":"2018-12-17","location":"Miami Beach, FL, United States"},"status":"public","department":[{"_id":"DaAl"}],"year":"2019","date_created":"2019-11-26T15:07:49Z","external_id":{"isi":["000458114800023"]},"oa_version":"None","publication_status":"published","author":[{"full_name":"Khirirat, Sarit","first_name":"Sarit","last_name":"Khirirat"},{"last_name":"Johansson","first_name":"Mikael","full_name":"Johansson, Mikael"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"publication":"2018 IEEE Conference on Decision and Control","date_published":"2019-01-21T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"21","article_number":"8619625","scopus_import":"1","_id":"7122","abstract":[{"lang":"eng","text":"Data-rich applications in machine-learning and control have motivated an intense research on large-scale optimization. Novel algorithms have been proposed and shown to have optimal convergence rates in terms of iteration counts. However, their practical performance is severely degraded by the cost of exchanging high-dimensional gradient vectors between computing nodes. Several gradient compression heuristics have recently been proposed to reduce communications, but few theoretical results exist that quantify how they impact algorithm convergence. This paper establishes and strengthens the convergence guarantees for gradient descent under a family of gradient compression techniques. For convex optimization problems, we derive admissible step sizes and quantify both the number of iterations and the number of bits that need to be exchanged to reach a target accuracy. Finally, we validate the performance of different gradient compression techniques in simulations. The numerical results highlight the properties of different gradient compression algorithms and confirm that fast convergence with limited information exchange is possible."}],"citation":{"mla":"Khirirat, Sarit, et al. “Gradient Compression for Communication-Limited Convex Optimization.” <i>2018 IEEE Conference on Decision and Control</i>, 8619625, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/cdc.2018.8619625\">10.1109/cdc.2018.8619625</a>.","ieee":"S. Khirirat, M. Johansson, and D.-A. Alistarh, “Gradient compression for communication-limited convex optimization,” in <i>2018 IEEE Conference on Decision and Control</i>, Miami Beach, FL, United States, 2019.","short":"S. Khirirat, M. Johansson, D.-A. Alistarh, in:, 2018 IEEE Conference on Decision and Control, IEEE, 2019.","ista":"Khirirat S, Johansson M, Alistarh D-A. 2019. Gradient compression for communication-limited convex optimization. 2018 IEEE Conference on Decision and Control. CDC: Conference on Decision and Control, 8619625.","chicago":"Khirirat, Sarit, Mikael Johansson, and Dan-Adrian Alistarh. “Gradient Compression for Communication-Limited Convex Optimization.” In <i>2018 IEEE Conference on Decision and Control</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/cdc.2018.8619625\">https://doi.org/10.1109/cdc.2018.8619625</a>.","ama":"Khirirat S, Johansson M, Alistarh D-A. Gradient compression for communication-limited convex optimization. In: <i>2018 IEEE Conference on Decision and Control</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/cdc.2018.8619625\">10.1109/cdc.2018.8619625</a>","apa":"Khirirat, S., Johansson, M., &#38; Alistarh, D.-A. (2019). Gradient compression for communication-limited convex optimization. In <i>2018 IEEE Conference on Decision and Control</i>. Miami Beach, FL, United States: IEEE. <a href=\"https://doi.org/10.1109/cdc.2018.8619625\">https://doi.org/10.1109/cdc.2018.8619625</a>"},"publisher":"IEEE","date_updated":"2023-09-06T11:14:55Z","isi":1,"language":[{"iso":"eng"}],"title":"Gradient compression for communication-limited convex optimization","article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Loss of functional cardiomyocytes is a major determinant of heart failure after myocardial infarction. Previous high throughput screening studies have identified a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate cardiac regeneration in mice. Here, we show that all of the most effective of these miRNAs activate nuclear localization of the master transcriptional cofactor Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization by targeting Cofilin2, a process that by itself activates YAP nuclear translocation. Thus, activation of YAP and modulation of the actin cytoskeleton are major components of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte proliferation."}],"publisher":"Elsevier","article_processing_charge":"Yes","language":[{"iso":"eng"}],"volume":27,"publication":"Cell Reports","date_published":"2019-05-28T00:00:00Z","intvolume":"        27","year":"2019","ddc":["576"],"oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["2211-1247"]},"doi":"10.1016/j.celrep.2019.05.005","quality_controlled":"1","has_accepted_license":"1","citation":{"ista":"Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI, Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili M, Samal A, Giacca M. 2019. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. Cell Reports. 27(9), 2759–2771.e5.","short":"C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I. Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo, M. Marsili, A. Samal, M. Giacca, Cell Reports 27 (2019) 2759–2771.e5.","mla":"Torrini, Consuelo, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>, vol. 27, no. 9, Elsevier, 2019, p. 2759–2771.e5, doi:<a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">10.1016/j.celrep.2019.05.005</a>.","ieee":"C. Torrini <i>et al.</i>, “Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation,” <i>Cell Reports</i>, vol. 27, no. 9. Elsevier, p. 2759–2771.e5, 2019.","apa":"Torrini, C., Cubero, R. J., Dirkx, E., Braga, L., Ali, H., Prosdocimo, G., … Giacca, M. (2019). Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">https://doi.org/10.1016/j.celrep.2019.05.005</a>","ama":"Torrini C, Cubero RJ, Dirkx E, et al. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. <i>Cell Reports</i>. 2019;27(9):2759-2771.e5. doi:<a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">10.1016/j.celrep.2019.05.005</a>","chicago":"Torrini, Consuelo, Ryan J Cubero, Ellen Dirkx, Luca Braga, Hashim Ali, Giulia Prosdocimo, Maria Ines Gutierrez, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">https://doi.org/10.1016/j.celrep.2019.05.005</a>."},"oa":1,"date_updated":"2021-01-12T08:11:56Z","title":"Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"9","day":"28","file_date_updated":"2020-07-14T12:47:50Z","_id":"7128","extern":"1","date_created":"2019-11-26T22:30:07Z","external_id":{"pmid":["31141697"]},"publication_status":"published","pmid":1,"author":[{"full_name":"Torrini, Consuelo","first_name":"Consuelo","last_name":"Torrini"},{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","orcid":"0000-0003-0002-1867","first_name":"Ryan J","full_name":"Cubero, Ryan J"},{"full_name":"Dirkx, Ellen","first_name":"Ellen","last_name":"Dirkx"},{"full_name":"Braga, Luca","last_name":"Braga","first_name":"Luca"},{"full_name":"Ali, Hashim","first_name":"Hashim","last_name":"Ali"},{"first_name":"Giulia","last_name":"Prosdocimo","full_name":"Prosdocimo, Giulia"},{"full_name":"Gutierrez, Maria Ines","last_name":"Gutierrez","first_name":"Maria Ines"},{"full_name":"Collesi, Chiara","last_name":"Collesi","first_name":"Chiara"},{"full_name":"Licastro, Danilo","last_name":"Licastro","first_name":"Danilo"},{"last_name":"Zentilin","first_name":"Lorena","full_name":"Zentilin, Lorena"},{"first_name":"Miguel","last_name":"Mano","full_name":"Mano, Miguel"},{"full_name":"Zacchigna, Serena","last_name":"Zacchigna","first_name":"Serena"},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"last_name":"Marsili","first_name":"Matteo","full_name":"Marsili, Matteo"},{"full_name":"Samal, Areejit","last_name":"Samal","first_name":"Areejit"},{"full_name":"Giacca, Mauro","last_name":"Giacca","first_name":"Mauro"}],"month":"05","type":"journal_article","file":[{"file_name":"torrini_cellreports_2019.pdf","date_created":"2019-11-26T22:30:43Z","date_updated":"2020-07-14T12:47:50Z","access_level":"open_access","relation":"main_file","file_size":4650750,"content_type":"application/pdf","file_id":"7129","checksum":"c5d855d07263bfec718673385d0ea2d7","creator":"rcubero"}],"page":"2759-2771.e5","keyword":["cardiomyocyte","cell cycle","Cofilin2","cytoskeleton","Hippo","microRNA","regeneration","YAP"],"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"}},{"_id":"7130","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","day":"17","article_number":"063402","acknowledgement":"We acknowledge interesting discussions with M Abbott, E Aurell, J Barbier, R Monasson, T Mora, I Nemenman, N Tishby and R Zecchina. This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation) (RJC and YR), by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (2016R1D1A1B03932264) (JJ), and, in part, by the ICTP through the OEA-AC-98 (JS).","arxiv":1,"title":"Statistical criticality arises in most informative representations","oa":1,"citation":{"ieee":"R. J. Cubero, J. Jo, M. Marsili, Y. Roudi, and J. Song, “Statistical criticality arises in most informative representations,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2019, no. 6. IOP Publishing, 2019.","mla":"Cubero, Ryan J., et al. “Statistical Criticality Arises in Most Informative Representations.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2019, no. 6, 063402, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">10.1088/1742-5468/ab16c8</a>.","short":"R.J. Cubero, J. Jo, M. Marsili, Y. Roudi, J. Song, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).","ista":"Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. 2019. Statistical criticality arises in most informative representations. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063402.","chicago":"Cubero, Ryan J, Junghyo Jo, Matteo Marsili, Yasser Roudi, and Juyong Song. “Statistical Criticality Arises in Most Informative Representations.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">https://doi.org/10.1088/1742-5468/ab16c8</a>.","ama":"Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. Statistical criticality arises in most informative representations. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2019;2019(6). doi:<a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">10.1088/1742-5468/ab16c8</a>","apa":"Cubero, R. J., Jo, J., Marsili, M., Roudi, Y., &#38; Song, J. (2019). Statistical criticality arises in most informative representations. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">https://doi.org/10.1088/1742-5468/ab16c8</a>"},"date_updated":"2021-01-12T08:11:57Z","keyword":["optimization under uncertainty","source coding","large deviation"],"status":"public","month":"06","type":"journal_article","publication_status":"published","author":[{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","first_name":"Ryan J","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J"},{"full_name":"Jo, Junghyo","last_name":"Jo","first_name":"Junghyo"},{"first_name":"Matteo","last_name":"Marsili","full_name":"Marsili, Matteo"},{"full_name":"Roudi, Yasser","last_name":"Roudi","first_name":"Yasser"},{"first_name":"Juyong","last_name":"Song","full_name":"Song, Juyong"}],"extern":"1","date_created":"2019-11-26T22:36:09Z","external_id":{"arxiv":["1808.00249"]},"volume":2019,"date_published":"2019-06-17T00:00:00Z","publication":"Journal of Statistical Mechanics: Theory and Experiment","intvolume":"      2019","article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We show that statistical criticality, i.e. the occurrence of power law frequency distributions, arises in samples that are maximally informative about the underlying generating process. In order to reach this conclusion, we first identify the frequency with which different outcomes occur in a sample, as the variable carrying useful information on the generative process. The entropy of the frequency, that we call relevance, provides an upper bound to the number of informative bits. This differs from the entropy of the data, that we take as a measure of resolution. Samples that maximise relevance at a given resolution—that we call maximally informative samples—exhibit statistical criticality. In particular, Zipf's law arises at the optimal trade-off between resolution (i.e. compression) and relevance. As a byproduct, we derive a bound of the maximal number of parameters that can be estimated from a dataset, in the absence of prior knowledge on the generative model.\r\n\r\nFurthermore, we relate criticality to the statistical properties of the representation of the data generating process. We show that, as a consequence of the concentration property of the asymptotic equipartition property, representations that are maximally informative about the data generating process are characterised by an exponential distribution of energy levels. This arises from a principle of minimal entropy, that is conjugate of the maximum entropy principle in statistical mechanics. This explains why statistical criticality requires no parameter fine tuning in maximally informative samples."}],"publisher":"IOP Publishing","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.00249"}],"doi":"10.1088/1742-5468/ab16c8","quality_controlled":"1","publication_identifier":{"issn":["1742-5468"]},"oa_version":"Preprint","article_type":"original","year":"2019"},{"quality_controlled":"1","conference":{"name":"ISIT: International Symposium on Information Theory","location":"Paris, France","start_date":"2019-07-07","end_date":"2019-07-12"},"doi":"10.1109/isit.2019.8849240","publication_identifier":{"isbn":["9781538692912"]},"oa_version":"Preprint","year":"2019","publication":"2019 IEEE International Symposium on Information Theory","date_published":"2019-07-01T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X<i are ϵ-close to be nearly flat (only a constant factor away). The argument is combinatorial (based on simplex coverings).\r\nThis result may be used as a generic tool for \\emph{exhibiting block-source structures}. We demonstrate this by reproving the fundamental converter due to Nisan and Zuckermann (\\emph{J. Computer and System Sciences, 1996}), which shows that sampling blocks from a min-entropy source roughly preserves the entropy rate. Our bound implies, only by straightforward chain rules, an additive loss of o(1) (for sufficiently many samples), which qualitatively meets the first tighter analysis of this problem due to Vadhan (\\emph{CRYPTO'03}), obtained by large deviation techniques. "}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.08476"}],"publisher":"IEEE","status":"public","month":"07","type":"conference","publication_status":"published","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","first_name":"Maciej","full_name":"Skórski, Maciej"}],"department":[{"_id":"KrPi"}],"date_created":"2019-11-28T10:19:21Z","external_id":{"isi":["000489100301043"],"arxiv":["1702.08476"]},"scopus_import":"1","_id":"7136","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"8849240","day":"01","isi":1,"arxiv":1,"title":"Strong chain rules for min-entropy under few bits spoiled","oa":1,"citation":{"apa":"Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In <i>2019 IEEE International Symposium on Information Theory</i>. Paris, France: IEEE. <a href=\"https://doi.org/10.1109/isit.2019.8849240\">https://doi.org/10.1109/isit.2019.8849240</a>","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In <i>2019 IEEE International Symposium on Information Theory</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/isit.2019.8849240\">https://doi.org/10.1109/isit.2019.8849240</a>.","ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: <i>2019 IEEE International Symposium on Information Theory</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/isit.2019.8849240\">10.1109/isit.2019.8849240</a>","ista":"Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240.","short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019.","mla":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” <i>2019 IEEE International Symposium on Information Theory</i>, 8849240, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/isit.2019.8849240\">10.1109/isit.2019.8849240</a>.","ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in <i>2019 IEEE International Symposium on Information Theory</i>, Paris, France, 2019."},"date_updated":"2023-09-06T11:15:41Z"},{"year":"2019","ddc":["580"],"oa_version":"Published Version","article_type":"original","publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]},"doi":"10.1038/s41422-019-0254-4","quality_controlled":"1","abstract":[{"lang":"eng","text":"Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content."}],"main_file_link":[{"url":"https://doi.org/10.1038/s41422-019-0254-4","open_access":"1"}],"publisher":"Springer Nature","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":29,"publication":"Cell Research","date_published":"2019-12-01T00:00:00Z","intvolume":"        29","department":[{"_id":"JiFr"}],"external_id":{"isi":["000500749600001"],"pmid":["31745287"]},"date_created":"2019-12-02T12:30:48Z","publication_status":"published","author":[{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","last_name":"Sinclair","first_name":"Scott A","orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A"},{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"type":"journal_article","month":"12","page":"965-966","status":"public","citation":{"mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” <i>Cell Research</i>, vol. 29, Springer Nature, 2019, pp. 965–66, doi:<a href=\"https://doi.org/10.1038/s41422-019-0254-4\">10.1038/s41422-019-0254-4</a>.","ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” <i>Cell Research</i>, vol. 29. Springer Nature, pp. 965–966, 2019.","short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966.","ama":"Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. <i>Cell Research</i>. 2019;29:965-966. doi:<a href=\"https://doi.org/10.1038/s41422-019-0254-4\">10.1038/s41422-019-0254-4</a>","chicago":"Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” <i>Cell Research</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41422-019-0254-4\">https://doi.org/10.1038/s41422-019-0254-4</a>.","apa":"Sinclair, S. A., &#38; Friml, J. (2019). Defying gravity: a plant’s quest for moisture. <i>Cell Research</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41422-019-0254-4\">https://doi.org/10.1038/s41422-019-0254-4</a>"},"oa":1,"date_updated":"2026-06-18T19:16:44Z","isi":1,"title":"Defying gravity: a plant's quest for moisture","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":"1","_id":"7143"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.05549"}],"publisher":"American Physical Society","abstract":[{"lang":"eng","text":"End-to-end correlated bound states are investigated in superconductor-semiconductor hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently identified from each wire end, and a cross-correlation function is computed that counts end-to-end coincidences, averaging over thousands of subgap features. Strong correlations in a short, 300-nm device are reduced by a factor of 4 in a long, 900-nm device. In addition, subgap conductance distributions are investigated, and correlations between the left and right distributions are identified based on their mutual information."}],"intvolume":"       100","volume":100,"date_published":"2019-11-15T00:00:00Z","publication":"Physical Review B","article_type":"original","oa_version":"Preprint","year":"2019","doi":"10.1103/physrevb.100.205412","quality_controlled":"1","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"title":"End-to-end correlated subgap states in hybrid nanowires","arxiv":1,"isi":1,"date_updated":"2024-02-28T13:13:51Z","oa":1,"citation":{"ieee":"G. L. R. Anselmetti <i>et al.</i>, “End-to-end correlated subgap states in hybrid nanowires,” <i>Physical Review B</i>, vol. 100, no. 20. American Physical Society, 2019.","mla":"Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” <i>Physical Review B</i>, vol. 100, no. 20, 205412, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevb.100.205412\">10.1103/physrevb.100.205412</a>.","short":"G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski, J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P. Higginbotham, Physical Review B 100 (2019).","ista":"Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.","chicago":"Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski, J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevb.100.205412\">https://doi.org/10.1103/physrevb.100.205412</a>.","ama":"Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap states in hybrid nanowires. <i>Physical Review B</i>. 2019;100(20). doi:<a href=\"https://doi.org/10.1103/physrevb.100.205412\">10.1103/physrevb.100.205412</a>","apa":"Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski, F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap states in hybrid nanowires. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.100.205412\">https://doi.org/10.1103/physrevb.100.205412</a>"},"_id":"7145","scopus_import":"1","article_number":"205412","day":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"20","author":[{"first_name":"G. L. R.","last_name":"Anselmetti","full_name":"Anselmetti, G. L. R."},{"last_name":"Martinez","first_name":"E. A.","full_name":"Martinez, E. A."},{"full_name":"Ménard, G. C.","first_name":"G. C.","last_name":"Ménard"},{"full_name":"Puglia, D.","first_name":"D.","last_name":"Puglia"},{"full_name":"Malinowski, F. K.","last_name":"Malinowski","first_name":"F. K."},{"last_name":"Lee","first_name":"J. S.","full_name":"Lee, J. S."},{"full_name":"Choi, S.","last_name":"Choi","first_name":"S."},{"first_name":"M.","last_name":"Pendharkar","full_name":"Pendharkar, M."},{"first_name":"C. J.","last_name":"Palmstrøm","full_name":"Palmstrøm, C. J."},{"full_name":"Marcus, C. M.","first_name":"C. M.","last_name":"Marcus"},{"full_name":"Casparis, L.","first_name":"L.","last_name":"Casparis"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P"}],"publication_status":"published","external_id":{"arxiv":["1908.05549"],"isi":["000495967500006"]},"date_created":"2019-12-04T16:02:25Z","department":[{"_id":"AnHi"}],"status":"public","type":"journal_article","month":"11"},{"volume":3,"ec_funded":1,"publication":"Nature Ecology & Evolution","date_published":"2019-11-25T00:00:00Z","intvolume":"         3","abstract":[{"lang":"eng","text":"Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity."}],"publisher":"Springer Nature","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2397-334X"]},"doi":"10.1038/s41559-019-1050-8","quality_controlled":"1","year":"2019","oa_version":"None","article_type":"original","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"12","day":"25","scopus_import":"1","_id":"7146","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"citation":{"apa":"Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-019-1050-8\">https://doi.org/10.1038/s41559-019-1050-8</a>","ama":"Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover. <i>Nature Ecology &#38; Evolution</i>. 2019;3(12):1632-1641. doi:<a href=\"https://doi.org/10.1038/s41559-019-1050-8\">10.1038/s41559-019-1050-8</a>","chicago":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41559-019-1050-8\">https://doi.org/10.1038/s41559-019-1050-8</a>.","ista":"Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology &#38; Evolution. 3(12), 1632–1641.","short":"B. Vicoso, Nature Ecology &#38; Evolution 3 (2019) 1632–1641.","mla":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12, Springer Nature, 2019, pp. 1632–41, doi:<a href=\"https://doi.org/10.1038/s41559-019-1050-8\">10.1038/s41559-019-1050-8</a>.","ieee":"B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,” <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12. Springer Nature, pp. 1632–1641, 2019."},"date_updated":"2025-04-14T07:41:21Z","isi":1,"title":"Molecular and evolutionary dynamics of animal sex-chromosome turnover","month":"11","type":"journal_article","page":"1632-1641","status":"public","department":[{"_id":"BeVi"}],"external_id":{"isi":["000500728800009"]},"date_created":"2019-12-04T16:05:25Z","publication_status":"published","author":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}]},{"status":"public","page":"155-187","month":"09","type":"conference","alternative_title":["LNCS"],"author":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","orcid":"0000-0001-7777-546X","last_name":"Igler"},{"full_name":"Petrov, Tatjana","last_name":"Petrov","first_name":"Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sezgin","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali"}],"publication_status":"published","date_created":"2019-12-04T16:07:50Z","external_id":{"isi":["000557875100009"]},"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"_id":"7147","scopus_import":"1","day":"17","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Transient memory in gene regulation","isi":1,"date_updated":"2026-04-16T10:26:49Z","citation":{"short":"C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187.","ista":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory in gene regulation. 17th International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773, 155–187.","ieee":"C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in <i>17th International Conference on Computational Methods in Systems Biology</i>, Trieste, Italy, 2019, vol. 11773, pp. 155–187.","mla":"Guet, Calin C., et al. “Transient Memory in Gene Regulation.” <i>17th International Conference on Computational Methods in Systems Biology</i>, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:<a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">10.1007/978-3-030-31304-3_9</a>.","apa":"Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., &#38; Sezgin, A. (2019). Transient memory in gene regulation. In <i>17th International Conference on Computational Methods in Systems Biology</i> (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">https://doi.org/10.1007/978-3-030-31304-3_9</a>","ama":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: <i>17th International Conference on Computational Methods in Systems Biology</i>. Vol 11773. Springer Nature; 2019:155-187. doi:<a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">10.1007/978-3-030-31304-3_9</a>","chicago":"Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In <i>17th International Conference on Computational Methods in Systems Biology</i>, 11773:155–87. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">https://doi.org/10.1007/978-3-030-31304-3_9</a>."},"project":[{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Design principles underlying genetic switch architecture","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/978-3-030-31304-3_9","conference":{"name":"CMSB: Computational Methods in Systems Biology","location":"Trieste, Italy","start_date":"2019-09-18","end_date":"2019-09-20"},"publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783030313043"],"issn":["0302-9743"],"isbn":["9783030313036"]},"oa_version":"None","year":"2019","intvolume":"     11773","publication":"17th International Conference on Computational Methods in Systems Biology","date_published":"2019-09-17T00:00:00Z","volume":11773,"language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions."}]},{"oa_version":"Preprint","article_type":"original","year":"2019","doi":"10.1007/s00446-016-0270-2","quality_controlled":"1","publication_identifier":{"issn":["0178-2770","1432-0452"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In this work, we use algebraic methods for studying distance computation and subgraph detection tasks in the congested clique model. Specifically, we adapt parallel matrix multiplication implementations to the congested clique, obtaining an O(n1−2/ω) round matrix multiplication algorithm, where ω<2.3728639 is the exponent of matrix multiplication. In conjunction with known techniques from centralised algorithmics, this gives significant improvements over previous best upper bounds in the congested clique model. The highlight results include:\r\n\r\n1.    triangle and 4-cycle counting in O(n0.158) rounds, improving upon the O(n1/3) algorithm of Dolev et al. [DISC 2012],\r\n2. a (1+o(1))-approximation of all-pairs shortest paths in O(n0.158) rounds, improving upon the O~(n1/2)-round (2+o(1))-approximation algorithm given by Nanongkai [STOC 2014], and\r\n 3. computing the girth in O(n0.158) rounds, which is the first non-trivial solution in this model.\r\n   \r\nIn addition, we present a novel constant-round combinatorial algorithm for detecting 4-cycles."}],"publisher":"Springer Nature","main_file_link":[{"url":"https://arxiv.org/abs/1503.04963","open_access":"1"}],"volume":32,"date_published":"2019-12-01T00:00:00Z","publication":"Distributed Computing","intvolume":"        32","publication_status":"published","author":[{"full_name":"Censor-Hillel, Keren","first_name":"Keren","last_name":"Censor-Hillel"},{"first_name":"Petteri","last_name":"Kaski","full_name":"Kaski, Petteri"},{"last_name":"Korhonen","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne"},{"full_name":"Lenzen, Christoph","last_name":"Lenzen","first_name":"Christoph"},{"full_name":"Paz, Ami","first_name":"Ami","last_name":"Paz"},{"last_name":"Suomela","first_name":"Jukka","full_name":"Suomela, Jukka"}],"extern":"1","date_created":"2019-12-05T09:49:49Z","external_id":{"arxiv":["1503.04963"]},"status":"public","month":"12","type":"journal_article","page":"461-478","arxiv":1,"title":"Algebraic methods in the congested clique","citation":{"mla":"Censor-Hillel, Keren, et al. “Algebraic Methods in the Congested Clique.” <i>Distributed Computing</i>, vol. 32, no. 6, Springer Nature, 2019, pp. 461–78, doi:<a href=\"https://doi.org/10.1007/s00446-016-0270-2\">10.1007/s00446-016-0270-2</a>.","ieee":"K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, and J. Suomela, “Algebraic methods in the congested clique,” <i>Distributed Computing</i>, vol. 32, no. 6. Springer Nature, pp. 461–478, 2019.","short":"K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, J. Suomela, Distributed Computing 32 (2019) 461–478.","ista":"Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. 2019. Algebraic methods in the congested clique. Distributed Computing. 32(6), 461–478.","chicago":"Censor-Hillel, Keren, Petteri Kaski, Janne Korhonen, Christoph Lenzen, Ami Paz, and Jukka Suomela. “Algebraic Methods in the Congested Clique.” <i>Distributed Computing</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00446-016-0270-2\">https://doi.org/10.1007/s00446-016-0270-2</a>.","ama":"Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. Algebraic methods in the congested clique. <i>Distributed Computing</i>. 2019;32(6):461-478. doi:<a href=\"https://doi.org/10.1007/s00446-016-0270-2\">10.1007/s00446-016-0270-2</a>","apa":"Censor-Hillel, K., Kaski, P., Korhonen, J., Lenzen, C., Paz, A., &#38; Suomela, J. (2019). Algebraic methods in the congested clique. <i>Distributed Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00446-016-0270-2\">https://doi.org/10.1007/s00446-016-0270-2</a>"},"oa":1,"date_updated":"2021-01-12T08:12:05Z","_id":"7150","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","day":"01"},{"article_processing_charge":"No","title":"Supplementary data for \"Programming temporal morphing of self-actuated shells\"","publisher":"Institute of Science and Technology Austria","date_updated":"2025-06-12T06:58:31Z","contributor":[{"last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Connor","last_name":"McMahan"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","first_name":"Jesus"},{"last_name":"Daraio","first_name":"Chiara"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"oa":1,"citation":{"ista":"Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7154\">10.15479/AT:ISTA:7154</a>.","short":"R. Guseinov, (2019).","ieee":"R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019.","mla":"Guseinov, Ruslan. <i>Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.”</i> Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7154\">10.15479/AT:ISTA:7154</a>.","apa":"Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7154\">https://doi.org/10.15479/AT:ISTA:7154</a>","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7154\">https://doi.org/10.15479/AT:ISTA:7154</a>.","ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7154\">10.15479/AT:ISTA:7154</a>"},"_id":"7154","file_date_updated":"2020-07-14T12:47:50Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"date_published":"2019-12-06T00:00:00Z","author":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","orcid":"0000-0001-9819-5077","last_name":"Guseinov","full_name":"Guseinov, Ruslan"}],"related_material":{"record":[{"status":"deleted","id":"8433","relation":"used_in_publication"},{"id":"7262","status":"public","relation":"used_in_publication"}]},"ddc":["000"],"oa_version":"Published Version","date_created":"2019-12-09T07:52:46Z","year":"2019","department":[{"_id":"BeBi"}],"has_accepted_license":"1","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","doi":"10.15479/AT:ISTA:7154","type":"research_data","month":"12","file":[{"file_id":"7155","checksum":"155133e6e188e85b3c0676a5e70b9341","content_type":"application/x-zip-compressed","file_size":65307107,"creator":"dernst","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-09T07:52:17Z","file_name":"temporal_morphing_supp_data.zip"}]},{"abstract":[{"text":"We propose an efficient microwave-photonic modulator as a resource for stationary entangled microwave-optical fields and develop the theory for deterministic entanglement generation and quantum state transfer in multi-resonant electro-optic systems. The device is based on a single crystal whispering gallery mode resonator integrated into a 3D-microwave cavity. The specific design relies on a new combination of thin-film technology and conventional machining that is optimized for the lowest dissipation rates in the microwave, optical, and mechanical domains. We extract important device properties from finite-element simulations and predict continuous variable entanglement generation rates on the order of a Mebit/s for optical pump powers of only a few tens of microwatts. We compare the quantum state transfer fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation and direct conversion protocols under realistic conditions. Combining the unique capabilities of circuit quantum electrodynamics with the resilience of fiber optic communication could facilitate long-distance solid-state qubit networks, new methods for quantum signal synthesis, quantum key distribution, and quantum enhanced detection, as well as more power-efficient classical sensing and modulation.","lang":"eng"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2019-12-01T00:00:00Z","publication":"npj Quantum Information","ec_funded":1,"volume":5,"intvolume":"         5","year":"2019","ddc":["530"],"oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["2056-6387"]},"quality_controlled":"1","doi":"10.1038/s41534-019-0220-5","has_accepted_license":"1","oa":1,"citation":{"chicago":"Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” <i>Npj Quantum Information</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41534-019-0220-5\">https://doi.org/10.1038/s41534-019-0220-5</a>.","ama":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. <i>npj Quantum Information</i>. 2019;5. doi:<a href=\"https://doi.org/10.1038/s41534-019-0220-5\">10.1038/s41534-019-0220-5</a>","apa":"Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., &#38; Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. <i>Npj Quantum Information</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41534-019-0220-5\">https://doi.org/10.1038/s41534-019-0220-5</a>","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” <i>Npj Quantum Information</i>, vol. 5, 108, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41534-019-0220-5\">10.1038/s41534-019-0220-5</a>.","ieee":"A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic entanglement source for microwave to telecom quantum state transfer,” <i>npj Quantum Information</i>, vol. 5. Springer Nature, 2019.","ista":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 5, 108.","short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. 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Shape expressions for specifying and extracting signal features. 19th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.","short":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309.","mla":"Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal Features.” <i>19th International Conference on Runtime Verification</i>, vol. 11757, Springer Nature, 2019, pp. 292–309, doi:<a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">10.1007/978-3-030-32079-9_17</a>.","ieee":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions for specifying and extracting signal features,” in <i>19th International Conference on Runtime Verification</i>, Porto, Portugal, 2019, vol. 11757, pp. 292–309.","apa":"Ničković, D., Qin, X., Ferrere, T., Mateis, C., &#38; Deshmukh, J. (2019). Shape expressions for specifying and extracting signal features. In <i>19th International Conference on Runtime Verification</i> (Vol. 11757, pp. 292–309). Porto, Portugal: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">https://doi.org/10.1007/978-3-030-32079-9_17</a>","chicago":"Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In <i>19th International Conference on Runtime Verification</i>, 11757:292–309. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">https://doi.org/10.1007/978-3-030-32079-9_17</a>.","ama":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for specifying and extracting signal features. In: <i>19th International Conference on Runtime Verification</i>. Vol 11757. Springer Nature; 2019:292-309. doi:<a href=\"https://doi.org/10.1007/978-3-030-32079-9_17\">10.1007/978-3-030-32079-9_17</a>"},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S11402-N23"}],"title":"Shape expressions for specifying and extracting signal features","isi":1,"day":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"7159","scopus_import":"1","year":"2019","oa_version":"None","publication_identifier":{"eisbn":["9783030320799"],"isbn":["9783030320782"],"issn":["0302-9743"]},"quality_controlled":"1","conference":{"start_date":"2019-10-08","location":"Porto, Portugal","end_date":"2019-10-11","name":"RV: Runtime Verification"},"doi":"10.1007/978-3-030-32079-9_17","publisher":"Springer Nature","abstract":[{"text":"Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a tremendous amount of generated, measured and recorded time-series data. Extracting temporal segments that encode patterns with useful information out of these huge amounts of data is an extremely difficult problem. We propose shape expressions as a declarative formalism for specifying, querying and extracting sophisticated temporal patterns from possibly noisy data. Shape expressions are regular expressions with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters as atomic predicates and additional constraints on these parameters. We equip shape expressions with a novel noisy semantics that combines regular expression matching semantics with statistical regression. We characterize essential properties of the formalism and propose an efficient approximate shape expression matching procedure. We demonstrate the wide applicability of this technique on two case studies. ","lang":"eng"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"     11757","date_published":"2019-10-01T00:00:00Z","publication":"19th International Conference on Runtime Verification","volume":11757},{"has_accepted_license":"1","doi":"10.1242/dev.176297","quality_controlled":"1","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"article_type":"original","oa_version":"Published Version","ddc":["570"],"year":"2019","intvolume":"       146","volume":146,"ec_funded":1,"publication":"Development","date_published":"2019-12-04T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"The Company of Biologists","abstract":[{"lang":"eng","text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube."}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","month":"12","type":"journal_article","file":[{"file_name":"2019_Development_Guerrero.pdf","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-12-13T07:34:06Z","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":7797881,"content_type":"application/pdf","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a","file_id":"7177"}],"author":[{"last_name":"Guerrero","first_name":"Pilar","full_name":"Guerrero, Pilar"},{"last_name":"Perez-Carrasco","first_name":"Ruben","full_name":"Perez-Carrasco, Ruben"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","orcid":"0000-0001-7896-7762","last_name":"Zagórski","full_name":"Zagórski, Marcin P"},{"last_name":"Page","first_name":"David","full_name":"Page, David"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"full_name":"Page, Karen M.","last_name":"Page","first_name":"Karen M."}],"pmid":1,"publication_status":"published","external_id":{"pmid":["31784457"],"isi":["000507575700004"]},"date_created":"2019-12-10T14:39:50Z","department":[{"_id":"AnKi"}],"_id":"7165","scopus_import":"1","file_date_updated":"2020-07-14T12:47:50Z","article_number":"dev176297","day":"04","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"23","title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","corr_author":"1","isi":1,"date_updated":"2025-04-14T07:27:30Z","project":[{"grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"oa":1,"citation":{"short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019).","ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297.","ieee":"P. Guerrero <i>et al.</i>, “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” <i>Development</i>, vol. 146, no. 23. The Company of Biologists, 2019.","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., &#38; Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>","chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>.","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. 2019;146(23). doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>"}},{"publication_identifier":{"eisbn":["978-3-658-26763-6"],"isbn":["978-3-658-26762-9"]},"type":"book_editor","month":"10","page":"XIV, 245","doi":"10.1007/978-3-658-26763-6","quality_controlled":"1","status":"public","year":"2019","department":[{"_id":"ChLa"}],"date_created":"2019-12-11T14:15:56Z","place":"Wiesbaden","edition":"1","publication_status":"published","oa_version":"None","related_material":{"link":[{"url":"https://ist.ac.at/en/news/book-release-how-machines-learn/","relation":"press_release","description":"News on IST Website"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2019-10-30T00:00:00Z","day":"30","editor":[{"first_name":"Kristian","last_name":"Kersting","full_name":"Kersting, Kristian"},{"full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Constantin","last_name":"Rothkopf","full_name":"Rothkopf, Constantin"}],"_id":"7171","abstract":[{"text":"Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens. Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten möchten. Auch für Schülerinnen und Schüler geeignet!","lang":"ger"}],"citation":{"apa":"Kersting, K., Lampert, C., &#38; Rothkopf, C. (Eds.). (2019). <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i> (1st ed.). Wiesbaden: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-658-26763-6\">https://doi.org/10.1007/978-3-658-26763-6</a>","ama":"Kersting K, Lampert C, Rothkopf C, eds. <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i>. 1st ed. Wiesbaden: Springer Nature; 2019. doi:<a href=\"https://doi.org/10.1007/978-3-658-26763-6\">10.1007/978-3-658-26763-6</a>","chicago":"Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i>. 1st ed. Wiesbaden: Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-658-26763-6\">https://doi.org/10.1007/978-3-658-26763-6</a>.","short":"K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.","ista":"Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.","ieee":"K. Kersting, C. Lampert, and C. Rothkopf, Eds., <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i>, 1st ed. Wiesbaden: Springer Nature, 2019.","mla":"Kersting, Kristian, et al., editors. <i>Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt</i>. 1st ed., Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1007/978-3-658-26763-6\">10.1007/978-3-658-26763-6</a>."},"date_updated":"2021-12-22T14:40:58Z","publisher":"Springer Nature","article_processing_charge":"No","title":"Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt","language":[{"iso":"ger"}]},{"status":"public","degree_awarded":"PhD","file":[{"creator":"mvasilev","checksum":"ef981c1a3b1d9da0edcbedcff4970d37","file_id":"7175","file_size":20454014,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_name":"Thesis_Mina_final_upload_7.docx","date_updated":"2020-07-14T12:47:51Z","date_created":"2019-12-12T09:32:36Z"},{"creator":"mvasilev","file_id":"7176","checksum":"3882c4585e46c9cfb486e4225cad54ab","file_size":11565025,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"Thesis_Mina_final_upload_7.pdf","date_created":"2019-12-12T09:33:10Z","date_updated":"2020-07-14T12:47:51Z"}],"page":"192","type":"dissertation","month":"12","alternative_title":["ISTA Thesis"],"author":[{"full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","first_name":"Mina K"}],"related_material":{"record":[{"status":"public","id":"449","relation":"part_of_dissertation"},{"id":"6377","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"1346","relation":"part_of_dissertation"}]},"publication_status":"published","date_created":"2019-12-11T21:24:39Z","department":[{"_id":"JiFr"}],"_id":"7172","supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:51Z","day":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","OA_place":"publisher","corr_author":"1","date_updated":"2026-04-08T13:54:45Z","citation":{"ieee":"M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019.","mla":"Vasileva, Mina K. <i>Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7172\">10.15479/AT:ISTA:7172</a>.","short":"M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019.","ista":"Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","chicago":"Vasileva, Mina K. “Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7172\">https://doi.org/10.15479/AT:ISTA:7172</a>.","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7172\">10.15479/AT:ISTA:7172</a>","apa":"Vasileva, M. K. (2019). <i>Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7172\">https://doi.org/10.15479/AT:ISTA:7172</a>"},"oa":1,"has_accepted_license":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.15479/AT:ISTA:7172","publication_identifier":{"eissn":["2663-337X"]},"oa_version":"Published Version","ddc":["570"],"year":"2019","date_published":"2019-12-12T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.\r\nThe first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.\r\nThe second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.\r\nThe third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.\r\nIn the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.\r\nIn the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes.","lang":"eng"}]}]