[{"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"citation":{"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.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.","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.","mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:10.1038/s41477-019-0542-5.","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 et al., “PIN-driven auxin transport emerged early in streptophyte evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019.","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. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["31712756"],"isi":["000496526100010"]},"article_processing_charge":"No","author":[{"last_name":"Skokan","full_name":"Skokan, Roman","first_name":"Roman"},{"last_name":"Medvecká","full_name":"Medvecká, Eva","first_name":"Eva"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"last_name":"Müller","full_name":"Müller, Karel","first_name":"Karel"},{"first_name":"Petr","full_name":"Skůpa, Petr","last_name":"Skůpa"},{"full_name":"Karady, Michal","last_name":"Karady","first_name":"Michal"},{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou"},{"last_name":"Janacek","full_name":"Janacek, Dorina P.","first_name":"Dorina P."},{"full_name":"Hammes, Ulrich Z.","last_name":"Hammes","first_name":"Ulrich Z."},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"title":"PIN-driven auxin transport emerged early in streptophyte evolution","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2019","has_accepted_license":"1","isi":1,"publication":"Nature Plants","day":"01","page":"1114-1119","date_created":"2019-11-25T09:08:04Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1038/s41477-019-0542-5","_id":"7106","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-06T11:09:49Z","ddc":["580"],"file_date_updated":"2020-10-14T08:54:49Z","department":[{"_id":"JiFr"}],"abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 5","month":"11","publication_status":"published","publication_identifier":{"issn":["2055-0278"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-10-14T08:54:49Z","file_size":1980851,"creator":"dernst","date_created":"2020-10-14T08:54:49Z","file_name":"2019_NaturePlants_Skokan_accepted.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"94e0426856aad9a9bd0135d5436efbf1","file_id":"8660","success":1}],"ec_funded":1,"issue":"11","volume":5},{"date_updated":"2023-09-06T11:08:52Z","department":[{"_id":"MiSi"}],"_id":"7105","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"language":[{"iso":"eng"}],"volume":21,"issue":"11","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891","open_access":"1"}],"scopus_import":"1","intvolume":" 21","month":"11","citation":{"ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5","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. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0411-5","ieee":"L. Yolland et al., “Persistent and polarized global actin flow is essential for directionality during cell migration,” Nature Cell Biology, 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.","mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5.","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.","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.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000495888300009"],"pmid":["31685997"]},"article_processing_charge":"No","author":[{"first_name":"Lawrence","last_name":"Yolland","full_name":"Yolland, Lawrence"},{"last_name":"Burki","full_name":"Burki, Mubarik","first_name":"Mubarik"},{"full_name":"Marcotti, Stefania","last_name":"Marcotti","first_name":"Stefania"},{"first_name":"Andrei","last_name":"Luchici","full_name":"Luchici, Andrei"},{"last_name":"Kenny","full_name":"Kenny, Fiona N.","first_name":"Fiona N."},{"first_name":"John Robert","full_name":"Davis, John Robert","last_name":"Davis"},{"last_name":"Serna-Morales","full_name":"Serna-Morales, Eduardo","first_name":"Eduardo"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","full_name":"Müller, Jan","last_name":"Müller"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"last_name":"Davidson","full_name":"Davidson, Andrew","first_name":"Andrew"},{"full_name":"Wood, Will","last_name":"Wood","first_name":"Will"},{"first_name":"Linus J.","last_name":"Schumacher","full_name":"Schumacher, Linus J."},{"first_name":"Robert G.","full_name":"Endres, Robert G.","last_name":"Endres"},{"full_name":"Miodownik, Mark","last_name":"Miodownik","first_name":"Mark"},{"first_name":"Brian M.","last_name":"Stramer","full_name":"Stramer, Brian M."}],"title":"Persistent and polarized global actin flow is essential for directionality during cell migration","year":"2019","isi":1,"publication":"Nature Cell Biology","day":"01","page":"1370-1381","date_created":"2019-11-25T08:55:00Z","doi":"10.1038/s41556-019-0411-5","date_published":"2019-11-01T00:00:00Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-5411"]},"publication_status":"published","volume":66,"issue":"3","oa_version":"None","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"}],"month":"05","intvolume":" 66","scopus_import":"1","date_updated":"2023-09-06T11:11:56Z","department":[{"_id":"ToHe"}],"_id":"7109","status":"public","type":"journal_article","article_type":"original","day":"01","publication":"Journal of the ACM","isi":1,"year":"2019","doi":"10.1145/3286976","date_published":"2019-05-01T00:00:00Z","date_created":"2019-11-26T10:22:32Z","publisher":"ACM","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to timed automata,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","short":"T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).","ama":"Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata. Journal of the ACM. 2019;66(3). doi:10.1145/3286976","apa":"Ferrere, T., Maler, O., Ničković, D., & Pnueli, A. (2019). From real-time logic to timed automata. Journal of the ACM. ACM. https://doi.org/10.1145/3286976","mla":"Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” Journal of the ACM, vol. 66, no. 3, 19, ACM, 2019, doi:10.1145/3286976.","ista":"Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed automata. Journal of the ACM. 66(3), 19.","chicago":"Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time Logic to Timed Automata.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3286976."},"title":"From real-time logic to timed automata","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"first_name":"Dejan","last_name":"Ničković","full_name":"Ničković, Dejan"},{"full_name":"Pnueli, Amir","last_name":"Pnueli","first_name":"Amir"}],"article_processing_charge":"No","external_id":{"isi":["000495406300005"]},"article_number":"19","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"184"}]},"volume":66,"issue":"3","publication_identifier":{"issn":["0004-5411"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1711.08436.pdf"}],"month":"06","intvolume":" 66","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"UlWa"}],"date_updated":"2023-09-06T11:10:58Z","type":"journal_article","article_type":"original","status":"public","_id":"7108","date_published":"2019-06-01T00:00:00Z","doi":"10.1145/3314024","date_created":"2019-11-26T10:13:59Z","isi":1,"year":"2019","day":"01","publication":"Journal of the ACM","quality_controlled":"1","publisher":"ACM","oa":1,"author":[{"last_name":"Goaoc","full_name":"Goaoc, Xavier","first_name":"Xavier"},{"id":"B593B804-1035-11EA-B4F1-947645A5BB83","first_name":"Pavel","full_name":"Patak, Pavel","last_name":"Patak"},{"last_name":"Patakova","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"},{"first_name":"Martin","full_name":"Tancer, Martin","last_name":"Tancer"},{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"article_processing_charge":"No","external_id":{"arxiv":["1711.08436"],"isi":["000495406300007"]},"title":"Shellability is NP-complete","citation":{"chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.","ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM, vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024.","ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. Journal of the ACM. 2019;66(3). doi:10.1145/3314024","apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024","short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019).","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"21"},{"_id":"7147","status":"public","type":"conference","conference":{"name":"CMSB: Computational Methods in Systems Biology","start_date":"2019-09-18","location":"Trieste, Italy","end_date":"2019-09-20"},"date_updated":"2023-09-06T11:18:08Z","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"oa_version":"None","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."}],"month":"09","intvolume":" 11773","alternative_title":["LNCS"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030313036","9783030313043"]},"publication_status":"published","volume":11773,"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture","grant_number":"24573"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","chicago":"Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference on Computational Methods in Systems Biology, 11773:155–87. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31304-3_9.","apa":"Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., & Sezgin, A. (2019). Transient memory in gene regulation. In 17th International Conference on Computational Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. https://doi.org/10.1007/978-3-030-31304-3_9","ama":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: 17th International Conference on Computational Methods in Systems Biology. Vol 11773. Springer Nature; 2019:155-187. doi:10.1007/978-3-030-31304-3_9","ieee":"C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in 17th International Conference on Computational Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187.","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.","mla":"Guet, Calin C., et al. “Transient Memory in Gene Regulation.” 17th International Conference on Computational Methods in Systems Biology, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:10.1007/978-3-030-31304-3_9."},"title":"Transient memory in gene regulation","author":[{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","last_name":"Petrov","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","full_name":"Sezgin, Ali","last_name":"Sezgin"}],"article_processing_charge":"No","external_id":{"isi":["000557875100009"]},"publisher":"Springer Nature","quality_controlled":"1","day":"17","publication":"17th International Conference on Computational Methods in Systems Biology","isi":1,"year":"2019","date_published":"2019-09-17T00:00:00Z","doi":"10.1007/978-3-030-31304-3_9","date_created":"2019-12-04T16:07:50Z","page":"155-187"},{"title":"Strong chain rules for min-entropy under few bits spoiled","external_id":{"arxiv":["1702.08476"],"isi":["000489100301043"]},"article_processing_charge":"No","author":[{"full_name":"Skórski, Maciej","last_name":"Skórski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In 2019 IEEE International Symposium on Information Theory. IEEE, 2019. https://doi.org/10.1109/isit.2019.8849240.","ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: 2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240","apa":"Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In 2019 IEEE International Symposium on Information Theory. Paris, France: IEEE. https://doi.org/10.1109/isit.2019.8849240","short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019.","ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in 2019 IEEE International Symposium on Information Theory, Paris, France, 2019.","mla":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” 2019 IEEE International Symposium on Information Theory, 8849240, IEEE, 2019, doi:10.1109/isit.2019.8849240."},"article_number":"8849240","date_created":"2019-11-28T10:19:21Z","doi":"10.1109/isit.2019.8849240","date_published":"2019-07-01T00:00:00Z","publication":"2019 IEEE International Symposium on Information Theory","day":"01","year":"2019","isi":1,"oa":1,"publisher":"IEEE","quality_controlled":"1","department":[{"_id":"KrPi"}],"date_updated":"2023-09-06T11:15:41Z","status":"public","conference":{"location":"Paris, France","end_date":"2019-07-12","start_date":"2019-07-07","name":"ISIT: International Symposium on Information Theory"},"type":"conference","_id":"7136","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781538692912"]},"month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1702.08476","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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|X2018 IEEE Conference on Decision and Control. IEEE, 2019. https://doi.org/10.1109/cdc.2018.8619625.","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.","mla":"Khirirat, Sarit, et al. “Gradient Compression for Communication-Limited Convex Optimization.” 2018 IEEE Conference on Decision and Control, 8619625, IEEE, 2019, doi:10.1109/cdc.2018.8619625.","ama":"Khirirat S, Johansson M, Alistarh D-A. Gradient compression for communication-limited convex optimization. In: 2018 IEEE Conference on Decision and Control. IEEE; 2019. doi:10.1109/cdc.2018.8619625","apa":"Khirirat, S., Johansson, M., & Alistarh, D.-A. (2019). Gradient compression for communication-limited convex optimization. In 2018 IEEE Conference on Decision and Control. Miami Beach, FL, United States: IEEE. https://doi.org/10.1109/cdc.2018.8619625","ieee":"S. Khirirat, M. Johansson, and D.-A. Alistarh, “Gradient compression for communication-limited convex optimization,” in 2018 IEEE Conference on Decision and Control, Miami Beach, FL, United States, 2019.","short":"S. Khirirat, M. Johansson, D.-A. Alistarh, in:, 2018 IEEE Conference on Decision and Control, IEEE, 2019."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Khirirat","full_name":"Khirirat, Sarit","first_name":"Sarit"},{"first_name":"Mikael","full_name":"Johansson, Mikael","last_name":"Johansson"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"article_processing_charge":"No","external_id":{"isi":["000458114800023"]},"title":"Gradient compression for communication-limited convex optimization","department":[{"_id":"DaAl"}]},{"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"title":"Molecular and evolutionary dynamics of animal sex-chromosome turnover","external_id":{"isi":["000500728800009"]},"article_processing_charge":"No","author":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"B. Vicoso, Nature Ecology & Evolution 3 (2019) 1632–1641.","ieee":"B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,” Nature Ecology & Evolution, vol. 3, no. 12. Springer Nature, pp. 1632–1641, 2019.","apa":"Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-019-1050-8","ama":"Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 2019;3(12):1632-1641. doi:10.1038/s41559-019-1050-8","mla":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution, vol. 3, no. 12, Springer Nature, 2019, pp. 1632–41, doi:10.1038/s41559-019-1050-8.","ista":"Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 3(12), 1632–1641.","chicago":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution. Springer Nature, 2019. https://doi.org/10.1038/s41559-019-1050-8."},"quality_controlled":"1","publisher":"Springer Nature","date_created":"2019-12-04T16:05:25Z","date_published":"2019-11-25T00:00:00Z","doi":"10.1038/s41559-019-1050-8","page":"1632-1641","publication":"Nature Ecology & Evolution","day":"25","year":"2019","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"7146","department":[{"_id":"BeVi"}],"date_updated":"2023-09-06T11:18:59Z","intvolume":" 3","month":"11","scopus_import":"1","oa_version":"None","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."}],"ec_funded":1,"volume":3,"issue":"12","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2397-334X"]}},{"author":[{"last_name":"Sinclair","orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"No","external_id":{"isi":["000500749600001"],"pmid":["31745287"]},"title":"Defying gravity: a plant's quest for moisture","citation":{"mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4.","apa":"Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4","ama":"Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. Cell Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4","ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.","short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.","chicago":"Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4.","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"965-966","doi":"10.1038/s41422-019-0254-4","date_published":"2019-12-01T00:00:00Z","date_created":"2019-12-02T12:30:48Z","isi":1,"year":"2019","day":"01","publication":"Cell Research","type":"journal_article","article_type":"original","status":"public","_id":"7143","department":[{"_id":"JiFr"}],"date_updated":"2023-09-06T11:20:58Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41422-019-0254-4"}],"month":"12","intvolume":" 29","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."}],"oa_version":"Published Version","pmid":1,"volume":29,"publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]},"publication_status":"published","language":[{"iso":"eng"}]},{"_id":"7156","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-06T11:22:39Z","ddc":["530"],"file_date_updated":"2020-07-14T12:47:50Z","department":[{"_id":"JoFi"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 5","month":"12","publication_status":"published","publication_identifier":{"issn":["2056-6387"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_NPJ_Rueda.pdf","date_created":"2019-12-09T08:25:06Z","creator":"dernst","file_size":1580132,"date_updated":"2020-07-14T12:47:50Z","checksum":"13e0ea1d4f9b5f5710780d9473364f58","file_id":"7157","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"volume":5,"article_number":"108","project":[{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"},{"name":"Hybrid Optomechanical Technologies","grant_number":"732894","call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","name":"Integrating superconducting quantum circuits","grant_number":"F07105"}],"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.” Npj Quantum Information. Springer Nature, 2019. https://doi.org/10.1038/s41534-019-0220-5.","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.","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information, vol. 5, 108, Springer Nature, 2019, doi:10.1038/s41534-019-0220-5.","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,” npj Quantum Information, vol. 5. Springer Nature, 2019.","short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019).","ama":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 2019;5. doi:10.1038/s41534-019-0220-5","apa":"Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., & Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-019-0220-5"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000502996200003"],"arxiv":["1909.01470"]},"author":[{"last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R"},{"first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","orcid":"0000-0001-9868-2166","full_name":"Hease, William J"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh"},{"last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"title":"Electro-optic entanglement source for microwave to telecom quantum state transfer","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2019","isi":1,"has_accepted_license":"1","publication":"npj Quantum Information","day":"01","date_created":"2019-12-09T08:18:56Z","doi":"10.1038/s41534-019-0220-5","date_published":"2019-12-01T00:00:00Z"},{"article_processing_charge":"No","external_id":{"isi":["000507575700004"],"pmid":["31784457"]},"author":[{"first_name":"Pilar","last_name":"Guerrero","full_name":"Guerrero, Pilar"},{"last_name":"Perez-Carrasco","full_name":"Perez-Carrasco, Ruben","first_name":"Ruben"},{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"first_name":"David","last_name":"Page","full_name":"Page, David"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"full_name":"Page, Karen M.","last_name":"Page","first_name":"Karen M."}],"title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","citation":{"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.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297.","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.","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:10.1242/dev.176297.","apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. The Company of Biologists. https://doi.org/10.1242/dev.176297","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 2019;146(23). doi:10.1242/dev.176297","ieee":"P. Guerrero et al., “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” Development, vol. 146, no. 23. The Company of Biologists, 2019.","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"}],"article_number":"dev176297","date_created":"2019-12-10T14:39:50Z","date_published":"2019-12-04T00:00:00Z","doi":"10.1242/dev.176297","year":"2019","has_accepted_license":"1","isi":1,"publication":"Development","day":"04","oa":1,"quality_controlled":"1","publisher":"The Company of Biologists","department":[{"_id":"AnKi"}],"file_date_updated":"2020-07-14T12:47:50Z","date_updated":"2023-09-06T11:26:36Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"7165","ec_funded":1,"issue":"23","volume":146,"publication_status":"published","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7177","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_Development_Guerrero.pdf","date_created":"2019-12-13T07:34:06Z","file_size":7797881,"date_updated":"2020-07-14T12:47:50Z","creator":"dernst"}],"scopus_import":"1","intvolume":" 146","month":"12","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version"},{"quality_controlled":"1","publisher":"Springer Nature","page":"292-309","date_published":"2019-10-01T00:00:00Z","doi":"10.1007/978-3-030-32079-9_17","date_created":"2019-12-09T08:47:55Z","isi":1,"year":"2019","day":"01","publication":"19th International Conference on Runtime Verification","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Dejan","last_name":"Ničković","full_name":"Ničković, Dejan"},{"full_name":"Qin, Xin","last_name":"Qin","first_name":"Xin"},{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143"},{"first_name":"Cristinel","full_name":"Mateis, Cristinel","last_name":"Mateis"},{"first_name":"Jyotirmoy","last_name":"Deshmukh","full_name":"Deshmukh, Jyotirmoy"}],"external_id":{"isi":["000570006300017"]},"article_processing_charge":"No","title":"Shape expressions for specifying and extracting signal features","citation":{"mla":"Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal Features.” 19th International Conference on Runtime Verification, vol. 11757, Springer Nature, 2019, pp. 292–309, doi:10.1007/978-3-030-32079-9_17.","short":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309.","ieee":"D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions for specifying and extracting signal features,” in 19th International Conference on Runtime Verification, Porto, Portugal, 2019, vol. 11757, pp. 292–309.","ama":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for specifying and extracting signal features. In: 19th International Conference on Runtime Verification. Vol 11757. Springer Nature; 2019:292-309. doi:10.1007/978-3-030-32079-9_17","apa":"Ničković, D., Qin, X., Ferrere, T., Mateis, C., & Deshmukh, J. (2019). Shape expressions for specifying and extracting signal features. In 19th International Conference on Runtime Verification (Vol. 11757, pp. 292–309). Porto, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-32079-9_17","chicago":"Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In 19th International Conference on Runtime Verification, 11757:292–309. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-32079-9_17.","ista":"Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions for specifying and extracting signal features. 19th International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","alternative_title":["LNCS"],"month":"10","intvolume":" 11757","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"}],"oa_version":"None","volume":11757,"publication_identifier":{"issn":["0302-9743"],"isbn":["9783030320782","9783030320799"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"end_date":"2019-10-11","location":"Porto, Portugal","start_date":"2019-10-08","name":"RV: Runtime Verification"},"status":"public","_id":"7159","department":[{"_id":"ToHe"}],"date_updated":"2023-09-06T11:24:10Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: International Symposium on Automated Technology for Verification and Analysis. Vol 11781. Springer Nature; 2019:462-478. doi:10.1007/978-3-030-31784-3_27","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In International Symposium on Automated Technology for Verification and Analysis (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in International Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” International Symposium on Automated Technology for Verification and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27.","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478.","chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In International Symposium on Automated Technology for Verification and Analysis, 11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27."},"title":"Deciding fast termination for probabilistic VASS with nondeterminism","article_processing_charge":"No","external_id":{"arxiv":["1907.11010"],"isi":["000723515700027"]},"author":[{"first_name":"Tomás","full_name":"Brázdil, Tomás","last_name":"Brázdil"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Antonín","full_name":"Kucera, Antonín","last_name":"Kucera"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný","full_name":"Novotný, Petr"},{"last_name":"Velan","full_name":"Velan, Dominik","first_name":"Dominik"}],"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"publication":"International Symposium on Automated Technology for Verification and Analysis","day":"21","year":"2019","isi":1,"date_created":"2019-12-15T23:00:44Z","doi":"10.1007/978-3-030-31784-3_27","date_published":"2019-10-21T00:00:00Z","page":"462-478","oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_updated":"2023-09-06T12:40:58Z","department":[{"_id":"KrCh"}],"_id":"7183","status":"public","conference":{"name":"ATVA: Automated TEchnology for Verification and Analysis","start_date":"2019-10-28","end_date":"2019-10-31","location":"Taipei, Taiwan"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783030317836"],"eissn":["16113349"],"issn":["03029743"]},"volume":11781,"oa_version":"Preprint","abstract":[{"text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2).","lang":"eng"}],"intvolume":" 11781","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1907.11010","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1"},{"file":[{"date_updated":"2020-07-14T12:47:52Z","file_size":1532505,"creator":"dernst","date_created":"2019-12-16T07:58:43Z","file_name":"2019_FrontiersPlant_Alcantara.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7185","checksum":"995aa838aec2064d93550de82b40bbd1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664462X"]},"publication_status":"published","issue":"11","volume":10,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.","lang":"eng"}],"month":"11","intvolume":" 10","scopus_import":"1","ddc":["580"],"date_updated":"2023-09-06T14:33:46Z","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"JiFr"}],"_id":"7182","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"14","publication":"Frontiers in Plant Science","has_accepted_license":"1","isi":1,"year":"2019","doi":"10.3389/fpls.2019.01437","date_published":"2019-11-14T00:00:00Z","date_created":"2019-12-15T23:00:43Z","publisher":"Frontiers","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science. Frontiers, 2019. https://doi.org/10.3389/fpls.2019.01437.","ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers, 2019, doi:10.3389/fpls.2019.01437.","ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437","apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437","ieee":"A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019.","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019)."},"title":"Systematic Y2H screening reveals extensive effector-complex formation","author":[{"last_name":"Alcântara","full_name":"Alcântara, André","first_name":"André"},{"first_name":"Jason","full_name":"Bosch, Jason","last_name":"Bosch"},{"first_name":"Fahimeh","full_name":"Nazari, Fahimeh","last_name":"Nazari"},{"last_name":"Hoffmann","full_name":"Hoffmann, Gesa","first_name":"Gesa"},{"last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"first_name":"Martin A.","last_name":"Darino","full_name":"Darino, Martin A."},{"first_name":"Toluwase","last_name":"Olukayode","full_name":"Olukayode, Toluwase"},{"full_name":"Reumann, Daniel","last_name":"Reumann","first_name":"Daniel"},{"first_name":"Laura","last_name":"Baggaley","full_name":"Baggaley, Laura"},{"first_name":"Armin","last_name":"Djamei","full_name":"Djamei, Armin"}],"article_processing_charge":"No","external_id":{"isi":["000499821700001"],"pmid":["31803201"]},"article_number":"1437"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"7180","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"DaSi"}],"date_updated":"2023-09-06T14:08:21Z","ddc":["570"],"scopus_import":"1","intvolume":" 10","month":"12","abstract":[{"text":"Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":10,"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-12-16T07:37:50Z","file_name":"2019_NatureComm_Retzer.pdf","date_updated":"2020-07-14T12:47:52Z","file_size":5156533,"creator":"dernst","file_id":"7184","checksum":"77e8720a8e0f3091b98159f85be40893","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"project":[{"name":"Modeling epithelial tissue mechanics during cell invasion","grant_number":"M02379","call_identifier":"FWF","_id":"264CBBAC-B435-11E9-9278-68D0E5697425"}],"article_number":"5516","external_id":{"pmid":["31797871"],"isi":["000500508100001"]},"article_processing_charge":"No","author":[{"last_name":"Retzer","full_name":"Retzer, Katarzyna","first_name":"Katarzyna"},{"id":"3425EC26-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Akhmanova","orcid":"0000-0003-1522-3162","full_name":"Akhmanova, Maria"},{"full_name":"Konstantinova, Nataliia","last_name":"Konstantinova","first_name":"Nataliia"},{"first_name":"Kateřina","last_name":"Malínská","full_name":"Malínská, Kateřina"},{"first_name":"Johannes","last_name":"Leitner","full_name":"Leitner, Johannes"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"}],"title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","citation":{"ama":"Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 2019;10. doi:10.1038/s41467-019-13543-1","apa":"Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., & Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13543-1","ieee":"K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications, vol. 10. Springer Nature, 2019.","short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019).","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications, vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1.","ista":"Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516.","chicago":"Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2019-12-15T23:00:43Z","date_published":"2019-12-01T00:00:00Z","doi":"10.1038/s41467-019-13543-1","year":"2019","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"01"},{"project":[{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"title":"Large multiple sequence alignments with a root-to-leaf regressive method","author":[{"first_name":"Edgar","last_name":"Garriga","full_name":"Garriga, Edgar"},{"last_name":"Di Tommaso","full_name":"Di Tommaso, Paolo","first_name":"Paolo"},{"first_name":"Cedrik","full_name":"Magis, Cedrik","last_name":"Magis"},{"first_name":"Ionas","last_name":"Erb","full_name":"Erb, Ionas"},{"first_name":"Leila","last_name":"Mansouri","full_name":"Mansouri, Leila"},{"first_name":"Athanasios","full_name":"Baltzis, Athanasios","last_name":"Baltzis"},{"first_name":"Hafid","full_name":"Laayouni, Hafid","last_name":"Laayouni"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"last_name":"Floden","full_name":"Floden, Evan","first_name":"Evan"},{"first_name":"Cedric","last_name":"Notredame","full_name":"Notredame, Cedric"}],"article_processing_charge":"No","external_id":{"pmid":["31792410"],"isi":["000500748900021"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","ieee":"E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6","ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6","chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.","ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470."},"publisher":"Springer Nature","quality_controlled":"1","oa":1,"doi":"10.1038/s41587-019-0333-6","date_published":"2019-12-01T00:00:00Z","date_created":"2019-12-15T23:00:43Z","page":"1466-1470","day":"01","publication":"Nature Biotechnology","isi":1,"year":"2019","status":"public","type":"journal_article","article_type":"original","_id":"7181","department":[{"_id":"FyKo"}],"date_updated":"2023-09-06T14:32:52Z","month":"12","intvolume":" 37","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6."}],"issue":"12","volume":37,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13059"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15461696"],"issn":["10870156"]},"publication_status":"published"},{"scopus_import":"1","month":"11","intvolume":" 8","abstract":[{"text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":8,"ec_funded":1,"publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","file":[{"creator":"dernst","file_size":2960543,"date_updated":"2020-07-14T12:47:53Z","file_name":"2019_eLife_Llorca.pdf","date_created":"2020-02-18T15:19:26Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"b460ecc33e1a68265e7adea775021f3a","file_id":"7503"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7202","file_date_updated":"2020-07-14T12:47:53Z","department":[{"_id":"SiHi"}],"date_updated":"2023-09-06T14:38:39Z","ddc":["570"],"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"doi":"10.7554/eLife.51381","date_published":"2019-11-18T00:00:00Z","date_created":"2019-12-22T23:00:42Z","isi":1,"has_accepted_license":"1","year":"2019","day":"18","publication":"eLife","project":[{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e51381","author":[{"first_name":"Alfredo","full_name":"Llorca, Alfredo","last_name":"Llorca"},{"full_name":"Ciceri, Gabriele","last_name":"Ciceri","first_name":"Gabriele"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","last_name":"Beattie","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753"},{"first_name":"Fong Kuan","full_name":"Wong, Fong Kuan","last_name":"Wong"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"first_name":"Eleni","last_name":"Serafeimidou-Pouliou","full_name":"Serafeimidou-Pouliou, Eleni"},{"last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian","first_name":"Marian"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen","last_name":"Streicher"},{"last_name":"Arnold","full_name":"Arnold, Sebastian J.","first_name":"Sebastian J."},{"last_name":"Meyer","full_name":"Meyer, Martin","first_name":"Martin"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Maravall","full_name":"Maravall, Miguel","first_name":"Miguel"},{"first_name":"Oscar","full_name":"Marín, Oscar","last_name":"Marín"}],"article_processing_charge":"No","external_id":{"pmid":["31736464"],"isi":["000508156800001"]},"title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381.","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife Sciences Publications, 2019, doi:10.7554/eLife.51381.","ieee":"A. Llorca et al., “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences Publications, 2019.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019).","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381","ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8. doi:10.7554/eLife.51381"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"doi":"10.1096/fj.201901543R","date_published":"2019-12-01T00:00:00Z","date_created":"2019-12-15T23:00:42Z","page":"13734-13746","day":"01","publication":"FASEB Journal","isi":1,"has_accepted_license":"1","year":"2019","quality_controlled":"1","publisher":"FASEB","oa":1,"title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses","author":[{"first_name":"Lisa","last_name":"Klotz","full_name":"Klotz, Lisa"},{"full_name":"Wendler, Olaf","last_name":"Wendler","first_name":"Olaf"},{"first_name":"Renato","last_name":"Frischknecht","full_name":"Frischknecht, Renato"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"full_name":"Schulze, Holger","last_name":"Schulze","first_name":"Holger"},{"full_name":"Enz, Ralf","last_name":"Enz","first_name":"Ralf"}],"external_id":{"isi":["000507466100054"],"pmid":["31585509"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R.","ieee":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” FASEB Journal, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.","short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","apa":"Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., & Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. FASEB. https://doi.org/10.1096/fj.201901543R","ama":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 2019;33(12):13734-13746. doi:10.1096/fj.201901543R","chicago":"Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R.","ista":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746."},"volume":33,"issue":"12","file":[{"creator":"shigemot","file_size":4766789,"date_updated":"2020-12-06T17:30:09Z","file_name":"Klotz et al 2019 EMBO Reports.pdf","date_created":"2020-12-06T17:30:09Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"79e3b72481dc32489911121cf3b7d8d0","file_id":"8922"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15306860"]},"publication_status":"published","month":"12","intvolume":" 33","scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity."}],"file_date_updated":"2020-12-06T17:30:09Z","department":[{"_id":"RySh"}],"ddc":["571","599"],"date_updated":"2023-09-06T14:34:36Z","status":"public","article_type":"original","type":"journal_article","_id":"7179"},{"year":"2019","isi":1,"publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","day":"17","date_created":"2019-12-22T23:00:42Z","doi":"10.1145/3295500.3356222","date_published":"2019-11-17T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM","citation":{"mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” International Conference for High Performance Computing, Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222","ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019. doi:10.1145/3295500.3356222","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in International Conference for High Performance Computing, Networking, Storage and Analysis, SC, Denver, CO, Unites States, 2019.","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019.","chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In International Conference for High Performance Computing, Networking, Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.","ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1802.08021"],"isi":["000545976800011"]},"article_processing_charge":"No","author":[{"last_name":"Renggli","full_name":"Renggli, Cedric","first_name":"Cedric"},{"id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A","first_name":"Saleh","full_name":"Ashkboos, Saleh","last_name":"Ashkboos"},{"first_name":"Mehdi","full_name":"Aghagolzadeh, Mehdi","last_name":"Aghagolzadeh"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hoefler","full_name":"Hoefler, Torsten","first_name":"Torsten"}],"title":"SparCML: High-performance sparse communication for machine learning","article_number":"a11","project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","publication_identifier":{"eissn":["21674337"],"isbn":["9781450362290"],"issn":["21674329"]},"language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.08021"}],"scopus_import":"1","month":"11","date_updated":"2023-09-06T14:37:55Z","department":[{"_id":"DaAl"}],"_id":"7201","conference":{"name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis","start_date":"2019-11-17","location":"Denver, CO, Unites States","end_date":"2019-11-19"},"type":"conference","status":"public"},{"type":"research_data_reference","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","_id":"13067","author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Zagrodzka, Zuzanna","last_name":"Zagrodzka","first_name":"Zuzanna"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","citation":{"ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK."},"date_updated":"2023-09-06T14:48:57Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"month":"12","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"oa_version":"Published Version","doi":"10.5061/DRYAD.TB2RBNZWK","related_material":{"record":[{"status":"public","id":"7205","relation":"used_in_publication"}]},"date_published":"2019-12-02T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-23T16:36:27Z","year":"2019","day":"02"},{"article_number":"641","external_id":{"isi":["000511618800007"]},"article_processing_charge":"No","author":[{"last_name":"Aganezov","full_name":"Aganezov, Sergey","first_name":"Sergey"},{"last_name":"Zban","full_name":"Zban, Ilya","first_name":"Ilya"},{"first_name":"Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","full_name":"Aksenov, Vitalii","last_name":"Aksenov"},{"full_name":"Alexeev, Nikita","last_name":"Alexeev","first_name":"Nikita"},{"full_name":"Schatz, Michael C.","last_name":"Schatz","first_name":"Michael C."}],"title":"Recovering rearranged cancer chromosomes from karyotype graphs","citation":{"ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4.","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"BMC","quality_controlled":"1","date_created":"2019-12-29T23:00:46Z","doi":"10.1186/s12859-019-3208-4","date_published":"2019-12-17T00:00:00Z","year":"2019","isi":1,"has_accepted_license":"1","publication":"BMC Bioinformatics","day":"17","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"7214","file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"DaAl"}],"date_updated":"2023-09-06T14:51:06Z","ddc":["570"],"scopus_import":"1","intvolume":" 20","month":"12","abstract":[{"lang":"eng","text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer."}],"oa_version":"Published Version","volume":20,"publication_status":"published","publication_identifier":{"eissn":["14712105"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7a30357efdcf8f66587ed495c0927724","file_id":"7221","date_updated":"2020-07-14T12:47:54Z","file_size":1917374,"creator":"dernst","date_created":"2020-01-02T16:10:58Z","file_name":"2019_BMCBioinfo_Aganezov.pdf"}]},{"day":"13","publication":"25th Anniversary of Euro-Par","isi":1,"year":"2019","date_published":"2019-08-13T00:00:00Z","doi":"10.1007/978-3-030-29400-7_23","date_created":"2020-01-05T23:00:46Z","page":"317-333","publisher":"Springer Nature","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.","mla":"Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels for programming via communicating sequential processes. In 25th Anniversary of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-29400-7_23","ama":"Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming via communicating sequential processes. In: 25th Anniversary of Euro-Par. Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 317–333.","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming via communicating sequential processes,” in 25th Anniversary of Euro-Par, Göttingen, Germany, 2019, vol. 11725, pp. 317–333."},"title":"Scalable FIFO channels for programming via communicating sequential processes","author":[{"full_name":"Koval, Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Elizarov","full_name":"Elizarov, Roman","first_name":"Roman"}],"external_id":{"isi":["000851061400023"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-0302-9399-4"],"issn":["0302-9743"]},"publication_status":"published","volume":11725,"oa_version":"None","abstract":[{"text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) and actor models, which share data via explicit communication. These models have been known for almost half a century, and have recently had started to gain significant traction among modern programming languages. The common abstraction for communication between several processes is the channel. Although channels are similar to producer-consumer data structures, they have different semantics and support additional operations, such as the select expression. Despite their growing popularity, most known implementations of channels use lock-based data structures and can be rather inefficient.\r\n\r\nIn this paper, we present the first efficient lock-free algorithm for implementing a communication channel for CSP programming. We provide implementations and experimental results in the Kotlin and Go programming languages. Our new algorithm outperforms existing implementations on many workloads, while providing non-blocking progress guarantee. Our design can serve as an example of how to construct general communication data structures for CSP and actor models. ","lang":"eng"}],"month":"08","intvolume":" 11725","alternative_title":["LNCS"],"scopus_import":"1","date_updated":"2023-09-06T14:53:59Z","department":[{"_id":"DaAl"}],"_id":"7228","status":"public","type":"conference","conference":{"name":"Euro-Par: European Conference on Parallel Processing","start_date":"2019-08-26","end_date":"2019-08-30","location":"Göttingen, Germany"}},{"abstract":[{"text":"We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system to label a stream of noisy observations of transit vehicle trajectories with the transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently to large transit networks, our system first retrieves a small set of candidate routes from a geometrically indexed data structure, then applies a fine-grained scoring step to choose the best match. Given that real-time data remains unavailable for the majority of the world’s transit agencies, these inferences can help feed a real-time map of a transit system’s trips, infer transit trip delays in real time, or measure and correct noisy transit tracking data. This system can run on vehicle observations from a variety of sources that don’t attach route information to vehicle observations, such as public imagery streams or user-contributed transit vehicle sightings.We abstract away the specifics of the sensing system and demonstrate the effectiveness of our system on a \"semisynthetic\" dataset of all New York City buses, where we simulate sensed trajectories by starting with fully labeled vehicle trajectories reported via the GTFS-Realtime protocol, removing the transit route IDs, and perturbing locations with synthetic noise. Using just the geometric shapes of the trajectories, we demonstrate that our system converges on the correct route ID within a few minutes, even after a vehicle switches from serving one trip to the next.","lang":"eng"}],"oa_version":"None","publisher":"IEEE","scopus_import":"1","quality_controlled":"1","month":"11","year":"2019","publication_status":"published","publication_identifier":{"isbn":["9781538670248"]},"isi":1,"publication":"2019 IEEE Intelligent Transportation Systems Conference","language":[{"iso":"eng"}],"day":"28","date_created":"2019-12-29T23:00:47Z","date_published":"2019-11-28T00:00:00Z","doi":"10.1109/ITSC.2019.8917514","_id":"7216","article_number":"8917514","conference":{"name":"ITSC: Intelligent Transportation Systems Conference","start_date":"2019-10-27","location":"Auckland, New Zealand","end_date":"2019-10-30"},"type":"conference","status":"public","citation":{"ista":"Osang GF, Cook J, Fabrikant A, Gruteser M. 2019. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. 2019 IEEE Intelligent Transportation Systems Conference. ITSC: Intelligent Transportation Systems Conference, 8917514.","chicago":"Osang, Georg F, James Cook, Alex Fabrikant, and Marco Gruteser. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” In 2019 IEEE Intelligent Transportation Systems Conference. IEEE, 2019. https://doi.org/10.1109/ITSC.2019.8917514.","ieee":"G. F. Osang, J. Cook, A. Fabrikant, and M. Gruteser, “LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale,” in 2019 IEEE Intelligent Transportation Systems Conference, Auckland, New Zealand, 2019.","short":"G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 2019.","apa":"Osang, G. F., Cook, J., Fabrikant, A., & Gruteser, M. (2019). LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In 2019 IEEE Intelligent Transportation Systems Conference. Auckland, New Zealand: IEEE. https://doi.org/10.1109/ITSC.2019.8917514","ama":"Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In: 2019 IEEE Intelligent Transportation Systems Conference. IEEE; 2019. doi:10.1109/ITSC.2019.8917514","mla":"Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” 2019 IEEE Intelligent Transportation Systems Conference, 8917514, IEEE, 2019, doi:10.1109/ITSC.2019.8917514."},"date_updated":"2023-09-06T14:50:28Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000521238102050"]},"article_processing_charge":"No","author":[{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"},{"first_name":"James","last_name":"Cook","full_name":"Cook, James"},{"first_name":"Alex","last_name":"Fabrikant","full_name":"Fabrikant, Alex"},{"first_name":"Marco","full_name":"Gruteser, Marco","last_name":"Gruteser"}],"title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","department":[{"_id":"HeEd"}]},{"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"]},"language":[{"iso":"eng"}],"volume":11750,"abstract":[{"lang":"eng","text":"Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 11750","month":"08","date_updated":"2023-09-06T14:55:15Z","department":[{"_id":"ToHe"}],"_id":"7231","conference":{"location":"Amsterdam, The Netherlands","end_date":"2019-08-29","start_date":"2019-08-27","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"type":"conference","status":"public","year":"2019","isi":1,"publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","day":"13","page":"123-141","date_created":"2020-01-05T23:00:47Z","doi":"10.1007/978-3-030-29662-9_8","date_published":"2019-08-13T00:00:00Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","citation":{"ista":"Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.","chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.","apa":"Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8","ama":"Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8","ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141.","short":"H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.","mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1907.11514"],"isi":["000611677700008"]},"article_processing_charge":"No","author":[{"last_name":"Kong","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"last_name":"Jiang","full_name":"Jiang, Yu","first_name":"Yu"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}]},{"title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","author":[{"first_name":"Niko Paresh","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","last_name":"Amin-Wetzel","full_name":"Amin-Wetzel, Niko Paresh"},{"first_name":"Lisa","last_name":"Neidhardt","full_name":"Neidhardt, Lisa"},{"last_name":"Yan","full_name":"Yan, Yahui","first_name":"Yahui"},{"last_name":"Mayer","full_name":"Mayer, Matthias P.","first_name":"Matthias P."},{"full_name":"Ron, David","last_name":"Ron","first_name":"David"}],"external_id":{"isi":["000512303700001"],"pmid":["31873072"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793","apa":"Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019). Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.50793","ieee":"N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications, 2019.","short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).","mla":"Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife, vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793.","ista":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 8, e50793.","chicago":"Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer, and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.50793."},"article_number":"e50793","doi":"10.7554/eLife.50793","date_published":"2019-12-24T00:00:00Z","date_created":"2020-01-19T23:00:39Z","day":"24","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2019","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"acknowledgement":"We thank the CIMR flow cytometry core facility team (Reiner Schulte, Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington lab for access to the Octet machine, Steffen Preissler for advice on data interpretation, Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.","file_date_updated":"2020-11-19T11:37:41Z","department":[{"_id":"MaDe"}],"ddc":["570"],"date_updated":"2023-09-06T14:58:02Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7340","volume":8,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","file_id":"8777","creator":"dernst","file_size":4817384,"date_updated":"2020-11-19T11:37:41Z","file_name":"2019_eLife_AminWetzel.pdf","date_created":"2020-11-19T11:37:41Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","month":"12","intvolume":" 8","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling.","lang":"eng"}]},{"article_number":"054108","citation":{"mla":"Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.","apa":"Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5064867","ama":"Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867","short":"T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).","ieee":"T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.","chicago":"Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.","ista":"Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000458109300009"],"arxiv":["1708.09364"]},"article_processing_charge":"No","author":[{"full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R"},{"first_name":"Joris","full_name":"Paijmans, Joris","last_name":"Paijmans"},{"first_name":"Laurens","full_name":"Bossen, Laurens","last_name":"Bossen"},{"last_name":"Miedema","full_name":"Miedema, Thomas","first_name":"Thomas"},{"full_name":"Wehrens, Martijn","last_name":"Wehrens","first_name":"Martijn"},{"full_name":"Becker, Nils B.","last_name":"Becker","first_name":"Nils B."},{"first_name":"Kazunari","full_name":"Kaizu, Kazunari","last_name":"Kaizu"},{"first_name":"Koichi","last_name":"Takahashi","full_name":"Takahashi, Koichi"},{"first_name":"Marileen","full_name":"Dogterom, Marileen","last_name":"Dogterom"},{"full_name":"ten Wolde, Pieter Rein","last_name":"ten Wolde","first_name":"Pieter Rein"}],"title":"eGFRD in all dimensions","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","year":"2019","isi":1,"publication":"The Journal of Chemical Physics","day":"07","date_created":"2020-01-30T10:34:36Z","doi":"10.1063/1.5064867","date_published":"2019-02-07T00:00:00Z","_id":"7422","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-06T14:59:28Z","department":[{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1708.09364","open_access":"1"}],"intvolume":" 150","month":"02","publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"language":[{"iso":"eng"}],"volume":150,"issue":"5"},{"isi":1,"year":"2019","day":"28","publication":"27th International Symposium on Graph Drawing and Network Visualization","page":"230-243","date_published":"2019-11-28T00:00:00Z","doi":"10.1007/978-3-030-35802-0_18","date_created":"2020-01-05T23:00:47Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"chicago":"Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization, 11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18.","ista":"Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 11904, 230–243.","mla":"Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18.","short":"A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.","ieee":"A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in 27th International Symposium on Graph Drawing and Network Visualization, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.","apa":"Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple drawings. In 27th International Symposium on Graph Drawing and Network Visualization (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18","ama":"Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th International Symposium on Graph Drawing and Network Visualization. Vol 11904. Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara","first_name":"Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Derka","full_name":"Derka, Martin","first_name":"Martin"},{"full_name":"Parada, Irene","last_name":"Parada","first_name":"Irene"}],"external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"article_processing_charge":"No","title":"Extending simple drawings","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-0303-5801-3"],"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":11904,"ec_funded":1,"abstract":[{"text":"Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G.","lang":"eng"}],"oa_version":"Preprint","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1908.08129","open_access":"1"}],"month":"11","intvolume":" 11904","date_updated":"2023-09-06T14:56:00Z","department":[{"_id":"UlWa"}],"_id":"7230","type":"conference","conference":{"location":"Prague, Czech Republic","end_date":"2019-09-20","start_date":"2019-09-17","name":"GD: Graph Drawing and Network Visualization"},"status":"public"},{"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"author":[{"last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oded","full_name":"Maler, Oded","last_name":"Maler"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000611677700004"]},"title":"Mixed-time signal temporal logic","citation":{"ista":"Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.","chicago":"Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal Logic.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.","apa":"Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal logic. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_4","ama":"Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4","short":"T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75.","ieee":"T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.","mla":"Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Springer Nature","page":"59-75","date_published":"2019-08-13T00:00:00Z","doi":"10.1007/978-3-030-29662-9_4","date_created":"2020-01-05T23:00:48Z","isi":1,"year":"2019","day":"13","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","type":"conference","conference":{"location":"Amsterdam, The Netherlands","end_date":"2019-08-29","start_date":"2019-08-27","name":"FORMATS: Formal Modeling and Anaysis of Timed Systems"},"status":"public","_id":"7232","department":[{"_id":"ToHe"}],"date_updated":"2023-09-06T14:57:17Z","scopus_import":"1","alternative_title":["LNCS"],"month":"08","intvolume":" 11750","abstract":[{"lang":"eng","text":"We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism which extends STL by capturing the discrete/ continuous time duality found in many cyber-physical systems (CPS), as well as mixed-signal electronic designs. In STL−MX, properties of components with continuous dynamics are expressed in STL, while specifications of components with discrete dynamics are written in LTL. To combine the two layers, we evaluate formulas on two traces, discrete- and continuous-time, and introduce two interface operators that map signals, properties and their satisfaction signals across the two time domains. We show that STL-mx has the expressive power of STL supplemented with an implicit T-periodic clock signal. We develop and implement an algorithm for monitoring STL-mx formulas and illustrate the approach using a mixed-signal example. "}],"oa_version":"None","volume":11750,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"]},"publication_status":"published","language":[{"iso":"eng"}]},{"article_number":"jcs233387","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science. The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387.","ista":"Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 132(11), jcs233387.","mla":"Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:10.1242/jcs.233387.","short":"P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä, A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).","ieee":"P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists, 2019.","ama":"Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387","apa":"Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A., … Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387"},"title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","article_processing_charge":"No","external_id":{"pmid":["31076515"],"isi":["000473327900017"]},"author":[{"first_name":"Pranshu","last_name":"Sahgal","full_name":"Sahgal, Pranshu"},{"first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H"},{"first_name":"Jaroslav","full_name":"Icha, Jaroslav","last_name":"Icha"},{"first_name":"Ilkka","full_name":"Paatero, Ilkka","last_name":"Paatero"},{"first_name":"Hellyeh","full_name":"Hamidi, Hellyeh","last_name":"Hamidi"},{"first_name":"Antti","last_name":"Arjonen","full_name":"Arjonen, Antti"},{"last_name":"Pietilä","full_name":"Pietilä, Mika","first_name":"Mika"},{"last_name":"Rokka","full_name":"Rokka, Anne","first_name":"Anne"},{"first_name":"Johanna","full_name":"Ivaska, Johanna","last_name":"Ivaska"}],"oa":1,"quality_controlled":"1","publisher":"The Company of Biologists","publication":"Journal of Cell Science","day":"07","year":"2019","isi":1,"date_created":"2020-01-30T10:31:42Z","doi":"10.1242/jcs.233387","date_published":"2019-06-07T00:00:00Z","_id":"7420","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-06T15:01:00Z","department":[{"_id":"MiSi"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic.","lang":"eng"}],"intvolume":" 132","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/jcs.233387"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"issue":"11","volume":132},{"department":[{"_id":"LaEr"}],"date_updated":"2023-09-06T14:58:39Z","type":"journal_article","article_type":"original","status":"public","_id":"7423","volume":55,"issue":"1","publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1704.05224","open_access":"1"}],"month":"02","intvolume":" 55","abstract":[{"lang":"eng","text":"We compare finite rank perturbations of the following three ensembles of complex rectangular random matrices: First, a generalised Wishart ensemble with one random and two fixed correlation matrices introduced by Borodin and Péché, second, the product of two independent random matrices where one has correlated entries, and third, the case when the two random matrices become also coupled through a fixed matrix. The singular value statistics of all three ensembles is shown to be determinantal and we derive double contour integral representations for their respective kernels. Three different kernels are found in the limit of infinite matrix dimension at the origin of the spectrum. They depend on finite rank perturbations of the correlation and coupling matrices and are shown to be integrable. The first kernel (I) is found for two independent matrices from the second, and two weakly coupled matrices from the third ensemble. It generalises the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel (III) is obtained for the generalised Wishart ensemble and for two strongly coupled matrices. It further generalises the perturbed Bessel kernel of Desrosiers and Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices, provides an interpolation between the kernels (I) and (III), generalising previous findings of part of the authors."}],"oa_version":"Preprint","author":[{"first_name":"Gernot","full_name":"Akemann, Gernot","last_name":"Akemann"},{"full_name":"Checinski, Tomasz","last_name":"Checinski","first_name":"Tomasz"},{"first_name":"Dangzheng","id":"2F947E34-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Dangzheng","last_name":"Liu"},{"last_name":"Strahov","full_name":"Strahov, Eugene","first_name":"Eugene"}],"article_processing_charge":"No","external_id":{"isi":["000456070200013"],"arxiv":["1704.05224"]},"title":"Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles","citation":{"apa":"Akemann, G., Checinski, T., Liu, D., & Strahov, E. (2019). Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics. https://doi.org/10.1214/18-aihp888","ama":"Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 2019;55(1):441-479. doi:10.1214/18-aihp888","ieee":"G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles,” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.","short":"G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri Poincaré, Probabilités et Statistiques 55 (2019) 441–479.","mla":"Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1, Institute of Mathematical Statistics, 2019, pp. 441–79, doi:10.1214/18-aihp888.","ista":"Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479.","chicago":"Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-aihp888."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"441-479","date_published":"2019-02-01T00:00:00Z","doi":"10.1214/18-aihp888","date_created":"2020-01-30T10:36:50Z","isi":1,"year":"2019","day":"01","publication":"Annales de l'Institut Henri Poincaré, Probabilités et Statistiques","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 28(8), 1877–1889.","chicago":"Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14990.","ama":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 2019;28(8):1877-1889. doi:10.1111/mec.14990","apa":"Toups, M. A., Rodrigues, N., Perrin, N., & Kirkpatrick, M. (2019). A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14990","ieee":"M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog,” Molecular Ecology, vol. 28, no. 8. Wiley, pp. 1877–1889, 2019.","short":"M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28 (2019) 1877–1889.","mla":"Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” Molecular Ecology, vol. 28, no. 8, Wiley, 2019, pp. 1877–89, doi:10.1111/mec.14990."},"title":"A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"first_name":"Nicolas","full_name":"Rodrigues, Nicolas","last_name":"Rodrigues"},{"full_name":"Perrin, Nicolas","last_name":"Perrin","first_name":"Nicolas"},{"first_name":"Mark","full_name":"Kirkpatrick, Mark","last_name":"Kirkpatrick"}],"article_processing_charge":"No","external_id":{"isi":["000468200800004"],"pmid":["30576024"]},"day":"01","publication":"Molecular Ecology","isi":1,"year":"2019","doi":"10.1111/mec.14990","date_published":"2019-04-01T00:00:00Z","date_created":"2020-01-30T10:33:05Z","page":"1877-1889","publisher":"Wiley","quality_controlled":"1","date_updated":"2023-09-06T15:00:13Z","department":[{"_id":"BeVi"}],"_id":"7421","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"publication_status":"published","issue":"8","volume":28,"pmid":1,"oa_version":"None","abstract":[{"text":"X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Y chromosomes. A new method based on gene trees shows both chromosomes are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical topologies, showing they have been coinherited since the reciprocal translocation occurred. Reciprocal translocations can thus reshape sex linkage on a much greater scale compared with inversions, the type of rearrangement that is much better known in sex chromosome evolution, and they can greatly amplify the power of sexually antagonistic selection to drive genomic rearrangement. Two more populations show evidence of other rearrangements, suggesting that this species has unprecedented structural polymorphism in its sex chromosomes.","lang":"eng"}],"month":"04","intvolume":" 28"},{"page":"277-291","date_created":"2020-01-30T09:26:14Z","doi":"10.1007/978-3-030-17656-3_10","date_published":"2019-04-24T00:00:00Z","year":"2019","isi":1,"publication":"Advances in Cryptology – EUROCRYPT 2019","day":"24","oa":1,"quality_controlled":"1","publisher":"Springer International Publishing","external_id":{"isi":["000483516200010"]},"article_processing_charge":"No","author":[{"full_name":"Abusalah, Hamza M","last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M"},{"first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","full_name":"Klein, Karen","last_name":"Klein"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"last_name":"Walter","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"title":"Reversible proofs of sequential work","citation":{"chicago":"Abusalah, Hamza M, Chethan Kamath Hosdurg, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “Reversible Proofs of Sequential Work.” In Advances in Cryptology – EUROCRYPT 2019, 11477:277–91. Springer International Publishing, 2019. https://doi.org/10.1007/978-3-030-17656-3_10.","ista":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2019. Reversible proofs of sequential work. Advances in Cryptology – EUROCRYPT 2019. International Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol. 11477, 277–291.","mla":"Abusalah, Hamza M., et al. “Reversible Proofs of Sequential Work.” Advances in Cryptology – EUROCRYPT 2019, vol. 11477, Springer International Publishing, 2019, pp. 277–91, doi:10.1007/978-3-030-17656-3_10.","ieee":"H. M. Abusalah, C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “Reversible proofs of sequential work,” in Advances in Cryptology – EUROCRYPT 2019, Darmstadt, Germany, 2019, vol. 11477, pp. 277–291.","short":"H.M. Abusalah, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2019, Springer International Publishing, 2019, pp. 277–291.","ama":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. Reversible proofs of sequential work. In: Advances in Cryptology – EUROCRYPT 2019. Vol 11477. Springer International Publishing; 2019:277-291. doi:10.1007/978-3-030-17656-3_10","apa":"Abusalah, H. M., Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2019). Reversible proofs of sequential work. In Advances in Cryptology – EUROCRYPT 2019 (Vol. 11477, pp. 277–291). Darmstadt, Germany: Springer International Publishing. https://doi.org/10.1007/978-3-030-17656-3_10"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ec_funded":1,"volume":11477,"publication_status":"published","publication_identifier":{"isbn":["9783030176556","9783030176563"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprint.iacr.org/2019/252","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 11477","month":"04","abstract":[{"lang":"eng","text":"Proofs of sequential work (PoSW) are proof systems where a prover, upon receiving a statement χ and a time parameter T computes a proof ϕ(χ,T) which is efficiently and publicly verifiable. The proof can be computed in T sequential steps, but not much less, even by a malicious party having large parallelism. A PoSW thus serves as a proof that T units of time have passed since χ\r\n\r\nwas received.\r\n\r\nPoSW were introduced by Mahmoody, Moran and Vadhan [MMV11], a simple and practical construction was only recently proposed by Cohen and Pietrzak [CP18].\r\n\r\nIn this work we construct a new simple PoSW in the random permutation model which is almost as simple and efficient as [CP18] but conceptually very different. Whereas the structure underlying [CP18] is a hash tree, our construction is based on skip lists and has the interesting property that computing the PoSW is a reversible computation.\r\nThe fact that the construction is reversible can potentially be used for new applications like constructing proofs of replication. We also show how to “embed” the sloth function of Lenstra and Weselowski [LW17] into our PoSW to get a PoSW where one additionally can verify correctness of the output much more efficiently than recomputing it (though recent constructions of “verifiable delay functions” subsume most of the applications this construction was aiming at)."}],"oa_version":"Submitted Version","department":[{"_id":"KrPi"}],"date_updated":"2023-09-06T15:26:06Z","conference":{"location":"Darmstadt, Germany","end_date":"2019-05-23","start_date":"2019-05-19","name":"International Conference on the Theory and Applications of Cryptographic Techniques"},"type":"conference","status":"public","_id":"7411"},{"project":[{"grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Isolation of synaptic vesicles from genetically engineered cultured neurons","author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine"},{"last_name":"Spanova","full_name":"Spanova, Miroslava","id":"44A924DC-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslava"},{"last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"last_name":"Kainrath","full_name":"Kainrath, Stephanie","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783"},{"full_name":"Sitte, Harald H.","last_name":"Sitte","first_name":"Harald H."},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"external_id":{"isi":["000456220900013"],"pmid":["30496761"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Mckenzie, Catherine, et al. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” Journal of Neuroscience Methods, vol. 312, Elsevier, 2019, pp. 114–21, doi:10.1016/j.jneumeth.2018.11.018.","ama":"Mckenzie C, Spanova M, Johnson AJ, et al. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 2019;312:114-121. doi:10.1016/j.jneumeth.2018.11.018","apa":"Mckenzie, C., Spanova, M., Johnson, A. J., Kainrath, S., Zheden, V., Sitte, H. H., & Janovjak, H. L. (2019). Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2018.11.018","ieee":"C. Mckenzie et al., “Isolation of synaptic vesicles from genetically engineered cultured neurons,” Journal of Neuroscience Methods, vol. 312. Elsevier, pp. 114–121, 2019.","short":"C. Mckenzie, M. Spanova, A.J. Johnson, S. Kainrath, V. Zheden, H.H. Sitte, H.L. Janovjak, Journal of Neuroscience Methods 312 (2019) 114–121.","chicago":"Mckenzie, Catherine, Miroslava Spanova, Alexander J Johnson, Stephanie Kainrath, Vanessa Zheden, Harald H. Sitte, and Harald L Janovjak. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” Journal of Neuroscience Methods. Elsevier, 2019. https://doi.org/10.1016/j.jneumeth.2018.11.018.","ista":"Mckenzie C, Spanova M, Johnson AJ, Kainrath S, Zheden V, Sitte HH, Janovjak HL. 2019. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 312, 114–121."},"quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.jneumeth.2018.11.018","date_published":"2019-01-15T00:00:00Z","date_created":"2020-01-30T09:12:19Z","page":"114-121","day":"15","publication":"Journal of Neuroscience Methods","isi":1,"year":"2019","status":"public","article_type":"original","type":"journal_article","_id":"7406","department":[{"_id":"HaJa"},{"_id":"Bio"}],"date_updated":"2023-09-06T15:27:29Z","month":"01","intvolume":" 312","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"Background\r\nSynaptic vesicles (SVs) are an integral part of the neurotransmission machinery, and isolation of SVs from their host neuron is necessary to reveal their most fundamental biochemical and functional properties in in vitro assays. Isolated SVs from neurons that have been genetically engineered, e.g. to introduce genetically encoded indicators, are not readily available but would permit new insights into SV structure and function. Furthermore, it is unclear if cultured neurons can provide sufficient starting material for SV isolation procedures.\r\n\r\nNew method\r\nHere, we demonstrate an efficient ex vivo procedure to obtain functional SVs from cultured rat cortical neurons after genetic engineering with a lentivirus.\r\n\r\nResults\r\nWe show that ∼108 plated cortical neurons allow isolation of suitable SV amounts for functional analysis and imaging. We found that SVs isolated from cultured neurons have neurotransmitter uptake comparable to that of SVs isolated from intact cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized an exogenous SV-targeted marker protein and demonstrated the high efficiency of SV modification.\r\n\r\nComparison with existing methods\r\nObtaining SVs from genetically engineered neurons currently generally requires the availability of transgenic animals, which is constrained by technical (e.g. cost and time) and biological (e.g. developmental defects and lethality) limitations.\r\n\r\nConclusions\r\nThese results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"volume":312,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0165-0270"]},"publication_status":"published"},{"oa":1,"quality_controlled":"1","publisher":"IMLS","page":"12481-12512","date_created":"2020-02-02T23:01:06Z","date_published":"2019-06-01T00:00:00Z","year":"2019","isi":1,"publication":"36th International Conference on Machine Learning, ICML 2019","day":"01","article_processing_charge":"No","external_id":{"arxiv":["1810.07766"],"isi":["000684034307036"]},"author":[{"full_name":"Yu, Chen","last_name":"Yu","first_name":"Chen"},{"full_name":"Tang, Hanlin","last_name":"Tang","first_name":"Hanlin"},{"full_name":"Renggli, Cedric","last_name":"Renggli","first_name":"Cedric"},{"full_name":"Kassing, Simon","last_name":"Kassing","first_name":"Simon"},{"last_name":"Singla","full_name":"Singla, Ankit","first_name":"Ankit"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"full_name":"Zhang, Ce","last_name":"Zhang","first_name":"Ce"},{"first_name":"Ji","last_name":"Liu","full_name":"Liu, Ji"}],"title":"Distributed learning over unreliable networks","citation":{"ista":"Yu C, Tang H, Renggli C, Kassing S, Singla A, Alistarh D-A, Zhang C, Liu J. 2019. Distributed learning over unreliable networks. 36th International Conference on Machine Learning, ICML 2019. ICML: International Conference on Machine Learning vol. 2019–June, 12481–12512.","chicago":"Yu, Chen, Hanlin Tang, Cedric Renggli, Simon Kassing, Ankit Singla, Dan-Adrian Alistarh, Ce Zhang, and Ji Liu. “Distributed Learning over Unreliable Networks.” In 36th International Conference on Machine Learning, ICML 2019, 2019–June:12481–512. IMLS, 2019.","apa":"Yu, C., Tang, H., Renggli, C., Kassing, S., Singla, A., Alistarh, D.-A., … Liu, J. (2019). Distributed learning over unreliable networks. In 36th International Conference on Machine Learning, ICML 2019 (Vol. 2019–June, pp. 12481–12512). Long Beach, CA, United States: IMLS.","ama":"Yu C, Tang H, Renggli C, et al. Distributed learning over unreliable networks. In: 36th International Conference on Machine Learning, ICML 2019. Vol 2019-June. IMLS; 2019:12481-12512.","ieee":"C. Yu et al., “Distributed learning over unreliable networks,” in 36th International Conference on Machine Learning, ICML 2019, Long Beach, CA, United States, 2019, vol. 2019–June, pp. 12481–12512.","short":"C. Yu, H. Tang, C. Renggli, S. Kassing, A. Singla, D.-A. Alistarh, C. Zhang, J. Liu, in:, 36th International Conference on Machine Learning, ICML 2019, IMLS, 2019, pp. 12481–12512.","mla":"Yu, Chen, et al. “Distributed Learning over Unreliable Networks.” 36th International Conference on Machine Learning, ICML 2019, vol. 2019–June, IMLS, 2019, pp. 12481–512."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://arxiv.org/abs/1810.07766","open_access":"1"}],"scopus_import":"1","month":"06","abstract":[{"text":"Most of today's distributed machine learning systems assume reliable networks: whenever two machines exchange information (e.g., gradients or models), the network should guarantee the delivery of the message. At the same time, recent work exhibits the impressive tolerance of machine learning algorithms to errors or noise arising from relaxed communication or synchronization. In this paper, we connect these two trends, and consider the following question: Can we design machine learning systems that are tolerant to network unreliability during training? With this motivation, we focus on a theoretical problem of independent interest-given a standard distributed parameter server architecture, if every communication between the worker and the server has a non-zero probability p of being dropped, does there exist an algorithm that still converges, and at what speed? The technical contribution of this paper is a novel theoretical analysis proving that distributed learning over unreliable network can achieve comparable convergence rate to centralized or distributed learning over reliable networks. Further, we prove that the influence of the packet drop rate diminishes with the growth of the number of parameter servers. We map this theoretical result onto a real-world scenario, training deep neural networks over an unreliable network layer, and conduct network simulation to validate the system improvement by allowing the networks to be unreliable.","lang":"eng"}],"oa_version":"Preprint","volume":"2019-June","publication_status":"published","publication_identifier":{"isbn":["9781510886988"]},"language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2019-06-15","location":"Long Beach, CA, United States","start_date":"2019-06-10"},"type":"conference","status":"public","_id":"7437","department":[{"_id":"DaAl"}],"date_updated":"2023-09-06T15:21:48Z"},{"oa":1,"publisher":"SIAM","quality_controlled":"1","year":"2019","isi":1,"publication":"SIAM Journal on Computing","day":"31","page":"1583-1602","date_created":"2020-01-30T09:27:32Z","doi":"10.1137/16m109332x","date_published":"2019-10-31T00:00:00Z","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Achlioptas D, Iliopoulos F, Kolmogorov V. 2019. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 48(5), 1583–1602.","chicago":"Achlioptas, Dimitris, Fotis Iliopoulos, and Vladimir Kolmogorov. “A Local Lemma for Focused Stochastical Algorithms.” SIAM Journal on Computing. SIAM, 2019. https://doi.org/10.1137/16m109332x.","ama":"Achlioptas D, Iliopoulos F, Kolmogorov V. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 2019;48(5):1583-1602. doi:10.1137/16m109332x","apa":"Achlioptas, D., Iliopoulos, F., & Kolmogorov, V. (2019). A local lemma for focused stochastical algorithms. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16m109332x","ieee":"D. Achlioptas, F. Iliopoulos, and V. Kolmogorov, “A local lemma for focused stochastical algorithms,” SIAM Journal on Computing, vol. 48, no. 5. SIAM, pp. 1583–1602, 2019.","short":"D. Achlioptas, F. Iliopoulos, V. Kolmogorov, SIAM Journal on Computing 48 (2019) 1583–1602.","mla":"Achlioptas, Dimitris, et al. “A Local Lemma for Focused Stochastical Algorithms.” SIAM Journal on Computing, vol. 48, no. 5, SIAM, 2019, pp. 1583–602, doi:10.1137/16m109332x."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000493900200005"],"arxiv":["1809.01537"]},"author":[{"first_name":"Dimitris","last_name":"Achlioptas","full_name":"Achlioptas, Dimitris"},{"first_name":"Fotis","last_name":"Iliopoulos","full_name":"Iliopoulos, Fotis"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}],"title":"A local lemma for focused stochastical algorithms","abstract":[{"text":"We develop a framework for the rigorous analysis of focused stochastic local search algorithms. These algorithms search a state space by repeatedly selecting some constraint that is violated in the current state and moving to a random nearby state that addresses the violation, while (we hope) not introducing many new violations. An important class of focused local search algorithms with provable performance guarantees has recently arisen from algorithmizations of the Lovász local lemma (LLL), a nonconstructive tool for proving the existence of satisfying states by introducing a background measure on the state space. While powerful, the state transitions of algorithms in this class must be, in a precise sense, perfectly compatible with the background measure. In many applications this is a very restrictive requirement, and one needs to step outside the class. Here we introduce the notion of measure distortion and develop a framework for analyzing arbitrary focused stochastic local search algorithms, recovering LLL algorithmizations as the special case of no distortion. Our framework takes as input an arbitrary algorithm of such type and an arbitrary probability measure and shows how to use the measure as a yardstick of algorithmic progress, even for algorithms designed independently of the measure.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1809.01537","open_access":"1"}],"scopus_import":"1","intvolume":" 48","month":"10","publication_status":"published","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"5","volume":48,"_id":"7412","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-06T15:25:29Z","department":[{"_id":"VlKo"}]},{"month":"11","intvolume":" 38","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Multiple importance sampling (MIS) has become an indispensable tool in Monte Carlo rendering, widely accepted as a near-optimal solution for combining different sampling techniques. But an MIS combination, using the common balance or power heuristics, often results in an overly defensive estimator, leading to high variance. We show that by generalizing the MIS framework, variance can be substantially reduced. Specifically, we optimize one of the combined sampling techniques so as to decrease the overall variance of the resulting MIS estimator. We apply the approach to the computation of direct illumination due to an HDR environment map and to the computation of global illumination using a path guiding algorithm. The implementation can be as simple as subtracting a constant value from the tabulated sampling density done entirely in a preprocessing step. This produces a consistent noise reduction in all our tests with no negative influence on run time, no artifacts or bias, and no failure cases."}],"volume":38,"issue":"6","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"7418","department":[{"_id":"ChWo"}],"date_updated":"2023-09-06T15:22:23Z","publisher":"ACM","quality_controlled":"1","doi":"10.1145/3355089.3356565","date_published":"2019-11-01T00:00:00Z","date_created":"2020-01-30T10:19:43Z","day":"01","publication":"ACM Transactions on Graphics","isi":1,"year":"2019","article_number":"151","title":"MIS compensation: Optimizing sampling techniques in multiple importance sampling","author":[{"first_name":"Ondřej","last_name":"Karlík","full_name":"Karlík, Ondřej"},{"full_name":"Šik, Martin","last_name":"Šik","first_name":"Martin"},{"last_name":"Vévoda","full_name":"Vévoda, Petr","first_name":"Petr"},{"first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"}],"external_id":{"isi":["000498397300001"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Karlík, Ondřej, Martin Šik, Petr Vévoda, Tomas Skrivan, and Jaroslav Křivánek. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356565.","ista":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. 2019. MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. 38(6), 151.","mla":"Karlík, Ondřej, et al. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no. 6, 151, ACM, 2019, doi:10.1145/3355089.3356565.","apa":"Karlík, O., Šik, M., Vévoda, P., Skrivan, T., & Křivánek, J. (2019). MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356565","ama":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356565","ieee":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, and J. Křivánek, “MIS compensation: Optimizing sampling techniques in multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","short":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, J. Křivánek, ACM Transactions on Graphics 38 (2019)."}},{"date_created":"2020-01-30T09:30:41Z","doi":"10.4310/acta.2019.v222.n2.a1","date_published":"2019-06-07T00:00:00Z","page":"219-335","publication":"Acta Mathematica","day":"07","year":"2019","isi":1,"oa":1,"publisher":"International Press of Boston","quality_controlled":"1","title":"Bogoliubov theory in the Gross–Pitaevskii limit","external_id":{"isi":["000495865300001"],"arxiv":["1801.01389"]},"article_processing_charge":"No","author":[{"full_name":"Boccato, Chiara","last_name":"Boccato","first_name":"Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brennecke","full_name":"Brennecke, Christian","first_name":"Christian"},{"first_name":"Serena","last_name":"Cenatiempo","full_name":"Cenatiempo, Serena"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Boccato, Chiara, et al. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” Acta Mathematica, vol. 222, no. 2, International Press of Boston, 2019, pp. 219–335, doi:10.4310/acta.2019.v222.n2.a1.","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Bogoliubov theory in the Gross–Pitaevskii limit,” Acta Mathematica, vol. 222, no. 2. International Press of Boston, pp. 219–335, 2019.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Acta Mathematica 222 (2019) 219–335.","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 2019;222(2):219-335. doi:10.4310/acta.2019.v222.n2.a1","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2019). Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. International Press of Boston. https://doi.org/10.4310/acta.2019.v222.n2.a1","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” Acta Mathematica. International Press of Boston, 2019. https://doi.org/10.4310/acta.2019.v222.n2.a1.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2019. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 222(2), 219–335."},"volume":222,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1871-2509"],"issn":["0001-5962"]},"intvolume":" 222","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.01389"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We consider Bose gases consisting of N particles trapped in a box with volume one and interacting through a repulsive potential with scattering length of order N−1 (Gross–Pitaevskii regime). We determine the ground state energy and the low-energy excitation spectrum, up to errors vanishing as N→∞. Our results confirm Bogoliubov’s predictions.","lang":"eng"}],"department":[{"_id":"RoSe"}],"date_updated":"2023-09-06T15:24:31Z","status":"public","article_type":"original","type":"journal_article","_id":"7413"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","article_type":"original","_id":"7393","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:57Z","ddc":["570"],"date_updated":"2023-09-06T15:35:56Z","intvolume":" 5","month":"12","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.","lang":"eng"}],"ec_funded":1,"issue":"12","volume":5,"language":[{"iso":"eng"}],"file":[{"file_name":"2019_ScienceAdvances_Morales.pdf","date_created":"2020-02-03T13:33:25Z","creator":"dernst","file_size":1869449,"date_updated":"2020-07-14T12:47:57Z","file_id":"7442","checksum":"af99a5dcdc66c6d6102051faf3be48d8","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["2375-2548"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"eaav9963","title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","article_processing_charge":"No","external_id":{"isi":["000505069600008"],"pmid":["31840052"]},"author":[{"last_name":"Morales","full_name":"Morales, Hernán E.","first_name":"Hernán E."},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.","ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963","ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019)."},"oa":1,"publisher":"AAAS","quality_controlled":"1","date_created":"2020-01-29T15:58:27Z","date_published":"2019-12-04T00:00:00Z","doi":"10.1126/sciadv.aav9963","publication":"Science Advances","day":"04","year":"2019","has_accepted_license":"1","isi":1},{"title":"Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit","external_id":{"isi":["000475349900001"],"arxiv":["1808.04080"]},"article_processing_charge":"No","author":[{"full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso","first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Choueiri","full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Lopez Alonso JM, Choueiri GH, Hof B. 2019. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 874, 699–719.","chicago":"Lopez Alonso, Jose M, George H Choueiri, and Björn Hof. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics. CUP, 2019. https://doi.org/10.1017/jfm.2019.486.","ama":"Lopez Alonso JM, Choueiri GH, Hof B. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 2019;874:699-719. doi:10.1017/jfm.2019.486","apa":"Lopez Alonso, J. M., Choueiri, G. H., & Hof, B. (2019). Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. CUP. https://doi.org/10.1017/jfm.2019.486","ieee":"J. M. Lopez Alonso, G. H. Choueiri, and B. Hof, “Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit,” Journal of Fluid Mechanics, vol. 874. CUP, pp. 699–719, 2019.","short":"J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874 (2019) 699–719.","mla":"Lopez Alonso, Jose M., et al. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics, vol. 874, CUP, 2019, pp. 699–719, doi:10.1017/jfm.2019.486."},"oa":1,"publisher":"CUP","quality_controlled":"1","date_created":"2020-01-29T16:05:19Z","date_published":"2019-09-10T00:00:00Z","doi":"10.1017/jfm.2019.486","page":"699-719","publication":"Journal of Fluid Mechanics","day":"10","year":"2019","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"7397","department":[{"_id":"BjHo"}],"date_updated":"2023-09-06T15:36:36Z","intvolume":" 874","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04080"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Polymer additives can substantially reduce the drag of turbulent flows and the upperlimit, the so called “maximum drag reduction” (MDR) asymptote is universal, i.e. inde-pendent of the type of polymer and solvent used. Until recently, the consensus was that,in this limit, flows are in a marginal state where only a minimal level of turbulence activ-ity persists. Observations in direct numerical simulations using minimal sized channelsappeared to support this view and reported long “hibernation” periods where turbu-lence is marginalized. In simulations of pipe flow we find that, indeed, with increasingWeissenberg number (Wi), turbulence expresses long periods of hibernation if the domainsize is small. However, with increasing pipe length, the temporal hibernation continuouslyalters to spatio-temporal intermittency and here the flow consists of turbulent puffs sur-rounded by laminar flow. Moreover, upon an increase in Wi, the flow fully relaminarises,in agreement with recent experiments. At even larger Wi, a different instability is en-countered causing a drag increase towards MDR. Our findings hence link earlier minimalflow unit simulations with recent experiments and confirm that the addition of polymersinitially suppresses Newtonian turbulence and leads to a reverse transition. The MDRstate on the other hand results from a separate instability and the underlying dynamicscorresponds to the recently proposed state of elasto-inertial-turbulence (EIT)."}],"volume":874,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]}},{"project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” Discrete and Computational Geometry, vol. 62, no. 4, Springer, 2019, pp. 865–878, doi:10.1007/s00454-018-0049-2.","ieee":"H. Edelsbrunner and A. Nikitenko, “Poisson–Delaunay Mosaics of Order k,” Discrete and Computational Geometry, vol. 62, no. 4. Springer, pp. 865–878, 2019.","short":"H. Edelsbrunner, A. Nikitenko, Discrete and Computational Geometry 62 (2019) 865–878.","apa":"Edelsbrunner, H., & Nikitenko, A. (2019). Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. Springer. https://doi.org/10.1007/s00454-018-0049-2","ama":"Edelsbrunner H, Nikitenko A. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 2019;62(4):865–878. doi:10.1007/s00454-018-0049-2","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” Discrete and Computational Geometry. Springer, 2019. https://doi.org/10.1007/s00454-018-0049-2.","ista":"Edelsbrunner H, Nikitenko A. 2019. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 62(4), 865–878."},"title":"Poisson–Delaunay Mosaics of Order k","author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000494042900008"],"arxiv":["1709.09380"]},"publisher":"Springer","quality_controlled":"1","oa":1,"day":"01","publication":"Discrete and Computational Geometry","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-12-01T00:00:00Z","doi":"10.1007/s00454-018-0049-2","date_created":"2018-12-16T22:59:20Z","page":"865–878","_id":"5678","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["516"],"date_updated":"2023-09-07T12:07:12Z","file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"HeEd"}],"oa_version":"Published Version","abstract":[{"text":"The order-k Voronoi tessellation of a locally finite set 𝑋⊆ℝ𝑛 decomposes ℝ𝑛 into convex domains whose points have the same k nearest neighbors in X. Assuming X is a stationary Poisson point process, we give explicit formulas for the expected number and total area of faces of a given dimension per unit volume of space. We also develop a relaxed version of discrete Morse theory and generalize by counting only faces, for which the k nearest points in X are within a given distance threshold.","lang":"eng"}],"month":"12","intvolume":" 62","scopus_import":"1","file":[{"checksum":"f9d00e166efaccb5a76bbcbb4dcea3b4","file_id":"5932","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_DiscreteCompGeometry_Edelsbrunner.pdf","date_created":"2019-02-06T10:10:46Z","creator":"dernst","file_size":599339,"date_updated":"2020-07-14T12:47:10Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"publication_status":"published","issue":"4","volume":62,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6287"}]},"ec_funded":1},{"date_published":"2019-01-02T00:00:00Z","doi":"10.1016/j.neuron.2018.11.015","date_created":"2019-01-13T22:59:10Z","page":"119-132.e4","day":"02","publication":"Neuron","isi":1,"year":"2019","publisher":"Elsevier","quality_controlled":"1","oa":1,"title":"Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze","author":[{"id":"310349D0-F248-11E8-B48F-1D18A9856A87","first_name":"Haibing","full_name":"Xu, Haibing","last_name":"Xu"},{"last_name":"Baracskay","full_name":"Baracskay, Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000454791500014"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Xu H, Baracskay P, O’Neill J, Csicsvari JL. 2019. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 101(1), 119–132.e4.","chicago":"Xu, Haibing, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2018.11.015.","apa":"Xu, H., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.11.015","ama":"Xu H, Baracskay P, O’Neill J, Csicsvari JL. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 2019;101(1):119-132.e4. doi:10.1016/j.neuron.2018.11.015","ieee":"H. Xu, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze,” Neuron, vol. 101, no. 1. Elsevier, p. 119–132.e4, 2019.","short":"H. Xu, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 101 (2019) 119–132.e4.","mla":"Xu, Haibing, et al. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron, vol. 101, no. 1, Elsevier, 2019, p. 119–132.e4, doi:10.1016/j.neuron.2018.11.015."},"project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/reading-rats-minds/","relation":"press_release"}],"record":[{"id":"837","status":"public","relation":"dissertation_contains"}]},"issue":"1","volume":101,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["10974199"]},"publication_status":"published","month":"01","intvolume":" 101","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.1016/j.neuron.2018.11.015"}],"oa_version":"Published Version","abstract":[{"text":"Hippocampus is needed for both spatial working and reference memories. Here, using a radial eight-arm maze, we examined how the combined demand on these memories influenced CA1 place cell assemblies while reference memories were partially updated. This was contrasted with control tasks requiring only working memory or the update of reference memory. Reference memory update led to the reward-directed place field shifts at newly rewarded arms and to the gradual strengthening of firing in passes between newly rewarded arms but not between those passes that included a familiar-rewarded arm. At the maze center, transient network synchronization periods preferentially replayed trajectories of the next chosen arm in reference memory tasks but the previously visited arm in the working memory task. Hence, reference memory demand was uniquely associated with a gradual, goal novelty-related reorganization of place cell assemblies and with trajectory replay that reflected the animal's decision of which arm to visit next.","lang":"eng"}],"department":[{"_id":"JoCs"}],"date_updated":"2023-09-07T12:06:37Z","status":"public","article_type":"original","type":"journal_article","_id":"5828"},{"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Moser T, Seiringer R. 2019. Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. 20(4), 1325–1365.","chicago":"Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting Impurity in a Fermi Gas.” Annales Henri Poincare. Springer, 2019. https://doi.org/10.1007/s00023-018-00757-0.","ama":"Moser T, Seiringer R. Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. 2019;20(4):1325–1365. doi:10.1007/s00023-018-00757-0","apa":"Moser, T., & Seiringer, R. (2019). Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-00757-0","ieee":"T. Moser and R. Seiringer, “Energy contribution of a point-interacting impurity in a Fermi gas,” Annales Henri Poincare, vol. 20, no. 4. Springer, pp. 1325–1365, 2019.","short":"T. Moser, R. Seiringer, Annales Henri Poincare 20 (2019) 1325–1365.","mla":"Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting Impurity in a Fermi Gas.” Annales Henri Poincare, vol. 20, no. 4, Springer, 2019, pp. 1325–1365, doi:10.1007/s00023-018-00757-0."},"title":"Energy contribution of a point-interacting impurity in a Fermi gas","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1807.00739"],"isi":["000462444300008"]},"author":[{"full_name":"Moser, Thomas","last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"quality_controlled":"1","publisher":"Springer","publication":"Annales Henri Poincare","day":"01","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-01-20T22:59:17Z","doi":"10.1007/s00023-018-00757-0","date_published":"2019-04-01T00:00:00Z","page":"1325–1365","_id":"5856","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["530"],"date_updated":"2023-09-07T12:37:42Z","file_date_updated":"2020-07-14T12:47:12Z","department":[{"_id":"RoSe"}],"oa_version":"Published Version","abstract":[{"text":"We give a bound on the ground-state energy of a system of N non-interacting fermions in a three-dimensional cubic box interacting with an impurity particle via point interactions. We show that the change in energy compared to the system in the absence of the impurity is bounded in terms of the gas density and the scattering length of the interaction, independently of N. Our bound holds as long as the ratio of the mass of the impurity to the one of the gas particles is larger than a critical value m∗ ∗≈ 0.36 , which is the same regime for which we recently showed stability of the system.","lang":"eng"}],"intvolume":" 20","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"255e42f957a8e2b10aad2499c750a8d6","file_id":"5894","date_updated":"2020-07-14T12:47:12Z","file_size":859846,"creator":"dernst","date_created":"2019-01-28T15:27:17Z","file_name":"2019_Annales_Moser.pdf"}],"publication_status":"published","publication_identifier":{"issn":["14240637"]},"ec_funded":1,"issue":"4","volume":20,"related_material":{"record":[{"status":"public","id":"52","relation":"dissertation_contains"}]}},{"oa_version":"Published Version","abstract":[{"text":"In many shear flows like pipe flow, plane Couette flow, plane Poiseuille flow, etc. turbulence emerges subcritically. Here, when subjected to strong enough perturbations, the flow becomes turbulent in spite of the laminar base flow being linearly stable. The nature of this instability has puzzled the scientific community for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally intermittent. In pipe flow the localized turbulent structures are referred to as puffs and in planar flows like plane Couette and channel flow, patches arise in the form of localized oblique bands. In this thesis, we study the onset of turbulence in channel flow in direct numerical simulations from a dynamical system theory perspective, as well as by performing experiments in a large aspect ratio channel.\r\n\r\nThe aim of the experimental work is to determine the critical Reynolds number where turbulence first becomes sustained. Recently, the onset of turbulence has been described in analogy to absorbing state phase transition (i.e. directed percolation). In particular, it has been shown that the critical point can be estimated from the competition between spreading and decay processes. Here, by performing experiments, we identify the mechanisms underlying turbulence proliferation in channel flow and find the critical Reynolds number, above which turbulence becomes sustained. Above the critical point, the continuous growth at the tip of the stripes outweighs the stochastic shedding of turbulent patches at the tail and the stripes expand. For growing stripes, the probability to decay decreases while the probability of stripe splitting increases. Consequently, and unlike for the puffs in pipe flow, neither of these two processes is time-independent i.e. memoryless. Coupling between stripe expansion and creation of new stripes via splitting leads to a significantly lower critical point ($Re_c=670+/-10$) than most earlier studies suggest. \r\n\r\nWhile the above approach sheds light on how turbulence first becomes sustained, it provides no insight into the origin of the stripes themselves. In the numerical part of the thesis we investigate how turbulent stripes form from invariant solutions of the Navier-Stokes equations. The origin of these turbulent stripes can be identified by applying concepts from the dynamical system theory. In doing so, we identify the exact coherent structures underlying stripes and their bifurcations and how they give rise to the turbulent attractor in phase space. We first report a family of localized nonlinear traveling wave solutions of the Navier-Stokes equations in channel flow. These solutions show structural similarities with turbulent stripes in experiments like obliqueness, quasi-streamwise streaks and vortices, etc. A parametric study of these traveling wave solution is performed, with parameters like Reynolds number, stripe tilt angle and domain size, including the stability of the solutions. These solutions emerge through saddle-node bifurcations and form a phase space skeleton for the turbulent stripes observed in the experiments. The lower branches of these TW solutions at different tilt angles undergo Hopf bifurcation and new solutions branches of relative periodic orbits emerge. These RPO solutions do not belong to the same family and therefore the routes to chaos for different angles are different. \r\n\r\nIn shear flows, turbulence at onset is transient in nature. Consequently,turbulence can not be tracked to lower Reynolds numbers, where the dynamics may simplify. Before this happens, turbulence becomes short-lived and laminarizes. In the last part of the thesis, we show that using numerical simulations we can continue turbulent stripes in channel flow past the 'relaminarization barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies and the fluctuations are no longer stochastic and the stripe settles down to a relative periodic orbit. This relative periodic orbit originates from the aforementioned traveling wave solutions. Starting from the relative periodic orbit, a small increase in speed i.e. Reynolds number gives rise to chaos and the attractor dimension sharply increases in contrast to the classical transition scenario where the instabilities affect the flow globally and give rise to much more gradual route to turbulence.","lang":"eng"}],"month":"10","alternative_title":["ISTA Thesis"],"file":[{"content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"6962","checksum":"7ba298ba0ce7e1d11691af6b8eaf0a0a","date_updated":"2020-07-14T12:47:46Z","file_size":45828099,"creator":"cparanjape","date_created":"2019-10-23T09:54:43Z","file_name":"Chaitanya_Paranjape_source_files_tex_figures.zip"},{"date_updated":"2020-07-14T12:47:46Z","file_size":19504197,"creator":"cparanjape","date_created":"2019-10-23T10:37:09Z","file_name":"Chaitanya_Paranjape_Thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6963","checksum":"642697618314e31ac31392da7909c2d9"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","_id":"6957","status":"public","keyword":["Instabilities","Turbulence","Nonlinear dynamics"],"type":"dissertation","ddc":["532"],"supervisor":[{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"date_updated":"2023-09-07T12:53:25Z","department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:47:46Z","publisher":"Institute of Science and Technology Austria","oa":1,"day":"24","has_accepted_license":"1","year":"2019","doi":"10.15479/AT:ISTA:6957","date_published":"2019-10-24T00:00:00Z","date_created":"2019-10-22T12:08:43Z","page":"138","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"C.S. Paranjape, Onset of Turbulence in Plane Poiseuille Flow, Institute of Science and Technology Austria, 2019.","ieee":"C. S. Paranjape, “Onset of turbulence in plane Poiseuille flow,” Institute of Science and Technology Austria, 2019.","apa":"Paranjape, C. S. (2019). Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6957","ama":"Paranjape CS. Onset of turbulence in plane Poiseuille flow. 2019. doi:10.15479/AT:ISTA:6957","mla":"Paranjape, Chaitanya S. Onset of Turbulence in Plane Poiseuille Flow. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6957.","ista":"Paranjape CS. 2019. Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria.","chicago":"Paranjape, Chaitanya S. “Onset of Turbulence in Plane Poiseuille Flow.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6957."},"title":"Onset of turbulence in plane Poiseuille flow","author":[{"last_name":"Paranjape","full_name":"Paranjape, Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","first_name":"Chaitanya S"}],"article_processing_charge":"No"},{"quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"doi":"10.1017/fms.2019.2","date_published":"2019-03-26T00:00:00Z","date_created":"2019-03-28T09:05:23Z","has_accepted_license":"1","isi":1,"year":"2019","day":"26","publication":"Forum of Mathematics, Sigma","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"e8","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"}],"article_processing_charge":"No","external_id":{"arxiv":["1705.10661"],"isi":["000488847100001"]},"title":"Random matrices with slow correlation decay","citation":{"ama":"Erdös L, Krüger TH, Schröder DJ. Random matrices with slow correlation decay. Forum of Mathematics, Sigma. 2019;7. doi:10.1017/fms.2019.2","apa":"Erdös, L., Krüger, T. H., & Schröder, D. J. (2019). Random matrices with slow correlation decay. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2019.2","ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Random matrices with slow correlation decay,” Forum of Mathematics, Sigma, vol. 7. Cambridge University Press, 2019.","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Forum of Mathematics, Sigma 7 (2019).","mla":"Erdös, László, et al. “Random Matrices with Slow Correlation Decay.” Forum of Mathematics, Sigma, vol. 7, e8, Cambridge University Press, 2019, doi:10.1017/fms.2019.2.","ista":"Erdös L, Krüger TH, Schröder DJ. 2019. Random matrices with slow correlation decay. Forum of Mathematics, Sigma. 7, e8.","chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Random Matrices with Slow Correlation Decay.” Forum of Mathematics, Sigma. Cambridge University Press, 2019. https://doi.org/10.1017/fms.2019.2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"03","intvolume":" 7","abstract":[{"lang":"eng","text":"We consider large random matrices with a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent away from the spectral edges, generalizing the recent result of Ajanki et al. [‘Stability of the matrix Dyson equation and random matrices with correlations’, Probab. Theory Related Fields 173(1–2) (2019), 293–373] to allow slow correlation decay and arbitrary expectation. The main novel tool is\r\na systematic diagrammatic control of a multivariate cumulant expansion."}],"oa_version":"Published Version","volume":7,"related_material":{"record":[{"relation":"dissertation_contains","id":"6179","status":"public"}]},"ec_funded":1,"publication_identifier":{"eissn":["20505094"]},"publication_status":"published","file":[{"file_name":"2019_Forum_Erdoes.pdf","date_created":"2019-09-17T14:24:13Z","creator":"dernst","file_size":1520344,"date_updated":"2020-07-14T12:47:22Z","checksum":"933a472568221c73b2c3ce8c87bf6d15","file_id":"6883","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6182","file_date_updated":"2020-07-14T12:47:22Z","department":[{"_id":"LaEr"}],"date_updated":"2023-09-07T12:54:12Z","ddc":["510"]},{"oa":1,"publisher":"MSP","quality_controlled":"1","publication":"Pure and Applied Analysis ","day":"12","year":"2019","date_created":"2019-03-28T10:21:17Z","date_published":"2019-10-12T00:00:00Z","doi":"10.2140/paa.2019.1.615","page":"615–707","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices, II: The Real Symmetric Case.” Pure and Applied Analysis . MSP, 2019. https://doi.org/10.2140/paa.2019.1.615.","ista":"Cipolloni G, Erdös L, Krüger TH, Schröder DJ. 2019. Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . 1(4), 615–707.","mla":"Cipolloni, Giorgio, et al. “Cusp Universality for Random Matrices, II: The Real Symmetric Case.” Pure and Applied Analysis , vol. 1, no. 4, MSP, 2019, pp. 615–707, doi:10.2140/paa.2019.1.615.","ama":"Cipolloni G, Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . 2019;1(4):615–707. doi:10.2140/paa.2019.1.615","apa":"Cipolloni, G., Erdös, L., Krüger, T. H., & Schröder, D. J. (2019). Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . MSP. https://doi.org/10.2140/paa.2019.1.615","ieee":"G. Cipolloni, L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices, II: The real symmetric case,” Pure and Applied Analysis , vol. 1, no. 4. MSP, pp. 615–707, 2019.","short":"G. Cipolloni, L. Erdös, T.H. Krüger, D.J. Schröder, Pure and Applied Analysis 1 (2019) 615–707."},"title":"Cusp universality for random matrices, II: The real symmetric case","external_id":{"arxiv":["1811.04055"]},"article_processing_charge":"No","author":[{"last_name":"Cipolloni","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"oa_version":"Preprint","abstract":[{"text":"We prove that the local eigenvalue statistics of real symmetric Wigner-type\r\nmatrices near the cusp points of the eigenvalue density are universal. Together\r\nwith the companion paper [arXiv:1809.03971], which proves the same result for\r\nthe complex Hermitian symmetry class, this completes the last remaining case of\r\nthe Wigner-Dyson-Mehta universality conjecture after bulk and edge\r\nuniversalities have been established in the last years. We extend the recent\r\nDyson Brownian motion analysis at the edge [arXiv:1712.03881] to the cusp\r\nregime using the optimal local law from [arXiv:1809.03971] and the accurate\r\nlocal shape analysis of the density from [arXiv:1506.05095, arXiv:1804.07752].\r\nWe also present a PDE-based method to improve the estimate on eigenvalue\r\nrigidity via the maximum principle of the heat flow related to the Dyson\r\nBrownian motion.","lang":"eng"}],"intvolume":" 1","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1811.04055","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2578-5893"],"eissn":["2578-5885"]},"ec_funded":1,"issue":"4","volume":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"6179","status":"public"}]},"_id":"6186","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-07T12:54:12Z","department":[{"_id":"LaEr"}]},{"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:44Z","file_size":3081855,"creator":"kschuh","date_created":"2019-10-01T10:53:45Z","file_name":"2019_PLoS_Cepeda-Humerez.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"81bdce1361c9aa8395d6fa635fb6ab47","file_id":"6925"}],"publication_status":"published","publication_identifier":{"eissn":["15537358"]},"related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"volume":15,"issue":"9","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks."}],"intvolume":" 15","month":"09","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-07T12:55:21Z","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:44Z","_id":"6900","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","publication":"PLoS computational biology","day":"03","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-09-22T22:00:37Z","date_published":"2019-09-03T00:00:00Z","doi":"10.1371/journal.pcbi.1007290","page":"e1007290","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007290.","ista":"Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290.","mla":"Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.","ama":"Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. PLoS computational biology. 2019;15(9):e1007290. doi:10.1371/journal.pcbi.1007290","apa":"Cepeda Humerez, S. A., Ruess, J., & Tkačik, G. (2019). Estimating information in time-varying signals. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007290","short":"S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.","ieee":"S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” PLoS computational biology, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019."},"title":"Estimating information in time-varying signals","external_id":{"pmid":["31479447"],"isi":["000489741800021"]},"article_processing_charge":"No","author":[{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","full_name":"Cepeda Humerez, Sarah A","last_name":"Cepeda Humerez"},{"last_name":"Ruess","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","first_name":"Jakob"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"department":[{"_id":"JiFr"}],"date_updated":"2023-09-07T12:54:35Z","status":"public","type":"journal_article","article_type":"original","_id":"6377","issue":"6","volume":15,"related_material":{"record":[{"relation":"dissertation_contains","id":"7172","status":"public"}]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15524469"],"issn":["15524450"]},"publication_status":"published","month":"06","intvolume":" 15","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acutely and reversibly perturb CME, the few chemical CME inhibitors that have been applied to plants are either ineffective or show undesirable side effects. Here, we identify the previously described endosidin9 (ES9) as an inhibitor of clathrin heavy chain (CHC) function in both Arabidopsis and human cells through affinity-based target isolation, in vitro binding studies and X-ray crystallography. Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the undesirable side effects of ES9 while retaining the ability to target CHC. ES9 and ES9-17 have expanded the chemical toolbox used to probe CHC function, and present chemical scaffolds for further design of more specific and potent CHC inhibitors across different systems."}],"title":"Disruption of endocytosis through chemical inhibition of clathrin heavy chain function","author":[{"last_name":"Dejonghe","full_name":"Dejonghe, Wim","first_name":"Wim"},{"full_name":"Sharma, Isha","last_name":"Sharma","first_name":"Isha"},{"last_name":"Denoo","full_name":"Denoo, Bram","first_name":"Bram"},{"first_name":"Steven","full_name":"De Munck, Steven","last_name":"De Munck"},{"first_name":"Qing","last_name":"Lu","full_name":"Lu, Qing"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"first_name":"Haydar","full_name":"Bulut, Haydar","last_name":"Bulut"},{"first_name":"Evelien","full_name":"Mylle, Evelien","last_name":"Mylle"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"last_name":"Vasileva","full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K"},{"first_name":"Daniel V.","full_name":"Savatin, Daniel V.","last_name":"Savatin"},{"first_name":"Wim","last_name":"Nerinckx","full_name":"Nerinckx, Wim"},{"last_name":"Staes","full_name":"Staes, An","first_name":"An"},{"first_name":"Andrzej","full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki"},{"first_name":"Dominique","full_name":"Audenaert, Dominique","last_name":"Audenaert"},{"first_name":"Klaas","last_name":"Yperman","full_name":"Yperman, Klaas"},{"first_name":"Annemieke","full_name":"Madder, Annemieke","last_name":"Madder"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Van Damme","full_name":"Van Damme, Daniël","first_name":"Daniël"},{"last_name":"Gevaert","full_name":"Gevaert, Kris","first_name":"Kris"},{"full_name":"Haucke, Volker","last_name":"Haucke","first_name":"Volker"},{"full_name":"Savvides, Savvas N.","last_name":"Savvides","first_name":"Savvas N."},{"first_name":"Johan","full_name":"Winne, Johan","last_name":"Winne"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"}],"external_id":{"isi":["000468195600018"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Dejonghe, Wim, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” Nature Chemical Biology, vol. 15, no. 6, Springer Nature, 2019, pp. 641–649, doi:10.1038/s41589-019-0262-1.","short":"W. Dejonghe, I. Sharma, B. Denoo, S. De Munck, Q. Lu, K. Mishev, H. Bulut, E. Mylle, R. De Rycke, M.K. Vasileva, D.V. Savatin, W. Nerinckx, A. Staes, A. Drozdzecki, D. Audenaert, K. Yperman, A. Madder, J. Friml, D. Van Damme, K. Gevaert, V. Haucke, S.N. Savvides, J. Winne, E. Russinova, Nature Chemical Biology 15 (2019) 641–649.","ieee":"W. Dejonghe et al., “Disruption of endocytosis through chemical inhibition of clathrin heavy chain function,” Nature Chemical Biology, vol. 15, no. 6. Springer Nature, pp. 641–649, 2019.","apa":"Dejonghe, W., Sharma, I., Denoo, B., De Munck, S., Lu, Q., Mishev, K., … Russinova, E. (2019). Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. Springer Nature. https://doi.org/10.1038/s41589-019-0262-1","ama":"Dejonghe W, Sharma I, Denoo B, et al. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. 2019;15(6):641–649. doi:10.1038/s41589-019-0262-1","chicago":"Dejonghe, Wim, Isha Sharma, Bram Denoo, Steven De Munck, Qing Lu, Kiril Mishev, Haydar Bulut, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” Nature Chemical Biology. Springer Nature, 2019. https://doi.org/10.1038/s41589-019-0262-1.","ista":"Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle E, De Rycke R, Vasileva MK, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN, Winne J, Russinova E. 2019. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. 15(6), 641–649."},"date_published":"2019-06-01T00:00:00Z","doi":"10.1038/s41589-019-0262-1","date_created":"2019-05-05T21:59:11Z","page":"641–649","day":"01","publication":"Nature Chemical Biology","isi":1,"year":"2019","publisher":"Springer Nature","quality_controlled":"1"},{"type":"dissertation","status":"public","_id":"7186","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"CaHe"}],"supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"date_updated":"2023-09-07T12:56:42Z","ddc":["570"],"alternative_title":["ISTA Thesis"],"month":"12","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"SSU"}],"abstract":[{"text":"Tissue morphogenesis in developmental or physiological processes is regulated by molecular\r\nand mechanical signals. While the molecular signaling cascades are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape changes have only recently been\r\nstudied in greater detail. To gain more insight into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process (epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature and formation of the junctional structure\r\nmediating this process has not been well described so far. Therefore, our main aim was to\r\ndetermine the nature, dynamics and potential function of the EVL-YSL junction during this\r\nepithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process\r\nof TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely renders the protein\r\nresponsive to flows. These flows are directed towards the junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive responses resulting in slower tissue spreading. We could further\r\ndemonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale polarization process mediated through the flow of phase-separated protein\r\nclusters might have implications for other processes such as immunological synapse\r\nformation, C. elegans zygote polarization and wound healing.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"1096","relation":"dissertation_contains"},{"relation":"part_of_dissertation","id":"7001","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_id":"7194","checksum":"585583c1c875c5d9525703a539668a7c","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2019-12-19T15:18:11Z","file_name":"DocumentSourceFiles.zip","creator":"cschwayer","date_updated":"2020-07-14T12:47:52Z","file_size":19431292},{"file_id":"7195","checksum":"9b9b24351514948d27cec659e632e2cd","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-12-19T15:19:21Z","file_name":"Thesis_CS_final.pdf","date_updated":"2020-07-14T12:47:52Z","file_size":19226428,"creator":"cschwayer"}],"language":[{"iso":"eng"}],"author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia","last_name":"Schwayer"}],"article_processing_charge":"No","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","citation":{"mla":"Schwayer, Cornelia. Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7186.","apa":"Schwayer, C. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7186","ama":"Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:10.15479/AT:ISTA:7186","short":"C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019.","ieee":"C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019.","chicago":"Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7186.","ista":"Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","oa":1,"page":"107","date_published":"2019-12-16T00:00:00Z","doi":"10.15479/AT:ISTA:7186","date_created":"2019-12-16T14:26:14Z","has_accepted_license":"1","year":"2019","day":"16"},{"oa":1,"publisher":"Institute of Science and Technology Austria","page":"104","date_created":"2019-07-26T11:14:34Z","date_published":"2019-08-08T00:00:00Z","doi":"10.15479/AT:ISTA:6681","year":"2019","has_accepted_license":"1","day":"08","article_processing_charge":"No","author":[{"first_name":"Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87","last_name":"Zhechev","full_name":"Zhechev, Stephan Y"}],"title":"Algorithmic aspects of homotopy theory and embeddability","citation":{"ieee":"S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,” Institute of Science and Technology Austria, 2019.","short":"S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute of Science and Technology Austria, 2019.","ama":"Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019. doi:10.15479/AT:ISTA:6681","apa":"Zhechev, S. Y. (2019). Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6681","mla":"Zhechev, Stephan Y. Algorithmic Aspects of Homotopy Theory and Embeddability. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6681.","ista":"Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria.","chicago":"Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6681."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"lang":"eng","text":"The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space."}],"oa_version":"Published Version","related_material":{"record":[{"id":"6774","status":"public","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"3231e7cbfca3b5687366f84f0a57a0c0","file_id":"6771","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-08-07T13:02:50Z","file_name":"Stephan_Zhechev_thesis.pdf","date_updated":"2020-07-14T12:47:37Z","file_size":1464227,"creator":"szhechev"},{"creator":"szhechev","date_updated":"2020-07-14T12:47:37Z","file_size":303988,"date_created":"2019-08-07T13:03:22Z","file_name":"Stephan_Zhechev_thesis.tex","access_level":"closed","relation":"source_file","content_type":"application/octet-stream","checksum":"85d65eb27b4377a9e332ee37a70f08b6","file_id":"6772"},{"file_id":"6773","checksum":"86b374d264ca2dd53e712728e253ee75","relation":"supplementary_material","access_level":"closed","content_type":"application/zip","file_name":"supplementary_material.zip","date_created":"2019-08-07T13:03:34Z","creator":"szhechev","file_size":1087004,"date_updated":"2020-07-14T12:47:37Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","_id":"6681","file_date_updated":"2020-07-14T12:47:37Z","department":[{"_id":"UlWa"}],"date_updated":"2023-09-07T13:10:36Z","supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"}],"ddc":["514"]},{"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1910.12628","open_access":"1"}],"publisher":"arXiv","month":"10","abstract":[{"text":"Suppose that $n\\neq p^k$ and $n\\neq 2p^k$ for all $k$ and all primes $p$. We prove that for any Hausdorff compactum $X$ with a free action of the symmetric group $\\mathfrak S_n$ there exists an $\\mathfrak S_n$-equivariant map $X \\to\r\n{\\mathbb R}^n$ whose image avoids the diagonal $\\{(x,x\\dots,x)\\in {\\mathbb R}^n|x\\in {\\mathbb R}\\}$.\r\n Previously, the special cases of this statement for certain $X$ were usually proved using the equivartiant obstruction theory. Such calculations are difficult and may become infeasible past the first (primary) obstruction. We\r\ntake a different approach which allows us to prove the vanishing of all obstructions simultaneously. The essential step in the proof is classifying the possible degrees of $\\mathfrak S_n$-equivariant maps from the boundary\r\n$\\partial\\Delta^{n-1}$ of $(n-1)$-simplex to itself. Existence of equivariant maps between spaces is important for many questions arising from discrete mathematics and geometry, such as Kneser's conjecture, the Square Peg conjecture, the Splitting Necklace problem, and the Topological Tverberg conjecture, etc. We demonstrate the utility of our result applying it to one such question, a specific instance of envy-free division problem.","lang":"eng"}],"oa_version":"Preprint","date_created":"2020-07-30T10:45:08Z","date_published":"2019-10-28T00:00:00Z","related_material":{"record":[{"status":"public","id":"11446","relation":"later_version"},{"status":"public","id":"8156","relation":"dissertation_contains"}]},"year":"2019","publication_status":"submitted","language":[{"iso":"eng"}],"publication":"arXiv","day":"28","type":"preprint","status":"public","project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory"}],"_id":"8182","article_number":"1910.12628","article_processing_charge":"No","external_id":{"arxiv":["1910.12628"]},"author":[{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"id":"ecf01965-d252-11ea-95a5-8ada5f6c6a67","first_name":"Sergey","last_name":"Kudrya","full_name":"Kudrya, Sergey"}],"department":[{"_id":"UlWa"}],"title":"Vanishing of all equivariant obstructions and the mapping degree","date_updated":"2023-09-07T13:12:17Z","citation":{"ista":"Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping degree. arXiv, 1910.12628.","chicago":"Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” ArXiv. arXiv, n.d.","ieee":"S. Avvakumov and S. Kudrya, “Vanishing of all equivariant obstructions and the mapping degree,” arXiv. arXiv.","short":"S. Avvakumov, S. Kudrya, ArXiv (n.d.).","apa":"Avvakumov, S., & Kudrya, S. (n.d.). Vanishing of all equivariant obstructions and the mapping degree. arXiv. arXiv.","ama":"Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping degree. arXiv.","mla":"Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” ArXiv, 1910.12628, arXiv."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]