[{"language":[{"iso":"eng"}],"doi":"10.1038/s42003-018-0078-7","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000461126500071"]},"month":"06","publication_identifier":{"issn":["2399-3642"]},"date_created":"2018-12-18T13:22:58Z","date_updated":"2024-02-21T13:48:42Z","volume":1,"author":[{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7196"},{"status":"public","relation":"popular_science","id":"5559"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"year":"2018","file_date_updated":"2020-07-14T12:47:10Z","ec_funded":1,"article_number":"71","date_published":"2018-06-14T00:00:00Z","publication":"Communications Biology","citation":{"short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018).","mla":"Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology, vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology. Springer Nature, 2018. https://doi.org/10.1038/s42003-018-0078-7.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71."},"day":"14","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"checksum":"a9db825fa3b64a51ff3de035ec973b3e","date_created":"2018-12-18T13:37:04Z","date_updated":"2020-07-14T12:47:10Z","relation":"main_file","file_id":"5752","content_type":"application/pdf","file_size":1804194,"creator":"dernst","access_level":"open_access","file_name":"2018_CommBiology_Pavlogiannis.pdf"}],"oa_version":"Published Version","pubrep_id":"1045","ddc":["004","519","576"],"title":"Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory","status":"public","intvolume":" 1","_id":"5751","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures."}],"issue":"1","type":"journal_article"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:11Z","abstract":[{"lang":"eng","text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants."}],"type":"research_data","oa_version":"Published Version","file":[{"creator":"cfraisse","file_size":369837892,"content_type":"application/zip","file_name":"FileS1.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:52Z","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_id":"5758","relation":"main_file"},{"relation":"main_file","file_id":"5759","date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","checksum":"3592e467b4d8206650860b612d6e12f3","file_name":"FileS2.zip","access_level":"open_access","file_size":84856909,"content_type":"application/zip","creator":"cfraisse"},{"date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","checksum":"c37ac5d5437c457338afc128c1240655","file_id":"5760","relation":"main_file","creator":"cfraisse","content_type":"text/plain","file_size":881133,"file_name":"FileS3.txt","access_level":"open_access"},{"creator":"cfraisse","file_size":883742,"content_type":"text/plain","access_level":"open_access","file_name":"FileS4.txt","checksum":"943dfd14da61817441e33e3e3cb8cdb9","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","file_id":"5761","relation":"main_file"},{"date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","relation":"main_file","file_id":"5762","file_size":2495437,"content_type":"text/plain","creator":"cfraisse","file_name":"FileS5.txt","access_level":"open_access"},{"creator":"cfraisse","content_type":"text/plain","file_size":15913457,"file_name":"FileS6.txt","access_level":"open_access","date_created":"2018-12-19T14:19:50Z","date_updated":"2020-07-14T12:47:11Z","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_id":"5763","relation":"main_file"},{"relation":"main_file","file_id":"5764","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_name":"FileS7.txt","access_level":"open_access","content_type":"text/plain","file_size":2584120,"creator":"cfraisse"},{"access_level":"open_access","file_name":"FileS8.txt","creator":"cfraisse","file_size":2446059,"content_type":"text/plain","file_id":"5765","relation":"main_file","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z"},{"checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","relation":"main_file","file_id":"5766","file_size":100737,"content_type":"text/plain","creator":"cfraisse","access_level":"open_access","file_name":"FileS9.txt"}],"date_updated":"2024-02-21T13:59:18Z","date_created":"2018-12-19T14:22:35Z","contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","last_name":"Puixeu Sala"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"6089"}]},"author":[{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["576"],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","year":"2018","_id":"5757","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"No","month":"12","day":"19","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"doi":"10.15479/at:ista:/5757","date_published":"2018-12-19T00:00:00Z","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"citation":{"chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757.","short":"C. Fraisse, (2018).","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757"},"oa":1},{"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:44:57Z","date_created":"2019-04-08T13:55:20Z","checksum":"d4dad55a7513f345706aaaba90cb1bb8","relation":"main_file","file_id":"6241","content_type":"application/pdf","file_size":5801709,"creator":"dernst","file_name":"2018_thesis_Alt.pdf","access_level":"open_access"},{"access_level":"closed","file_name":"2018_thesis_Alt_source.zip","creator":"dernst","content_type":"application/zip","file_size":3802059,"file_id":"6242","relation":"source_file","checksum":"d73fcf46300dce74c403f2b491148ab4","date_created":"2019-04-08T13:55:20Z","date_updated":"2020-07-14T12:44:57Z"}],"pubrep_id":"1040","status":"public","ddc":["515","519"],"title":"Dyson equation and eigenvalue statistics of random matrices","_id":"149","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2018-07-12T00:00:00Z","page":"456","citation":{"chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040.","mla":"Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","apa":"Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040"},"day":"12","article_processing_charge":"No","has_accepted_license":"1","date_created":"2018-12-11T11:44:53Z","date_updated":"2024-02-22T14:34:33Z","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1677"},{"id":"550","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6183"},{"id":"566","relation":"part_of_dissertation","status":"public"},{"id":"1010","relation":"part_of_dissertation","status":"public"},{"id":"6240","status":"public","relation":"part_of_dissertation"},{"id":"6184","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"LaEr"}],"year":"2018","file_date_updated":"2020-07-14T12:44:57Z","publist_id":"7772","ec_funded":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:TH_1040","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"07","publication_identifier":{"issn":["2663-337X"]}},{"abstract":[{"text":"Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field.","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"415","status":"public","title":"Effect of a magnetic field on molecule–solvent angular momentum transfer","intvolume":" 148","day":"14","article_processing_charge":"No","scopus_import":"1","date_published":"2018-03-14T00:00:00Z","publication":"The Journal of Chemical Physics","citation":{"ista":"Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307.","apa":"Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5017591","ieee":"W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” The Journal of Chemical Physics, vol. 148, no. 10. AIP Publishing, 2018.","ama":"Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591","chicago":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5017591.","mla":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591.","short":"W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018)."},"article_type":"original","publist_id":"7408","ec_funded":1,"article_number":"104307","author":[{"full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10759"}]},"date_updated":"2024-02-28T13:01:59Z","date_created":"2018-12-11T11:46:21Z","volume":148,"acknowledgement":"We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","year":"2018","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","month":"03","doi":"10.1063/1.5017591","language":[{"iso":"eng"}],"external_id":{"isi":["000427517200065"],"arxiv":["1711.09904"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09904"}],"quality_controlled":"1","isi":1,"project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}]},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"30","citation":{"mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336"},"publication":"ACM Transactions on Graphics","date_published":"2018-07-30T00:00:00Z","alternative_title":["SIGGRAPH"],"type":"journal_article","issue":"4","abstract":[{"text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface.","lang":"eng"}],"intvolume":" 37","status":"public","title":"Water surface wavelets","ddc":["000"],"_id":"134","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"5744","relation":"main_file","date_created":"2018-12-18T09:59:23Z","date_updated":"2020-07-14T12:44:45Z","checksum":"db75ebabe2ec432bf41389e614d6ef62","file_name":"2018_ACM_Jeschke.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":22185016}],"month":"07","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"external_id":{"isi":["000448185000055"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1145/3197517.3201336","article_number":"94","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"publist_id":"7789","file_date_updated":"2020-07-14T12:44:45Z","publisher":"ACM","department":[{"_id":"ChWo"}],"publication_status":"published","year":"2018","volume":37,"date_updated":"2024-02-28T13:58:51Z","date_created":"2018-12-11T11:44:48Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/"}]},"author":[{"first_name":"Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"},{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"last_name":"Mueller Fischer","first_name":"Matthias","full_name":"Mueller Fischer, Matthias"},{"full_name":"Chentanez, Nuttapong","first_name":"Nuttapong","last_name":"Chentanez"},{"first_name":"Miles","last_name":"Macklin","full_name":"Macklin, Miles"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"}]},{"article_number":"165301","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2018","date_updated":"2024-02-28T13:15:09Z","date_created":"2019-04-17T10:53:38Z","volume":121,"author":[{"first_name":"Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"last_name":"Tscherbul","first_name":"Timur","full_name":"Tscherbul, Timur"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","description":"News on IST Homepage","relation":"press_release"}]},"month":"10","quality_controlled":"1","isi":1,"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"oa":1,"external_id":{"arxiv":["1803.07990"],"isi":["000447468400008"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.121.165301","type":"journal_article","abstract":[{"lang":"eng","text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment."}],"issue":"16","status":"public","title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","intvolume":" 121","_id":"6339","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","day":"16","article_processing_charge":"No","publication":"Physical Review Letters","citation":{"ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301."},"date_published":"2018-10-16T00:00:00Z"},{"month":"10","oa":1,"external_id":{"arxiv":["1803.07990"]},"main_file_link":[{"url":"https://arxiv.org/abs/1803.07990","open_access":"1"}],"quality_controlled":"1","project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"doi":"10.1103/PhysRevLett.121.165301","language":[{"iso":"eng"}],"article_number":"165301","publist_id":"8025","year":"2018","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","author":[{"full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","first_name":"Giacomo"},{"first_name":"Timur","last_name":"Tscherbul","full_name":"Tscherbul, Timur"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"date_created":"2018-12-11T11:46:22Z","date_updated":"2024-02-28T13:14:53Z","volume":121,"scopus_import":"1","day":"16","article_processing_charge":"No","publication":"Physical Review Letters","citation":{"apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301."},"date_published":"2018-10-16T00:00:00Z","type":"journal_article","abstract":[{"text":"We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. ","lang":"eng"}],"issue":"16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"417","status":"public","title":"Diagrammatic Monte Carlo approach to rotating molecular impurities","intvolume":" 121","oa_version":"Preprint"},{"month":"04","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"doi":"10.1105/tpc.17.00785","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["29511054"],"isi":["000429441400018"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2022-05-23T09:12:38Z","publist_id":"7417","ec_funded":1,"author":[{"last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek"},{"orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","last_name":"Kania","full_name":"Kania, Urszula"},{"first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"full_name":"De Jaeger, Geert","last_name":"De Jaeger","first_name":"Geert"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6269"}]},"date_updated":"2024-03-28T23:30:06Z","date_created":"2018-12-11T11:46:20Z","volume":30,"acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","year":"2018","pmid":1,"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-04-09T00:00:00Z","publication":"The Plant Cell","citation":{"mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785.","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018."},"article_type":"original","page":"700 - 716","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_PlantCell_Adamowski.pdf","file_size":4407538,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"11406","checksum":"4e165e653b67d3f0684697f21aace5a1","success":1,"date_updated":"2022-05-23T09:12:38Z","date_created":"2022-05-23T09:12:38Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"412","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","ddc":["580"],"status":"public","intvolume":" 30"},{"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"With the advent of optogenetics, it became possible to change the activity of a targeted population of neurons in a temporally controlled manner. To combine the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics, we have developed a closed-loop recording system that allows for the actual electrophysiological signal to be used as a trigger for the laser light mediating the optogenetic intervention. We have optimized the weight, size, and shape of the corresponding implant to make it compatible with the size, force, and movements of a behaving mouse, and we have shown that the system can efficiently block sharp wave ripple (SWR) events using those events themselves as a trigger. To demonstrate the full potential of the optogenetic recording system we present a pilot study addressing the contribution of SWR events to learning in a complex behavioral task."}],"intvolume":" 5","ddc":["570"],"status":"public","title":"Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5914","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3746884,"creator":"dernst","access_level":"open_access","file_name":"2018_ENeuro_Guerrero.pdf","checksum":"f4915d45fc7ad4648b7b7a13fdecca01","date_created":"2019-02-05T12:48:36Z","date_updated":"2020-07-14T12:47:13Z","relation":"main_file","file_id":"5921"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","citation":{"ieee":"D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience, 2018.","apa":"Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K. (2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018","ista":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 5(4), e0087.","ama":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018","chicago":"Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.","short":"D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018).","mla":"Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018."},"publication":"eNeuro","date_published":"2018-07-27T00:00:00Z","article_number":"e0087","ec_funded":1,"file_date_updated":"2020-07-14T12:47:13Z","publisher":"Society of Neuroscience","department":[{"_id":"JoCs"}],"publication_status":"published","year":"2018","volume":5,"date_created":"2019-02-03T22:59:16Z","date_updated":"2024-03-28T23:30:10Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6849"}]},"author":[{"first_name":"Dámaris K","last_name":"Rangel Guerrero","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374","full_name":"Rangel Guerrero, Dámaris K"},{"full_name":"Donnett, James G.","first_name":"James G.","last_name":"Donnett"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"},{"full_name":"Kovács, Krisztián","orcid":"0000-0001-6251-1007","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","last_name":"Kovács","first_name":"Krisztián"}],"month":"07","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"I2072-B27","_id":"257D4372-B435-11E9-9278-68D0E5697425","name":"Interneuron plasticity during spatial learning","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000443994700007"]},"language":[{"iso":"eng"}],"doi":"10.1523/ENEURO.0087-18.2018"},{"day":"23","article_processing_charge":"No","scopus_import":"1","date_published":"2018-03-23T00:00:00Z","publication":"Science","citation":{"mla":"Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662.","short":"M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411.","chicago":"Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662.","ama":"Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411. doi:10.1126/science.aal3662","ista":"Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411.","apa":"Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aal3662","ieee":"M. Brown et al., “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018."},"article_type":"original","page":"1408 - 1411","abstract":[{"lang":"eng","text":"During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined."}],"issue":"6382","type":"journal_article","oa_version":"Published Version","_id":"402","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice","status":"public","intvolume":" 359","month":"03","doi":"10.1126/science.aal3662","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aal3662"}],"external_id":{"isi":["000428043600047"],"pmid":["29567714"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publist_id":"7428","author":[{"full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Markus"},{"full_name":"Assen, Frank P","first_name":"Frank P","last_name":"Assen","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119"},{"orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"first_name":"Jun","last_name":"Abe","full_name":"Abe, Jun"},{"last_name":"Schachner","first_name":"Helga","full_name":"Schachner, Helga"},{"full_name":"Asfour, Gabriele","last_name":"Asfour","first_name":"Gabriele"},{"full_name":"Bagó Horváth, Zsuzsanna","last_name":"Bagó Horváth","first_name":"Zsuzsanna"},{"full_name":"Stein, Jens","first_name":"Jens","last_name":"Stein"},{"last_name":"Uhrin","first_name":"Pavel","full_name":"Uhrin, Pavel"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6947"}]},"date_updated":"2024-03-28T23:30:09Z","date_created":"2018-12-11T11:46:16Z","volume":359,"acknowledgement":"M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line.","year":"2018","pmid":1,"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"MiSi"}]},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"88","citation":{"chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_992.","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018.","mla":"Tarlungeanu, Dora-Clara. The Branched Chain Amino Acids in Autism Spectrum Disorders . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_992.","apa":"Tarlungeanu, D.-C. (2018). The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:10.15479/AT:ISTA:th_992"},"date_published":"2018-03-01T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. ","lang":"eng"}],"status":"public","title":"The branched chain amino acids in autism spectrum disorders ","ddc":["570","616"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"395","oa_version":"Published Version","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":43684035,"creator":"dernst","access_level":"closed","embargo_to":"open_access","file_name":"2018_Thesis_Tarlungeanu_source.docx","checksum":"9f5231c96e0ad945040841a8630232da","date_created":"2019-04-05T09:19:17Z","date_updated":"2021-02-11T23:30:15Z","relation":"source_file","file_id":"6217"},{"creator":"dernst","content_type":"application/pdf","file_size":30511532,"access_level":"open_access","file_name":"2018_Thesis_Tarlungeanu.pdf","checksum":"0c33c370aa2010df5c552db57a6d01e9","date_updated":"2021-02-11T11:17:16Z","date_created":"2019-04-05T09:19:17Z","file_id":"6218","embargo":"2018-03-15","relation":"main_file"}],"pubrep_id":"992","publication_identifier":{"issn":["2663-337X"]},"month":"03","project":[{"_id":"25473368-B435-11E9-9278-68D0E5697425","grant_number":"F03523","name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"supervisor":[{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_992","publist_id":"7434","file_date_updated":"2021-02-11T23:30:15Z","department":[{"_id":"GaNo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","date_updated":"2023-09-07T12:38:59Z","date_created":"2018-12-11T11:46:14Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1183"}]},"author":[{"full_name":"Tarlungeanu, Dora-Clara","last_name":"Tarlungeanu","first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87"}]},{"year":"2018","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","last_name":"Case","full_name":"Case, Matthew J"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"682"}]},"date_created":"2018-12-11T11:44:22Z","date_updated":"2023-09-07T12:39:22Z","file_date_updated":"2021-02-11T23:30:13Z","publist_id":"8003","oa":1,"doi":"10.15479/AT:ISTA:th_1032","supervisor":[{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"51","status":"public","title":"From the left to the right: A tale of asymmetries, environments, and hippocampal development","ddc":["571","576"],"pubrep_id":"1032","file":[{"embargo_to":"open_access","file_name":"2018_Thesis_Case_Source.doc","access_level":"closed","file_size":141270528,"content_type":"application/msword","creator":"dernst","relation":"source_file","file_id":"6251","date_updated":"2021-02-11T23:30:13Z","date_created":"2019-04-09T07:16:26Z","checksum":"dcc7b55619d8509dd62b8e99d6cdee44"},{"file_name":"2018_Thesis_Case.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":15193621,"file_id":"6252","embargo":"2019-07-05","relation":"main_file","date_created":"2019-04-09T07:16:23Z","date_updated":"2021-02-11T11:17:14Z","checksum":"f69fdd5c8709c4e618aa8c1a1221153d"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Asymmetries have long been known about in the central nervous system. From gross anatomical differences, such as the presence of the parapineal organ in only one hemisphere of the developing zebrafish, to more subtle differences in activity between both hemispheres, as seen in freely roaming animals or human participants under PET and fMRI imaging analysis. The presence of asymmetries has been demonstrated to have huge behavioural implications, with their disruption often leading to the generation of neurological disorders, memory problems, changes in personality, and in an organism's health and well-being. For my Ph.D. work I aimed to tackle two important avenues of research. The first being the process of input-side dependency in the hippocampus, with the goal of finding a key gene responsible for its development (Gene X). The second project was to do with experience-induced laterality formation in the hippocampus. Specifically, how laterality in the synapse density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental enrichment. Through unilateral tracer injections into the CA3, I was able to selectively measure the properties of synapses within the CA1 and investigate how they differed based upon which hemisphere the presynaptic neurone originated. Having found the existence of a previously unreported reversed (left-isomerism) i.v. mutant, through morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate a key gene responsible for the process of left or right determination of inputs to the CA1 s.r.. This work relates to the previous finding of input-side dependent asymmetry in the wild-type rodent, where the origin of the projecting neurone to the CA1 will determine the morphology of a synapse, to a greater degree than the hemisphere in which the projection terminates. Using left- and right-isomerism i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like (Evl) as a potential target for Gene X. In relation to this topic, I also highlight my work in the recently published paper of how knockout of PirB can lead to a lack of input-side dependency in the murine hippocampus. For the second question, I show that the environmental enrichment paradigm will lead to an asymmetry in the synapse densities in the hippocampus of mice. I also highlight that the nature of the enrichment is of less consequence than the process of enrichment itself. I demonstrate that the CA3 region will dramatically alter its projection targets, in relation to environmental stimulation, with the asymmetry in synaptic density, caused by enrichment, relying heavily on commissural fibres. I also highlight the vital importance of input-side dependent asymmetry, as a necessary component of experience-dependent laterality formation in the CA1 s.r.. However, my results suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism also at play. Upon further investigation, I highlight the significant, and highly important, finding that the changes seen in the CA1 s.r. were predominantly caused through projections from the left-CA3, with the right-CA3 having less involvement in this mechanism.","lang":"eng"}],"citation":{"short":"M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development, Institute of Science and Technology Austria, 2018.","mla":"Case, Matthew J. From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1032.","chicago":"Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1032.","ama":"Case MJ. From the left to the right: A tale of asymmetries, environments, and hippocampal development. 2018. doi:10.15479/AT:ISTA:th_1032","apa":"Case, M. J. (2018). From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1032","ieee":"M. J. Case, “From the left to the right: A tale of asymmetries, environments, and hippocampal development,” Institute of Science and Technology Austria, 2018.","ista":"Case MJ. 2018. From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria."},"page":"186","date_published":"2018-06-27T00:00:00Z","day":"27","article_processing_charge":"No","has_accepted_license":"1"},{"publist_id":"8046","file_date_updated":"2021-02-11T11:17:16Z","author":[{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","first_name":"Susanne","last_name":"Laukoter","full_name":"Laukoter, Susanne"}],"date_created":"2018-12-11T11:44:08Z","date_updated":"2023-09-07T12:40:44Z","year":"2018","department":[{"_id":"SiHi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"11","doi":"10.15479/AT:ISTA:th1057","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"degree_awarded":"PhD","oa":1,"abstract":[{"lang":"eng","text":"Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1057","oa_version":"Published Version","file":[{"file_name":"Thesis_LaukoterSusanne_FINAL.docx","embargo_to":"open_access","access_level":"closed","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":17949175,"file_id":"6396","relation":"source_file","date_updated":"2019-11-23T23:30:03Z","date_created":"2019-05-10T07:47:04Z","checksum":"41fdbf5fdce312802935d88a8ad9932c"},{"access_level":"open_access","file_name":"Thesis_LaukoterSusanne_FINAL.pdf","file_size":21187245,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6397","embargo":"2019-11-21","checksum":"53001a9a0c9e570e598d861bb0af28aa","date_updated":"2021-02-11T11:17:16Z","date_created":"2019-05-10T07:47:04Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10","ddc":["570"],"title":"Role of genomic imprinting in cerebral cortex development","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"21","date_published":"2018-11-21T00:00:00Z","citation":{"ama":"Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:10.15479/AT:ISTA:th1057","ieee":"S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018.","apa":"Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057","ista":"Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria.","short":"S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018.","mla":"Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057.","chicago":"Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057."},"page":"1 - 139"},{"date_created":"2018-12-11T11:45:49Z","date_updated":"2023-09-07T12:39:44Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1321"}]},"author":[{"full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiSi"}],"publication_status":"published","year":"2018","acknowledgement":"First of all I would like to thank Michael Sixt for giving me the opportunity to work in \r\nhis group and for his support throughout the years. He is a truly inspiring person and \r\nthe best boss one can imagine. I would also like to thank all current and past \r\nmembers of the Sixt group for their help and the great working atmosphere in the lab. \r\nIt is a true privilege to work with such a bright, funny and friendly group of people and \r\nI’m proud that I could be part of it. Furthermore, I would like to say ‘thank you’ to Daria Siekhaus for all the meetings and discussion we had throughout the years \r\nand to Federica Benvenuti for being part of my committee. I am also grateful to Jack \r\nMerrin in the nanofabrication facility and all the people working in the bioimaging-\r\n, the electron microscopy- and the preclinical facilities.","publist_id":"7542","file_date_updated":"2021-02-11T23:30:17Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"doi":"10.15479/AT:ISTA:th_998","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"04","file":[{"file_id":"6219","relation":"source_file","checksum":"d5e3edbac548c26c1fa43a4b37a54a4c","date_updated":"2021-02-11T23:30:17Z","date_created":"2019-04-05T09:23:11Z","access_level":"closed","file_name":"PhD_thesis_AlexLeithner_final_version.docx","embargo_to":"open_access","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":29027671},{"date_updated":"2021-02-11T11:17:16Z","date_created":"2019-04-05T09:23:11Z","checksum":"071f7476db29e41146824ebd0697cb10","relation":"main_file","embargo":"2019-04-15","file_id":"6220","file_size":66045341,"content_type":"application/pdf","creator":"dernst","file_name":"PhD_thesis_AlexLeithner.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"998","ddc":["571","599","610"],"title":"Branched actin networks in dendritic cell biology","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"323","abstract":[{"lang":"eng","text":"In the here presented thesis, we explore the role of branched actin networks in cell migration and antigen presentation, the two most relevant processes in dendritic cell biology. Branched actin networks construct lamellipodial protrusions at the leading edge of migrating cells. These are typically seen as adhesive structures, which mediate force transduction to the extracellular matrix that leads to forward locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found that the resulting cells lack lamellipodial protrusions. Instead, depending on the maturation state, one or multiple filopodia were formed. By challenging these cells in a variety of migration assays we found that lamellipodial protrusions are dispensable for the locomotion of leukocytes and actually dampen the speed of migration. However, lamellipodia are critically required to negotiate complex environments that DCs experience while they travel to the next draining lymph node. Taken together our results suggest that leukocyte lamellipodia have rather a sensory- than a force transducing function. Furthermore, we show for the first time structure and dynamics of dendritic cell F-actin at the immunological synapse with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension, leading to an altered ultrastructure of the immunological synapse and severe T cell priming defects. These results point towards a previously unappreciated role of the cellular mechanics of dendritic cells in T cell activation. Additionally, we present a novel cell culture based system for the differentiation of dendritic cells from conditionally immortalized hematopoietic precursors. These precursor cells are genetically tractable via the CRISPR/Cas9 system while they retain their ability to differentiate into highly migratory dendritic cells and other immune cells. This will foster the study of all aspects of dendritic cell biology and beyond. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2018-04-12T00:00:00Z","page":"99","citation":{"chicago":"Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_998.","short":"A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute of Science and Technology Austria, 2018.","mla":"Leithner, Alexander F. Branched Actin Networks in Dendritic Cell Biology. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_998.","ieee":"A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute of Science and Technology Austria, 2018.","apa":"Leithner, A. F. (2018). Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_998","ista":"Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria.","ama":"Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:10.15479/AT:ISTA:th_998"},"has_accepted_license":"1","article_processing_charge":"No","day":"12"},{"status":"public","title":"Identification and characterization of novel auxin-cytokinin cross-talk components","ddc":["570"],"_id":"539","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"6226","date_created":"2019-04-05T09:37:56Z","date_updated":"2020-12-02T23:30:08Z","checksum":"0c9d6d1c80d9857e6e545213467bbcb2","embargo_to":"open_access","file_name":"2018_Hurny_thesis_source.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":28112114,"creator":"dernst"},{"file_name":"2018_Hurny_thesis.pdf","access_level":"open_access","file_size":12524427,"content_type":"application/pdf","creator":"dernst","relation":"main_file","embargo":"2019-07-10","file_id":"6227","date_updated":"2020-12-02T09:52:16Z","date_created":"2019-04-05T09:37:55Z","checksum":"ecbe481a1413d270bd501b872c7ed54f"}],"pubrep_id":"930","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth."}],"page":"147","citation":{"mla":"Hurny, Andrej. Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_930.","short":"A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018.","chicago":"Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_930.","ama":"Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:10.15479/AT:ISTA:th_930","ista":"Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria.","apa":"Hurny, A. (2018). Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_930","ieee":"A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018."},"date_published":"2018-01-01T00:00:00Z","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"EvBe"}],"year":"2018","date_created":"2018-12-11T11:47:03Z","date_updated":"2023-09-07T12:41:06Z","author":[{"full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Hurny","first_name":"Andrej"}],"related_material":{"record":[{"id":"1024","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2020-12-02T23:30:08Z","publist_id":"7277","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"degree_awarded":"PhD","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_930","month":"01","publication_identifier":{"issn":["2663-337X"]}},{"abstract":[{"text":"The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"6236","checksum":"7db4415e435590fa33542c7b0a0321d7","date_updated":"2021-02-11T23:30:22Z","date_created":"2019-04-08T13:36:01Z","access_level":"closed","embargo_to":"open_access","file_name":"2018_Thesis_Gridchyn_source.docx","file_size":7666687,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst"},{"embargo":"2019-08-29","file_id":"6237","relation":"main_file","date_created":"2019-04-08T13:36:01Z","date_updated":"2021-02-11T11:17:18Z","checksum":"f96f3fe8979f7b1e6db6acaca962b10c","file_name":"2018_Thesis_Gridchyn.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":6034153}],"pubrep_id":"1042","status":"public","title":"Reactivation content is important for consolidation of spatial memory","ddc":["573"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"48","article_processing_charge":"No","has_accepted_license":"1","day":"27","date_published":"2018-08-27T00:00:00Z","page":"104","citation":{"chicago":"Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1042.","short":"I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018.","mla":"Gridchyn, Igor. Reactivation Content Is Important for Consolidation of Spatial Memory. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1042.","ieee":"I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018.","apa":"Gridchyn, I. (2018). Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1042","ista":"Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria.","ama":"Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:10.15479/AT:ISTA:th_1042"},"publist_id":"8006","file_date_updated":"2021-02-11T23:30:22Z","date_updated":"2023-09-07T12:42:44Z","date_created":"2018-12-11T11:44:21Z","author":[{"last_name":"Gridchyn","first_name":"Igor","orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","full_name":"Gridchyn, Igor"}],"department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","publication_identifier":{"issn":["2663-337X"]},"month":"08","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:th_1042","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Siekhaus, Daria E","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th1064","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"07","date_created":"2018-12-11T11:44:08Z","date_updated":"2023-09-07T12:43:10Z","author":[{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","last_name":"Belyaeva","full_name":"Belyaeva, Vera"}],"department":[{"_id":"DaSi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","publist_id":"8047","file_date_updated":"2021-02-11T11:17:16Z","date_published":"2018-07-01T00:00:00Z","page":"96","citation":{"mla":"Belyaeva, Vera. Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1064.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018.","chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1064.","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:10.15479/AT:ISTA:th1064","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","apa":"Belyaeva, V. (2018). Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1064"},"has_accepted_license":"1","article_processing_charge":"No","day":"01","oa_version":"Published Version","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":102737483,"creator":"dernst","embargo_to":"open_access","file_name":"2018_Thesis_Belyaeva_source.docx","access_level":"closed","date_updated":"2020-07-14T12:48:14Z","date_created":"2019-04-08T14:13:12Z","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","relation":"source_file","file_id":"6243"},{"date_updated":"2021-02-11T11:17:16Z","date_created":"2019-04-08T14:14:08Z","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","embargo":"2019-11-19","file_id":"6244","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":88077843,"file_name":"2018_Thesis_Belyaeva.pdf","access_level":"open_access"}],"pubrep_id":"1064","title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","status":"public","ddc":["570"],"_id":"9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"oa":1,"doi":"10.15479/at:ista:th_1055","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"publication_identifier":{"issn":["2663-337X"]},"month":"10","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HaJa"}],"publication_status":"published","related_material":{"record":[{"id":"7132","status":"public","relation":"new_edition"}]},"author":[{"full_name":"Mckenzie, Catherine","last_name":"Mckenzie","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-04-09T14:13:39Z","date_updated":"2023-09-07T13:02:37Z","file_date_updated":"2021-02-11T11:17:16Z","citation":{"ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria.","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","apa":"Mckenzie, C. (2018). Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th_1055","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:10.15479/at:ista:th_1055","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:th_1055.","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission . Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:th_1055.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018."},"page":"95","date_published":"2018-10-31T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"31","_id":"6266","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["571","573"],"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","status":"public","pubrep_id":"1055","oa_version":"Published Version","file":[{"creator":"dernst","file_size":4906420,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_Thesis_McKenzie.pdf","checksum":"9d2c2dca04b00e485470c28b262af59a","date_created":"2019-04-09T14:12:40Z","date_updated":"2021-02-11T11:17:16Z","file_id":"6267","embargo":"2019-11-24","relation":"main_file"},{"date_created":"2019-04-09T14:12:40Z","date_updated":"2020-07-14T12:47:25Z","checksum":"50b58c272899601bc6fd9642c4dc97f1","relation":"source_file","file_id":"6268","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":5053545,"creator":"dernst","embargo_to":"open_access","file_name":"2018_Thesis_McKenzie_source.docx","access_level":"closed"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. "}]},{"date_published":"2018-06-22T00:00:00Z","citation":{"ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:10.15479/AT:ISTA:TH_1031","ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","apa":"Capek, D. (2018). Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1031","ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria.","short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","mla":"Capek, Daniel. Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1031.","chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1031."},"page":"95","has_accepted_license":"1","article_processing_charge":"No","day":"22","pubrep_id":"1031","file":[{"content_type":"application/pdf","file_size":31576521,"creator":"dernst","file_name":"2018_Thesis_Capek.pdf","access_level":"open_access","date_updated":"2021-02-11T11:17:17Z","date_created":"2019-04-08T13:42:26Z","checksum":"d3eca3dcacb67bffdde6e6609c31cdd0","relation":"main_file","embargo":"2019-06-25","file_id":"6238"},{"access_level":"closed","embargo_to":"open_access","file_name":"2018_Thesis_Capek_source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":38992956,"creator":"dernst","relation":"source_file","file_id":"6239","checksum":"876deb14067e638aba65d209668bd821","date_created":"2019-04-08T13:42:27Z","date_updated":"2021-02-11T23:30:21Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"50","ddc":["570","591","596"],"status":"public","title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration","abstract":[{"lang":"eng","text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:TH_1031","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"06","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1100"},{"id":"661","status":"public","relation":"part_of_dissertation"},{"id":"676","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","first_name":"Daniel","last_name":"Capek"}],"date_created":"2018-12-11T11:44:21Z","date_updated":"2023-09-07T12:48:16Z","year":"2018","department":[{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publist_id":"8004","file_date_updated":"2021-02-11T23:30:21Z"},{"publication_identifier":{"issn":["2663-337X"]},"month":"10","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"doi":"10.15479/AT:ISTA:th1059","oa":1,"publist_id":"8029","file_date_updated":"2021-02-11T11:17:14Z","date_updated":"2023-09-07T12:48:43Z","date_created":"2018-12-11T11:44:14Z","related_material":{"record":[{"id":"704","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Steinrück, Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719","first_name":"Magdalena","last_name":"Steinrück"}],"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","has_accepted_license":"1","article_processing_charge":"No","day":"30","date_published":"2018-10-30T00:00:00Z","page":"109","citation":{"chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1059.","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","mla":"Steinrück, Magdalena. The Influence of Sequence Context on the Evolution of Bacterial Gene Expression. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1059.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","apa":"Steinrück, M. (2018). The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1059","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:10.15479/AT:ISTA:th1059"},"abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"date_created":"2019-02-08T10:51:22Z","date_updated":"2020-07-14T12:45:43Z","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","file_id":"5941","relation":"source_file","creator":"dernst","file_size":9190845,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Steinrueck_final.docx","embargo_to":"open_access","access_level":"closed"},{"file_id":"5942","embargo":"2019-11-02","relation":"main_file","checksum":"3def8b7854c8b42d643597ce0215efac","date_created":"2019-02-08T10:51:22Z","date_updated":"2021-02-11T11:17:14Z","access_level":"open_access","file_name":"Thesis_Steinrueck_final.pdf","creator":"dernst","content_type":"application/pdf","file_size":7521973}],"pubrep_id":"1059","ddc":["576","579"],"title":"The influence of sequence context on the evolution of bacterial gene expression","status":"public","_id":"26","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"year":"2018","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"GeKa"}],"author":[{"first_name":"Arne","last_name":"Hollmann","full_name":"Hollmann, Arne"},{"full_name":"Jirovec, Daniel","first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"},{"first_name":"Maciej","last_name":"Kucharski","full_name":"Kucharski, Maciej"},{"full_name":"Kissinger, Dietmar","last_name":"Kissinger","first_name":"Dietmar"},{"full_name":"Fischer, Gunter","first_name":"Gunter","last_name":"Fischer"},{"full_name":"Schreiber, Lars R.","last_name":"Schreiber","first_name":"Lars R."}],"related_material":{"record":[{"id":"10058","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:27Z","date_created":"2019-01-10T14:22:23Z","volume":89,"article_number":"114701","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.09522"}],"oa":1,"external_id":{"arxiv":["1804.09522"],"isi":["000451735700054"]},"isi":1,"quality_controlled":"1","doi":"10.1063/1.5038258","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["00346748"]},"_id":"5816","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"30 GHz-voltage controlled oscillator operating at 4 K","status":"public","intvolume":" 89","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field.","lang":"eng"}],"issue":"11","publication":"Review of Scientific Instruments","citation":{"ama":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 2018;89(11). doi:10.1063/1.5038258","ieee":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R. Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” Review of Scientific Instruments, vol. 89, no. 11. AIP Publishing, 2018.","apa":"Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., & Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258","ista":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 89(11), 114701.","short":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018).","mla":"Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments, vol. 89, no. 11, 114701, AIP Publishing, 2018, doi:10.1063/1.5038258.","chicago":"Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments. AIP Publishing, 2018. https://doi.org/10.1063/1.5038258."},"date_published":"2018-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6263","status":"public","title":"Genetic determinants of antibiotic resistance evolution","ddc":["570","576","579"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_Thesis_Lukacisinova.pdf","creator":"dernst","content_type":"application/pdf","file_size":5656866,"file_id":"6264","embargo":"2020-01-25","relation":"main_file","checksum":"fc60585c9eaad868ac007004ef130908","date_updated":"2021-02-11T11:17:17Z","date_created":"2019-04-09T13:49:24Z"},{"checksum":"264057ec0a92ab348cc83b41f021ba92","date_created":"2019-04-09T13:49:23Z","date_updated":"2020-07-14T12:47:25Z","relation":"source_file","file_id":"6265","file_size":5168054,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst","access_level":"closed","embargo_to":"open_access","file_name":"2018_Thesis_Lukacisinova_source.docx"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Antibiotic resistance can emerge spontaneously through genomic mutation and render treatment ineffective. To counteract this process, in addition to the discovery and description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand its determinantsis needed. To address this challenge, this thesisuncoversnew genetic determinants of resistance evolvability using a customized robotic setup, exploressystematic ways in which resistance evolution is perturbed due to dose-responsecharacteristics of drugs and mutation rate differences,and mathematically investigates the evolutionary fate of one specific type of evolvability modifier -a stress-induced mutagenesis allele.We find severalgenes which strongly inhibit or potentiate resistance evolution. In order to identify them, we first developedan automated high-throughput feedback-controlled protocol whichkeeps the population size and selection pressure approximately constant for hundreds of cultures by dynamically re-diluting the cultures and adjusting the antibiotic concentration. We implementedthis protocol on a customized liquid handling robot and propagated 100 different gene deletion strains of Escherichia coliin triplicate for over 100 generations in tetracycline and in chloramphenicol, and comparedtheir adaptation rates.We find a diminishing returns pattern, where initially sensitive strains adapted more compared to less sensitive ones. Our data uncover that deletions of certain genes which do not affect mutation rate,including efflux pump components, a chaperone and severalstructural and regulatory genes can strongly and reproducibly alterresistance evolution. Sequencing analysis of evolved populations indicates that epistasis with resistance mutations is the most likelyexplanation. This work could inspire treatment strategies in which targeted inhibitors of evolvability mechanisms will be given alongside antibiotics to slow down resistance evolution and extend theefficacy of antibiotics.We implemented astochasticpopulation genetics model, toverifyways in which general properties, namely, dose-response characteristics of drugs and mutation rates, influence evolutionary dynamics. In particular, under the exposure to antibiotics with shallow dose-response curves,bacteria have narrower distributions of fitness effects of new mutations. We show that in silicothis also leads to slower resistance evolution. We see and confirm with experiments that increased mutation rates, apart from speeding up evolution, also leadto high reproducibility of phenotypic adaptation in a context of continually strong selection pressure.Knowledge of these patterns can aid in predicting the dynamics of antibiotic resistance evolutionand adapting treatment schemes accordingly.Focusing on a previously described type of evolvability modifier –a stress-induced mutagenesis allele –we find conditions under which it can persist in a population under periodic selectionakin to clinical treatment. We set up a deterministic infinite populationcontinuous time model tracking the frequencies of a mutator and resistance allele and evaluate various treatment schemes in how well they maintain a stress-induced mutator allele. In particular,a high diversity of stresses is crucial for the persistence of the mutator allele. This leads to a general trade-off where exactly those diversifying treatment schemes which are likely to decrease levels of resistance could lead to stronger selection of highly evolvable genotypes.In the long run, this work will lead to a deeper understanding of the genetic and cellular mechanisms involved in antibiotic resistance evolution and could inspire new strategies for slowing down its rate. ","lang":"eng"}],"citation":{"ama":"Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:10.15479/AT:ISTA:th1072","ista":"Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria.","apa":"Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072","ieee":"M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018.","mla":"Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072.","short":"M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018.","chicago":"Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072."},"page":"91","date_published":"2018-12-28T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"28","year":"2018","department":[{"_id":"ToBo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1619"},{"status":"public","relation":"part_of_dissertation","id":"696"},{"id":"1027","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Lukacisinova, Marta","first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"}],"date_updated":"2023-09-22T09:20:37Z","date_created":"2019-04-09T13:57:15Z","file_date_updated":"2021-02-11T11:17:17Z","oa":1,"doi":"10.15479/AT:ISTA:th1072","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["2663-337X"]},"month":"12"},{"month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000426693300011"]},"oa":1,"project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638"},{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","call_identifier":"FWF","name":"The role of Drosophila TNF alpha in immune cell invasion"},{"name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis","grant_number":"LSC16-021 ","_id":"2637E9C0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1534/g3.117.300452","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"publist_id":"7271","ec_funded":1,"file_date_updated":"2020-07-14T12:46:56Z","year":"2018","acknowledgement":" A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner by DOC Fellowships from the Austrian Academy of Sciences, ","department":[{"_id":"DaSi"}],"publisher":"Genetics Society of America","publication_status":"published","related_material":{"record":[{"id":"6530","relation":"research_paper"},{"id":"6543","relation":"research_paper"},{"id":"11193","status":"public","relation":"dissertation_contains"},{"id":"6546","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Attila","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","full_name":"György, Attila"},{"last_name":"Roblek","first_name":"Marko","orcid":"0000-0001-9588-1389","id":"3047D808-F248-11E8-B48F-1D18A9856A87","full_name":"Roblek, Marko"},{"full_name":"Ratheesh, Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7190-0776","first_name":"Aparna","last_name":"Ratheesh"},{"last_name":"Valosková","first_name":"Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","full_name":"Valosková, Katarina"},{"full_name":"Belyaeva, Vera","first_name":"Vera","last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"Wachner"},{"full_name":"Matsubayashi, Yutaka","first_name":"Yutaka","last_name":"Matsubayashi"},{"first_name":"Besaiz","last_name":"Sanchez Sanchez","full_name":"Sanchez Sanchez, Besaiz"},{"full_name":"Stramer, Brian","first_name":"Brian","last_name":"Stramer"},{"first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"}],"volume":8,"date_created":"2018-12-11T11:47:05Z","date_updated":"2024-03-28T23:30:30Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"chicago":"György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/g3.117.300452.","mla":"György, Attila, et al. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics, vol. 8, no. 3, Genetics Society of America, 2018, pp. 845–57, doi:10.1534/g3.117.300452.","short":"A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner, Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes, Genetics 8 (2018) 845–857.","ista":"György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857.","ieee":"A. György et al., “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” G3: Genes, Genomes, Genetics, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.","apa":"György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.117.300452","ama":"György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 2018;8(3):845-857. doi:10.1534/g3.117.300452"},"publication":"G3: Genes, Genomes, Genetics","page":"845 - 857","date_published":"2018-03-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"text":"Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult.","lang":"eng"}],"_id":"544","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 8","ddc":["570"],"title":"Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues","status":"public","pubrep_id":"990","oa_version":"Published Version","file":[{"file_id":"4905","relation":"main_file","checksum":"7d9d28b915159078a4ca7add568010e8","date_updated":"2020-07-14T12:46:56Z","date_created":"2018-12-12T10:11:48Z","access_level":"open_access","file_name":"IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf","creator":"system","file_size":2251222,"content_type":"application/pdf"}]},{"publist_id":"7192","ec_funded":1,"file_date_updated":"2020-07-14T12:47:20Z","publisher":"Springer","department":[{"_id":"RySh"}],"publication_status":"published","year":"2018","volume":223,"date_created":"2018-12-11T11:47:29Z","date_updated":"2024-03-28T23:30:31Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9562"}]},"author":[{"last_name":"Luján","first_name":"Rafael","full_name":"Luján, Rafael"},{"full_name":"Aguado, Carolina","last_name":"Aguado","first_name":"Carolina"},{"full_name":"Ciruela, Francisco","first_name":"Francisco","last_name":"Ciruela"},{"full_name":"Cózar, Javier","first_name":"Javier","last_name":"Cózar"},{"full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De La Ossa","first_name":"Luis","full_name":"De La Ossa, Luis"},{"full_name":"Bettler, Bernhard","last_name":"Bettler","first_name":"Bernhard"},{"full_name":"Wickman, Kevin","first_name":"Kevin","last_name":"Wickman"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"}],"month":"04","project":[{"name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000428419500030"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00429-017-1568-y","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Metabotropic GABAB receptors mediate slow inhibitory effects presynaptically and postsynaptically through the modulation of different effector signalling pathways. Here, we analysed the distribution of GABAB receptors using highly sensitive SDS-digested freeze-fracture replica labelling in mouse cerebellar Purkinje cells. Immunoreactivity for GABAB1 was observed on presynaptic and, more abundantly, on postsynaptic compartments, showing both scattered and clustered distribution patterns. Quantitative analysis of immunoparticles revealed a somato-dendritic gradient, with the density of immunoparticles increasing 26-fold from somata to dendritic spines. To understand the spatial relationship of GABAB receptors with two key effector ion channels, the G protein-gated inwardly rectifying K+ (GIRK/Kir3) channel and the voltage-dependent Ca2+ channel, biochemical and immunohistochemical approaches were performed. Co-immunoprecipitation analysis demonstrated that GABAB receptors co-assembled with GIRK and CaV2.1 channels in the cerebellum. Using double-labelling immunoelectron microscopic techniques, co-clustering between GABAB1 and GIRK2 was detected in dendritic spines, whereas they were mainly segregated in the dendritic shafts. In contrast, co-clustering of GABAB1 and CaV2.1 was detected in dendritic shafts but not spines. Presynaptically, although no significant co-clustering of GABAB1 and GIRK2 or CaV2.1 channels was detected, inter-cluster distance for GABAB1 and GIRK2 was significantly smaller in the active zone than in the dendritic shafts, and that for GABAB1 and CaV2.1 was significantly smaller in the active zone than in the dendritic shafts and spines. Thus, GABAB receptors are associated with GIRK and CaV2.1 channels in different subcellular compartments. These data provide a better framework for understanding the different roles played by GABAB receptors and their effector ion channels in the cerebellar network."}],"intvolume":" 223","title":"Differential association of GABAB receptors with their effector ion channels in Purkinje cells","status":"public","ddc":["571"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"612","file":[{"checksum":"a55b3103476ecb5f4f983d8801807e8b","date_created":"2018-12-12T10:15:36Z","date_updated":"2020-07-14T12:47:20Z","relation":"main_file","file_id":"5157","content_type":"application/pdf","file_size":5542926,"creator":"system","access_level":"open_access","file_name":"IST-2018-1013-v1+1_2018_Kleindienst_Differential.pdf"}],"oa_version":"Published Version","pubrep_id":"1013","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"1565 - 1587","article_type":"original","citation":{"chicago":"Luján, Rafael, Carolina Aguado, Francisco Ciruela, Javier Cózar, David Kleindienst, Luis De La Ossa, Bernhard Bettler, et al. “Differential Association of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain Structure and Function. Springer, 2018. https://doi.org/10.1007/s00429-017-1568-y.","mla":"Luján, Rafael, et al. “Differential Association of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain Structure and Function, vol. 223, no. 3, Springer, 2018, pp. 1565–87, doi:10.1007/s00429-017-1568-y.","short":"R. Luján, C. Aguado, F. Ciruela, J. Cózar, D. Kleindienst, L. De La Ossa, B. Bettler, K. Wickman, M. Watanabe, R. Shigemoto, Y. Fukazawa, Brain Structure and Function 223 (2018) 1565–1587.","ista":"Luján R, Aguado C, Ciruela F, Cózar J, Kleindienst D, De La Ossa L, Bettler B, Wickman K, Watanabe M, Shigemoto R, Fukazawa Y. 2018. Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. 223(3), 1565–1587.","apa":"Luján, R., Aguado, C., Ciruela, F., Cózar, J., Kleindienst, D., De La Ossa, L., … Fukazawa, Y. (2018). Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. Springer. https://doi.org/10.1007/s00429-017-1568-y","ieee":"R. Luján et al., “Differential association of GABAB receptors with their effector ion channels in Purkinje cells,” Brain Structure and Function, vol. 223, no. 3. Springer, pp. 1565–1587, 2018.","ama":"Luján R, Aguado C, Ciruela F, et al. Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. 2018;223(3):1565-1587. doi:10.1007/s00429-017-1568-y"},"publication":"Brain Structure and Function","date_published":"2018-04-01T00:00:00Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"02","scopus_import":"1","date_published":"2018-11-02T00:00:00Z","article_type":"original","citation":{"ama":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-06899-3","ista":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. 2018. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 9(1), 4605.","ieee":"C. Espinoza Martinez, J. Guzmán, X. Zhang, and P. M. Jonas, “Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","apa":"Espinoza Martinez, C., Guzmán, J., Zhang, X., & Jonas, P. M. (2018). Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06899-3","mla":"Espinoza Martinez, Claudia, et al. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” Nature Communications, vol. 9, no. 1, 4605, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06899-3.","short":"C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications 9 (2018).","chicago":"Espinoza Martinez, Claudia , José Guzmán, Xiaomin Zhang, and Peter M Jonas. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06899-3."},"publication":"Nature Communications","issue":"1","abstract":[{"lang":"eng","text":"Parvalbumin-positive (PV+) GABAergic interneurons in hippocampal microcircuits are thought to play a key role in several higher network functions, such as feedforward and feedback inhibition, network oscillations, and pattern separation. Fast lateral inhibition mediated by GABAergic interneurons may implement a winner-takes-all mechanism in the hippocampal input layer. However, it is not clear whether the functional connectivity rules of granule cells (GCs) and interneurons in the dentate gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings from up to seven GCs and up to four PV+ interneurons in the dentate gyrus, we find that connectivity is structured in space, synapse-specific, and enriched in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV+ interneuron) is ~ 10-times more abundant than recurrent inhibition (in which a GC inhibits itself). Thus, unique connectivity rules may enable the dentate gyrus to perform specific higher-order computations"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"5715","checksum":"9fe2a63bd95a5067d896c087d07998f3","date_created":"2018-12-17T15:41:57Z","date_updated":"2020-07-14T12:45:28Z","access_level":"open_access","file_name":"2018_NatureComm_Espinoza.pdf","content_type":"application/pdf","file_size":4651930,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 9","status":"public","ddc":["570"],"title":"Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus","_id":"21","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"11","language":[{"iso":"eng"}],"doi":"10.1038/s41467-018-06899-3","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000449069700009"]},"publist_id":"8034","ec_funded":1,"file_date_updated":"2020-07-14T12:45:28Z","article_number":"4605","volume":9,"date_created":"2018-12-11T11:44:12Z","date_updated":"2024-03-28T23:30:31Z","related_material":{"record":[{"id":"6363","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","first_name":"Claudia "},{"last_name":"Guzmán","first_name":"José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José"},{"full_name":"Zhang, Xiaomin","last_name":"Zhang","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"}],"publisher":"Nature Publishing Group","department":[{"_id":"PeJo"}],"publication_status":"published","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J..","year":"2018"},{"ec_funded":1,"publist_id":"7988","file_date_updated":"2020-07-14T12:47:34Z","article_number":"11","related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Goharshady","first_name":"Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"volume":118,"date_created":"2018-12-11T11:44:27Z","date_updated":"2024-03-28T23:30:34Z","year":"2018","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","publication_identifier":{"isbn":["978-3-95977-087-3"]},"month":"09","doi":"10.4230/LIPIcs.CONCUR.2018.11","conference":{"end_date":"2018-09-07","location":"Beijing, China","start_date":"2018-09-04","name":"CONCUR: Conference on Concurrency Theory"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1806.03108"]},"project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Crypto-currencies are digital assets designed to work as a medium of exchange, e.g., Bitcoin, but they are susceptible to attacks (dishonest behavior of participants). A framework for the analysis of attacks in crypto-currencies requires (a) modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior; (b) concurrent interactions between participants; and (c) analysis of long-term monetary gains. Traditional game-theoretic approaches for the analysis of security protocols consider either qualitative temporal properties such as safety and termination, or the very special class of one-shot (stateless) games. However, to analyze general attacks on protocols for crypto-currencies, both stateful analysis and quantitative objectives are necessary. In this work our main contributions are as follows: (a) we show how a class of concurrent mean-payo games, namely ergodic games, can model various attacks that arise naturally in crypto-currencies; (b) we present the first practical implementation of algorithms for ergodic games that scales to model realistic problems for crypto-currencies; and (c) we present experimental results showing that our framework can handle games with thousands of states and millions of transitions."}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:34Z","date_created":"2018-12-17T12:08:00Z","checksum":"68a055b1aaa241cc38375083cf832a7d","relation":"main_file","file_id":"5696","content_type":"application/pdf","file_size":1078309,"creator":"dernst","file_name":"2018_CONCUR_Chatterjee.pdf","access_level":"open_access"}],"_id":"66","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 118","status":"public","title":"Ergodic mean-payoff games for the analysis of attacks in crypto-currencies","ddc":["000"],"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-09-01T00:00:00Z","citation":{"ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.11","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and Y. Velner, “Ergodic mean-payoff games for the analysis of attacks in crypto-currencies,” presented at the CONCUR: Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Velner, Y. (2018). Ergodic mean-payoff games for the analysis of attacks in crypto-currencies (Vol. 118). Presented at the CONCUR: Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. 2018. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 118, 11.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, Y. Velner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Chatterjee, Krishnendu, et al. Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies. Vol. 118, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.11.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Yaron Velner. “Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11."}},{"month":"04","doi":"10.1007/978-3-319-89884-1_26","conference":{"location":"Thessaloniki, Greece","start_date":"2018-04-16","end_date":"2018-04-19","name":"ESOP: European Symposium on Programming"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","publist_id":"7554","ec_funded":1,"file_date_updated":"2020-07-14T12:46:00Z","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir","full_name":"Goharshady, Amir"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"volume":10801,"date_created":"2018-12-11T11:45:45Z","date_updated":"2024-03-28T23:30:33Z","year":"2018","acknowledgement":"The research was partially supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games).","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","citation":{"ista":"Chatterjee K, Goharshady AK, Velner Y. 2018. Quantitative analysis of smart contracts. ESOP: European Symposium on Programming, LNCS, vol. 10801, 739–767.","apa":"Chatterjee, K., Goharshady, A. K., & Velner, Y. (2018). Quantitative analysis of smart contracts (Vol. 10801, pp. 739–767). Presented at the ESOP: European Symposium on Programming, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89884-1_26","ieee":"K. Chatterjee, A. K. Goharshady, and Y. Velner, “Quantitative analysis of smart contracts,” presented at the ESOP: European Symposium on Programming, Thessaloniki, Greece, 2018, vol. 10801, pp. 739–767.","ama":"Chatterjee K, Goharshady AK, Velner Y. Quantitative analysis of smart contracts. In: Vol 10801. Springer; 2018:739-767. doi:10.1007/978-3-319-89884-1_26","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Yaron Velner. “Quantitative Analysis of Smart Contracts,” 10801:739–67. Springer, 2018. https://doi.org/10.1007/978-3-319-89884-1_26.","mla":"Chatterjee, Krishnendu, et al. Quantitative Analysis of Smart Contracts. Vol. 10801, Springer, 2018, pp. 739–67, doi:10.1007/978-3-319-89884-1_26.","short":"K. Chatterjee, A.K. Goharshady, Y. Velner, in:, Springer, 2018, pp. 739–767."},"page":"739 - 767","abstract":[{"lang":"eng","text":"Smart contracts are computer programs that are executed by a network of mutually distrusting agents, without the need of an external trusted authority. Smart contracts handle and transfer assets of considerable value (in the form of crypto-currency like Bitcoin). Hence, it is crucial that their implementation is bug-free. We identify the utility (or expected payoff) of interacting with such smart contracts as the basic and canonical quantitative property for such contracts. We present a framework for such quantitative analysis of smart contracts. Such a formal framework poses new and novel research challenges in programming languages, as it requires modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior and modeling utilities which are not specified as standard temporal properties such as safety and termination. While game-theoretic incentives have been analyzed in the security community, their analysis has been restricted to the very special case of stateless games. However, to analyze smart contracts, stateful analysis is required as it must account for the different program states of the protocol. Our main contributions are as follows: we present (i)~a simplified programming language for smart contracts; (ii)~an automatic translation of the programs to state-based games; (iii)~an abstraction-refinement approach to solve such games; and (iv)~experimental results on real-world-inspired smart contracts."}],"type":"conference","alternative_title":["LNCS"],"file":[{"checksum":"9c8a8338c571903b599b6ca93abd2cce","date_created":"2018-12-17T15:45:49Z","date_updated":"2020-07-14T12:46:00Z","file_id":"5716","relation":"main_file","creator":"dernst","file_size":1394993,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_ESOP_Chatterjee.pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"311","intvolume":" 10801","ddc":["000"],"title":"Quantitative analysis of smart contracts","status":"public"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:27Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2018","department":[{"_id":"KrCh"}],"publisher":"IEEE","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"author":[{"full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Behrouz, Ali","first_name":"Ali","last_name":"Behrouz"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"date_updated":"2024-03-28T23:30:34Z","date_created":"2019-04-18T10:37:35Z","publication_identifier":{"isbn":["978-1-5386-7975-3 "]},"month":"09","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000481634500196"],"arxiv":["1805.09104"]},"oa":1,"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","isi":1,"doi":"10.1109/Cybermatics_2018.2018.00231","conference":{"name":"IEEE International Conference on Blockchain","end_date":"2018-08-03","start_date":"2018-07-30","location":"Halifax, Canada"},"language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"We present a secure approach for maintaining andreporting credit history records on the Blockchain. Our ap-proach removes third-parties such as credit reporting agen-cies from the lending process and replaces them with smartcontracts. This allows customers to interact directly with thelenders or banks while ensuring the integrity, unmalleabilityand privacy of their credit data. Additionally, each customerhas full control over complete or selective disclosure of hercredit records, eliminating the risk of privacy violations or databreaches. Moreover, our approach provides strong guaranteesfor the lenders as well. A lender can check both correctness andcompleteness of the credit data disclosed to her. This is the firstapproach that can perform all credit reporting tasks withouta central authority or changing the financial mechanisms*.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6340","ddc":["000"],"title":"Secure Credit Reporting on the Blockchain","status":"public","oa_version":"Submitted Version","file":[{"creator":"akafshda","content_type":"application/pdf","file_size":624338,"access_level":"open_access","file_name":"blockchain2018.pdf","checksum":"b25c9bb7cf6e7e6634e692d26d41ead8","date_created":"2019-04-18T10:36:39Z","date_updated":"2020-07-14T12:47:27Z","file_id":"6341","relation":"main_file"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"short":"A.K. Goharshady, A. Behrouz, K. Chatterjee, in:, Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–1348.","mla":"Goharshady, Amir Kafshdar, et al. “Secure Credit Reporting on the Blockchain.” Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–48, doi:10.1109/Cybermatics_2018.2018.00231.","chicago":"Goharshady, Amir Kafshdar, Ali Behrouz, and Krishnendu Chatterjee. “Secure Credit Reporting on the Blockchain.” In Proceedings of the IEEE International Conference on Blockchain, 1343–48. IEEE, 2018. https://doi.org/10.1109/Cybermatics_2018.2018.00231.","ama":"Goharshady AK, Behrouz A, Chatterjee K. Secure Credit Reporting on the Blockchain. In: Proceedings of the IEEE International Conference on Blockchain. IEEE; 2018:1343-1348. doi:10.1109/Cybermatics_2018.2018.00231","ieee":"A. K. Goharshady, A. Behrouz, and K. Chatterjee, “Secure Credit Reporting on the Blockchain,” in Proceedings of the IEEE International Conference on Blockchain, Halifax, Canada, 2018, pp. 1343–1348.","apa":"Goharshady, A. K., Behrouz, A., & Chatterjee, K. (2018). Secure Credit Reporting on the Blockchain. In Proceedings of the IEEE International Conference on Blockchain (pp. 1343–1348). Halifax, Canada: IEEE. https://doi.org/10.1109/Cybermatics_2018.2018.00231","ista":"Goharshady AK, Behrouz A, Chatterjee K. 2018. Secure Credit Reporting on the Blockchain. Proceedings of the IEEE International Conference on Blockchain. IEEE International Conference on Blockchain, 1343–1348."},"publication":"Proceedings of the IEEE International Conference on Blockchain","page":"1343-1348","date_published":"2018-09-01T00:00:00Z"},{"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1437"},{"relation":"earlier_version","status":"public","id":"5441"},{"relation":"earlier_version","status":"public","id":"5442"},{"status":"public","relation":"dissertation_contains","id":"8934"}]},"date_created":"2019-02-14T14:31:52Z","date_updated":"2024-03-28T23:30:34Z","volume":40,"year":"2018","publication_status":"published","publisher":"Association for Computing Machinery (ACM)","department":[{"_id":"KrCh"}],"ec_funded":1,"article_number":"9","doi":"10.1145/3210257","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.07565"}],"external_id":{"arxiv":["1510.07565"],"isi":["000444694800001"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"month":"08","publication_identifier":{"issn":["0164-0925"]},"oa_version":"Preprint","_id":"6009","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","intvolume":" 40","abstract":[{"text":"We study algorithmic questions wrt algebraic path properties in concurrent systems, where the transitions of the system are labeled from a complete, closed semiring. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.\r\n","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2018-08-01T00:00:00Z","publication":"ACM Transactions on Programming Languages and Systems","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 40 (2018).","mla":"Chatterjee, Krishnendu, et al. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3, 9, Association for Computing Machinery (ACM), 2018, doi:10.1145/3210257.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3210257.","ama":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 2018;40(3). doi:10.1145/3210257","apa":"Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A. (2018). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3210257","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3. Association for Computing Machinery (ACM), 2018.","ista":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2018. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 40(3), 9."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"abstract":[{"lang":"eng","text":"We consider the stochastic shortest path (SSP)problem for succinct Markov decision processes(MDPs), where the MDP consists of a set of vari-ables, and a set of nondeterministic rules that up-date the variables. First, we show that several ex-amples from the AI literature can be modeled assuccinct MDPs. Then we present computationalapproaches for upper and lower bounds for theSSP problem: (a) for computing upper bounds, ourmethod is polynomial-time in the implicit descrip-tion of the MDP; (b) for lower bounds, we present apolynomial-time (in the size of the implicit descrip-tion) reduction to quadratic programming. Our ap-proach is applicable even to infinite-state MDPs.Finally, we present experimental results to demon-strate the effectiveness of our approach on severalclassical examples from the AI literature."}],"type":"conference","oa_version":"Preprint","status":"public","title":"Computational approaches for stochastic shortest path on succinct MDPs","intvolume":" 2018","_id":"5977","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"17","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-17T00:00:00Z","page":"4700-4707","publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","citation":{"apa":"Chatterjee, K., Fu, H., Goharshady, A. K., & Okati, N. (2018). Computational approaches for stochastic shortest path on succinct MDPs. In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence (Vol. 2018, pp. 4700–4707). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/653","ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and N. Okati, “Computational approaches for stochastic shortest path on succinct MDPs,” in Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4700–4707.","ista":"Chatterjee K, Fu H, Goharshady AK, Okati N. 2018. Computational approaches for stochastic shortest path on succinct MDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4700–4707.","ama":"Chatterjee K, Fu H, Goharshady AK, Okati N. Computational approaches for stochastic shortest path on succinct MDPs. In: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. Vol 2018. IJCAI; 2018:4700-4707. doi:10.24963/ijcai.2018/653","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Nastaran Okati. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018:4700–4707. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/653.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, N. Okati, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4700–4707.","mla":"Chatterjee, Krishnendu, et al. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, vol. 2018, IJCAI, 2018, pp. 4700–07, doi:10.24963/ijcai.2018/653."},"ec_funded":1,"date_created":"2019-02-13T13:26:27Z","date_updated":"2024-03-28T23:30:34Z","volume":2018,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir"},{"last_name":"Okati","first_name":"Nastaran","full_name":"Okati, Nastaran"}],"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publisher":"IJCAI","department":[{"_id":"KrCh"}],"year":"2018","month":"07","publication_identifier":{"issn":["10450823"],"isbn":["978-099924112-7"]},"language":[{"iso":"eng"}],"conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","end_date":"2018-07-19","location":"Stockholm, Sweden","start_date":"2018-07-13"},"doi":"10.24963/ijcai.2018/653","quality_controlled":"1","isi":1,"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"external_id":{"isi":["000764175404118"],"arxiv":["1804.08984"]},"main_file_link":[{"url":"https://arxiv.org/abs/1804.08984","open_access":"1"}],"oa":1},{"file":[{"creator":"dernst","file_size":2210020,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_FlowTurbulenceCombust_Kuehnen.pdf","checksum":"d7c0bade150faabca150b0a9986e60ca","date_created":"2018-12-17T15:52:37Z","date_updated":"2020-07-14T12:46:25Z","file_id":"5717","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 100","title":"Relaminarization by steady modification of the streamwise velocity profile in a pipe","status":"public","ddc":["530"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"422","issue":"4","abstract":[{"text":"We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device which injects fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the skin friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant local skin friction drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle.","lang":"eng"}],"type":"journal_article","date_published":"2018-01-01T00:00:00Z","page":"919 - 942","citation":{"mla":"Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion, vol. 100, no. 4, Springer, 2018, pp. 919–42, doi:10.1007/s10494-018-9896-4.","short":"J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942.","chicago":"Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion. Springer, 2018. https://doi.org/10.1007/s10494-018-9896-4.","ama":"Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 2018;100(4):919-942. doi:10.1007/s10494-018-9896-4","ista":"Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942.","ieee":"J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady modification of the streamwise velocity profile in a pipe,” Flow Turbulence and Combustion, vol. 100, no. 4. Springer, pp. 919–942, 2018.","apa":"Kühnen, J., Scarselli, D., Schaner, M., & Hof, B. (2018). Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. Springer. https://doi.org/10.1007/s10494-018-9896-4"},"publication":"Flow Turbulence and Combustion","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","volume":100,"date_updated":"2024-03-28T23:30:36Z","date_created":"2018-12-11T11:46:23Z","related_material":{"record":[{"id":"7258","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Kühnen, Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179","first_name":"Jakob","last_name":"Kühnen"},{"full_name":"Scarselli, Davide","first_name":"Davide","last_name":"Scarselli","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271"},{"last_name":"Schaner","first_name":"Markus","id":"316CE034-F248-11E8-B48F-1D18A9856A87","full_name":"Schaner, Markus"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"publisher":"Springer","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2018","ec_funded":1,"publist_id":"7401","file_date_updated":"2020-07-14T12:46:25Z","language":[{"iso":"eng"}],"doi":"10.1007/s10494-018-9896-4","project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000433113900004"]},"oa":1,"month":"01"},{"oa_version":"Preprint","_id":"461","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 14","status":"public","title":"Destabilizing turbulence in pipe flow","abstract":[{"text":"Turbulence is the major cause of friction losses in transport processes and it is responsible for a drastic drag increase in flows over bounding surfaces. While much effort is invested into developing ways to control and reduce turbulence intensities, so far no methods exist to altogether eliminate turbulence if velocities are sufficiently large. We demonstrate for pipe flow that appropriate distortions to the velocity profile lead to a complete collapse of turbulence and subsequently friction losses are reduced by as much as 90%. Counterintuitively, the return to laminar motion is accomplished by initially increasing turbulence intensities or by transiently amplifying wall shear. Since neither the Reynolds number nor the shear stresses decrease (the latter often increase), these measures are not indicative of turbulence collapse. Instead, an amplification mechanism measuring the interaction between eddies and the mean shear is found to set a threshold below which turbulence is suppressed beyond recovery.","lang":"eng"}],"type":"journal_article","date_published":"2018-01-08T00:00:00Z","citation":{"chicago":"Kühnen, Jakob, Baofang Song, Davide Scarselli, Nazmi B Budanur, Michael Riedl, Ashley Willis, Marc Avila, and Björn Hof. “Destabilizing Turbulence in Pipe Flow.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-017-0018-3.","mla":"Kühnen, Jakob, et al. “Destabilizing Turbulence in Pipe Flow.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 386–90, doi:10.1038/s41567-017-0018-3.","short":"J. Kühnen, B. Song, D. Scarselli, N.B. Budanur, M. Riedl, A. Willis, M. Avila, B. Hof, Nature Physics 14 (2018) 386–390.","ista":"Kühnen J, Song B, Scarselli D, Budanur NB, Riedl M, Willis A, Avila M, Hof B. 2018. Destabilizing turbulence in pipe flow. Nature Physics. 14, 386–390.","ieee":"J. Kühnen et al., “Destabilizing turbulence in pipe flow,” Nature Physics, vol. 14. Nature Publishing Group, pp. 386–390, 2018.","apa":"Kühnen, J., Song, B., Scarselli, D., Budanur, N. B., Riedl, M., Willis, A., … Hof, B. (2018). Destabilizing turbulence in pipe flow. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-017-0018-3","ama":"Kühnen J, Song B, Scarselli D, et al. Destabilizing turbulence in pipe flow. Nature Physics. 2018;14:386-390. doi:10.1038/s41567-017-0018-3"},"publication":"Nature Physics","page":"386-390","article_processing_charge":"No","day":"08","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12726"},{"id":"14530","status":"public","relation":"dissertation_contains"},{"id":"7258","relation":"dissertation_contains","status":"public"}]},"author":[{"first_name":"Jakob","last_name":"Kühnen","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob"},{"last_name":"Song","first_name":"Baofang","full_name":"Song, Baofang"},{"full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","first_name":"Davide"},{"full_name":"Budanur, Nazmi B","first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010"},{"full_name":"Riedl, Michael","last_name":"Riedl","first_name":"Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Willis","first_name":"Ashley","full_name":"Willis, Ashley"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"volume":14,"date_created":"2018-12-11T11:46:36Z","date_updated":"2024-03-28T23:30:36Z","year":"2018","acknowledgement":"We acknowledge the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 737549) and the Deutsche Forschungsgemeinschaft (Project No. FOR 1182) for financial support. We thank our technician P. Maier for providing highly valuable ideas and greatly supporting us in all technical aspects. We thank M. Schaner for technical drawings, construction and design. We thank M. Schwegel for a Matlab code to post-process experimental data.","publisher":"Nature Publishing Group","department":[{"_id":"BjHo"}],"publication_status":"published","ec_funded":1,"publist_id":"7360","doi":"10.1038/s41567-017-0018-3","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1711.06543","open_access":"1"}],"oa":1,"external_id":{"isi":["000429434100020"]},"project":[{"call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589"},{"name":"Eliminating turbulence in oil pipelines","call_identifier":"H2020","_id":"25104D44-B435-11E9-9278-68D0E5697425","grant_number":"737549"}],"isi":1,"quality_controlled":"1","month":"01"},{"day":"29","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2018-01-29T00:00:00Z","publication":"PLoS Genetics","citation":{"short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","mla":"Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics, vol. 14, no. 1, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007177.","chicago":"Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007177.","ama":"Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 2018;14(1). doi:10.1371/journal.pgen.1007177","ieee":"T. Prat et al., “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” PLoS Genetics, vol. 14, no. 1. Public Library of Science, 2018.","apa":"Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007177","ista":"Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1)."},"abstract":[{"lang":"eng","text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development."}],"issue":"1","type":"journal_article","pubrep_id":"967","oa_version":"Published Version","file":[{"file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","access_level":"open_access","creator":"system","file_size":24709062,"content_type":"application/pdf","file_id":"4843","relation":"main_file","date_created":"2018-12-12T10:10:52Z","date_updated":"2020-07-14T12:46:30Z","checksum":"0276d66788ec076f4924164a39e6a712"}],"_id":"449","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","ddc":["581"],"status":"public","intvolume":" 14","month":"01","doi":"10.1371/journal.pgen.1007177","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000423718600034"]},"isi":1,"quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"file_date_updated":"2020-07-14T12:46:30Z","publist_id":"7373","ec_funded":1,"author":[{"full_name":"Prat, Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Prat"},{"last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K","last_name":"Vasileva","full_name":"Vasileva, Mina K"},{"id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar","first_name":"Gergely","full_name":"Molnar, Gergely"},{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"full_name":"Schmid, Markus","last_name":"Schmid","first_name":"Markus"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1127"},{"status":"public","relation":"dissertation_contains","id":"7172"},{"status":"public","relation":"dissertation_contains","id":"8822"}]},"date_created":"2018-12-11T11:46:32Z","date_updated":"2024-03-28T23:30:38Z","volume":14,"year":"2018","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"JiFr"}]},{"abstract":[{"text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"file_id":"5714","relation":"main_file","checksum":"266b03f4fb8198e83141617aaa99dcab","date_updated":"2020-07-14T12:45:20Z","date_created":"2018-12-17T15:38:56Z","access_level":"open_access","file_name":"2018_ScientificReports_Grones.pdf","creator":"dernst","file_size":2413876,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"191","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["581"],"status":"public","title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","intvolume":" 8","day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-06T00:00:00Z","publication":"Scientific Reports","citation":{"chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports. Springer, 2018. https://doi.org/10.1038/s41598-018-28188-1.","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports, vol. 8, no. 1, 10279, Springer, 2018, doi:10.1038/s41598-018-28188-1.","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279.","ieee":"P. Grones et al., “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” Scientific Reports, vol. 8, no. 1. Springer, 2018.","apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., & Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. Springer. https://doi.org/10.1038/s41598-018-28188-1","ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-28188-1"},"file_date_updated":"2020-07-14T12:45:20Z","publist_id":"7729","ec_funded":1,"article_number":"10279","author":[{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abas, Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda F","last_name":"Abas"},{"last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"last_name":"Jones","first_name":"Angharad","full_name":"Jones, Angharad"},{"first_name":"Sascha","last_name":"Waidmann","full_name":"Waidmann, Sascha"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8822"}]},"date_created":"2018-12-11T11:45:06Z","date_updated":"2024-03-28T23:30:38Z","volume":8,"year":"2018","publication_status":"published","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Springer","month":"07","doi":"10.1038/s41598-018-28188-1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000437673200053"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"},{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}]},{"date_published":"2018-01-01T00:00:00Z","citation":{"ama":"Abualia R, Benková E, Lacombe B. Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. 2018;87:115-138. doi:10.1016/bs.abr.2018.09.007","ista":"Abualia R, Benková E, Lacombe B. 2018. Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. 87, 115–138.","ieee":"R. Abualia, E. Benková, and B. Lacombe, “Transporters and mechanisms of hormone transport in arabidopsis,” Advances in Botanical Research, vol. 87. Elsevier, pp. 115–138, 2018.","apa":"Abualia, R., Benková, E., & Lacombe, B. (2018). Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. Elsevier. https://doi.org/10.1016/bs.abr.2018.09.007","mla":"Abualia, Rashed, et al. “Transporters and Mechanisms of Hormone Transport in Arabidopsis.” Advances in Botanical Research, vol. 87, Elsevier, 2018, pp. 115–38, doi:10.1016/bs.abr.2018.09.007.","short":"R. Abualia, E. Benková, B. Lacombe, Advances in Botanical Research 87 (2018) 115–138.","chicago":"Abualia, Rashed, Eva Benková, and Benoît Lacombe. “Transporters and Mechanisms of Hormone Transport in Arabidopsis.” Advances in Botanical Research. Elsevier, 2018. https://doi.org/10.1016/bs.abr.2018.09.007."},"publication":"Advances in Botanical Research","page":"115 - 138","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"47","intvolume":" 87","title":"Transporters and mechanisms of hormone transport in arabidopsis","status":"public","abstract":[{"text":"Plant hormones as signalling molecules play an essential role in the control of plant growth and development. Typically, sites of hormonal action are usually distant from the site of biosynthesis thus relying on efficient transport mechanisms. Over the last decades, molecular identification of proteins and protein complexes involved in hormonal transport has started. Advanced screens for genes involved in hormonal transport in combination with transport assays using heterologous systems such as yeast, insect, or tobacco BY2 cells or Xenopus oocytes provided important insights into mechanisms underlying distribution of hormones in plant body and led to identification of principal transporters for each hormone. This review gives a short overview of the mechanisms of hormonal transport and transporters identified in Arabidopsis thaliana.","lang":"eng"}],"type":"journal_article","doi":"10.1016/bs.abr.2018.09.007","language":[{"iso":"eng"}],"external_id":{"isi":["000453657800006"]},"quality_controlled":"1","isi":1,"month":"01","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10303"}]},"author":[{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed","full_name":"Abualia, Rashed"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"full_name":"Lacombe, Benoît","first_name":"Benoît","last_name":"Lacombe"}],"volume":87,"date_updated":"2024-03-28T23:30:40Z","date_created":"2018-12-11T11:44:20Z","year":"2018","department":[{"_id":"EvBe"}],"publisher":"Elsevier","publication_status":"published","publist_id":"8007"},{"date_published":"2018-05-18T00:00:00Z","page":"606 - 616","publication":"Nature Immunology","citation":{"ama":"Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 2018;19(6):606-616. doi:10.1038/s41590-018-0109-z","apa":"Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/s41590-018-0109-z","ieee":"M. Hons et al., “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” Nature Immunology, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018.","ista":"Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616.","short":"M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616.","mla":"Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:10.1038/s41590-018-0109-z.","chicago":"Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41590-018-0109-z."},"day":"18","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","intvolume":" 19","_id":"15","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux.","lang":"eng"}],"issue":"6","type":"journal_article","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41590-018-0109-z","isi":1,"quality_controlled":"1","project":[{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687"},{"grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221"}],"external_id":{"pmid":["29777221"],"isi":["000433041500026"]},"oa":1,"month":"05","date_created":"2018-12-11T11:44:10Z","date_updated":"2024-03-28T23:30:40Z","volume":19,"author":[{"full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","first_name":"Miroslav"},{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","first_name":"Aglaja","last_name":"Kopf","full_name":"Kopf, Aglaja"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","first_name":"Alexander F","last_name":"Leithner","full_name":"Leithner, Alexander F"},{"full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723"},{"first_name":"Jun","last_name":"Abe","full_name":"Abe, Jun"},{"full_name":"Renkawitz, Jörg","first_name":"Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369"},{"full_name":"Stein, Jens","first_name":"Jens","last_name":"Stein"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"related_material":{"record":[{"id":"6891","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MiSi"},{"_id":"Bio"}],"acknowledgement":"This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014).","year":"2018","pmid":1,"ec_funded":1,"publist_id":"8040"},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"2542 - 2544","citation":{"apa":"Contreras, X., & Hippenmeyer, S. (2018). Incorrect trafficking route leads to autism. Brain a Journal of Neurology. Oxford University Press. https://doi.org/10.1093/brain/awy218","ieee":"X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,” Brain a journal of neurology, vol. 141, no. 9. Oxford University Press, pp. 2542–2544, 2018.","ista":"Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism. Brain a journal of neurology. 141(9), 2542–2544.","ama":"Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. Brain a journal of neurology. 2018;141(9):2542-2544. doi:10.1093/brain/awy218","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” Brain a Journal of Neurology. Oxford University Press, 2018. https://doi.org/10.1093/brain/awy218.","short":"X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” Brain a Journal of Neurology, vol. 141, no. 9, Oxford University Press, 2018, pp. 2542–44, doi:10.1093/brain/awy218."},"publication":"Brain a journal of neurology","date_published":"2018-09-01T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate cortical development and core behaviours related to autism disorders in mice’ by Szczurkowska et al. "}],"intvolume":" 141","status":"public","title":"Incorrect trafficking route leads to autism","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"28","oa_version":"None","month":"09","quality_controlled":"1","isi":1,"external_id":{"isi":["000446548100012"]},"language":[{"iso":"eng"}],"doi":"10.1093/brain/awy218","publisher":"Oxford University Press","department":[{"_id":"SiHi"}],"publication_status":"published","year":"2018","volume":141,"date_updated":"2024-03-28T23:30:42Z","date_created":"2018-12-11T11:44:14Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7902"}]},"author":[{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}]},{"language":[{"iso":"eng"}],"doi":"10.21769/BioProtoc.2685","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["2331-8325"]},"month":"01","volume":8,"date_created":"2018-12-11T11:46:30Z","date_updated":"2024-03-28T23:30:43Z","related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin"},{"last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"department":[{"_id":"JiFr"},{"_id":"Bio"}],"publisher":"Bio-protocol","publication_status":"published","year":"2018","acknowledgement":"This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ","ec_funded":1,"publist_id":"7381","file_date_updated":"2020-07-14T12:46:29Z","date_published":"2018-01-05T00:00:00Z","article_type":"original","citation":{"ista":"Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1).","apa":"Li, L., Krens, G., Fendrych, M., & Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-Protocol. Bio-protocol. https://doi.org/10.21769/BioProtoc.2685","ieee":"L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” Bio-protocol, vol. 8, no. 1. Bio-protocol, 2018.","ama":"Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 2018;8(1). doi:10.21769/BioProtoc.2685","chicago":"Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol. Bio-protocol, 2018. https://doi.org/10.21769/BioProtoc.2685.","mla":"Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol, vol. 8, no. 1, Bio-protocol, 2018, doi:10.21769/BioProtoc.2685.","short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018)."},"publication":"Bio-protocol","has_accepted_license":"1","article_processing_charge":"No","day":"05","file":[{"access_level":"open_access","file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","creator":"system","content_type":"application/pdf","file_size":11352389,"file_id":"5299","relation":"main_file","checksum":"6644ba698206eda32b0abf09128e63e3","date_created":"2018-12-12T10:17:43Z","date_updated":"2020-07-14T12:46:29Z"}],"oa_version":"Published Version","pubrep_id":"970","intvolume":" 8","ddc":["576","581"],"title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"442","issue":"1","abstract":[{"lang":"eng","text":"The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH."}],"type":"journal_article"},{"related_material":{"record":[{"status":"public","relation":"popular_science","id":"6074"},{"relation":"dissertation_contains","status":"public","id":"12364"}],"link":[{"url":"https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"full_name":"Deliu, Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","last_name":"Deliu","first_name":"Elena"},{"last_name":"Arecco","first_name":"Niccoló","full_name":"Arecco, Niccoló"},{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Morandell","full_name":"Morandell, Jasmin"},{"full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","first_name":"Christoph"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","first_name":"Ximena","full_name":"Contreras, Ximena"},{"first_name":"Charles","last_name":"Girardot","full_name":"Girardot, Charles"},{"full_name":"Käsper, Eva","last_name":"Käsper","first_name":"Eva"},{"full_name":"Kozlova, Alena","last_name":"Kozlova","first_name":"Alena","id":"C50A9596-02D0-11E9-976E-E38CFE5CBC1D"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi","last_name":"Kishi","full_name":"Kishi, Kasumi"},{"first_name":"Ilaria","last_name":"Chiaradia","id":"B6467F20-02D0-11E9-BDA5-E960C241894A","orcid":"0000-0002-9529-4464","full_name":"Chiaradia, Ilaria"},{"last_name":"Noh","first_name":"Kyung","full_name":"Noh, Kyung"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"}],"volume":21,"date_created":"2018-12-11T11:44:05Z","date_updated":"2024-03-28T23:30:45Z","year":"2018","acknowledgement":"This work was supported by the Simons Foundation Autism Research Initiative (grant 401299) to G.N. and the DFG (SPP1738 grant NO 1249) to K.-M.N.","publisher":"Nature Publishing Group","department":[{"_id":"GaNo"},{"_id":"EdHa"}],"publication_status":"published","publist_id":"8054","file_date_updated":"2020-07-14T12:45:58Z","doi":"10.1038/s41593-018-0266-2","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"oa":1,"external_id":{"isi":["000451324700010"]},"project":[{"grant_number":"401299","_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders"}],"quality_controlled":"1","isi":1,"month":"11","pubrep_id":"1071","file":[{"date_created":"2019-04-09T07:41:57Z","date_updated":"2020-07-14T12:45:58Z","checksum":"60abd0f05b7cdc08a6b0ec460884084f","relation":"main_file","file_id":"6255","file_size":8167169,"content_type":"application/pdf","creator":"dernst","file_name":"2017_NatureNeuroscience_Deliu.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"3","intvolume":" 21","title":"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition","ddc":["570"],"status":"public","issue":"12","abstract":[{"lang":"eng","text":"SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder."}],"type":"journal_article","date_published":"2018-11-19T00:00:00Z","citation":{"chicago":"Deliu, Elena, Niccoló Arecco, Jasmin Morandell, Christoph Dotter, Ximena Contreras, Charles Girardot, Eva Käsper, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience. Nature Publishing Group, 2018. https://doi.org/10.1038/s41593-018-0266-2.","short":"E. Deliu, N. Arecco, J. Morandell, C. Dotter, X. Contreras, C. Girardot, E. Käsper, A. Kozlova, K. Kishi, I. Chiaradia, K. Noh, G. Novarino, Nature Neuroscience 21 (2018) 1717–1727.","mla":"Deliu, Elena, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience, vol. 21, no. 12, Nature Publishing Group, 2018, pp. 1717–27, doi:10.1038/s41593-018-0266-2.","ieee":"E. Deliu et al., “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition,” Nature Neuroscience, vol. 21, no. 12. Nature Publishing Group, pp. 1717–1727, 2018.","apa":"Deliu, E., Arecco, N., Morandell, J., Dotter, C., Contreras, X., Girardot, C., … Novarino, G. (2018). Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/s41593-018-0266-2","ista":"Deliu E, Arecco N, Morandell J, Dotter C, Contreras X, Girardot C, Käsper E, Kozlova A, Kishi K, Chiaradia I, Noh K, Novarino G. 2018. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 21(12), 1717–1727.","ama":"Deliu E, Arecco N, Morandell J, et al. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 2018;21(12):1717-1727. doi:10.1038/s41593-018-0266-2"},"publication":"Nature Neuroscience","page":"1717 - 1727","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"19","scopus_import":"1"},{"citation":{"apa":"Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Indirect reciprocity with private, noisy, and incomplete information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1810565115","ieee":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity with private, noisy, and incomplete information,” PNAS, vol. 115, no. 48. National Academy of Sciences, pp. 12241–12246, 2018.","ista":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246.","ama":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 2018;115(48):12241-12246. doi:10.1073/pnas.1810565115","chicago":"Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1810565115.","short":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 12241–12246.","mla":"Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS, vol. 115, no. 48, National Academy of Sciences, 2018, pp. 12241–46, doi:10.1073/pnas.1810565115."},"publication":"PNAS","page":"12241-12246","date_published":"2018-11-27T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"27","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"2","intvolume":" 115","title":"Indirect reciprocity with private, noisy, and incomplete information","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"48","abstract":[{"text":"Indirect reciprocity explores how humans act when their reputation is at stake, and which social norms they use to assess the actions of others. A crucial question in indirect reciprocity is which social norms can maintain stable cooperation in a society. Past research has highlighted eight such norms, called “leading-eight” strategies. This past research, however, is based on the assumption that all relevant information about other population members is publicly available and that everyone agrees on who is good or bad. Instead, here we explore the reputation dynamics when information is private and noisy. We show that under these conditions, most leading-eight strategies fail to evolve. Those leading-eight strategies that do evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other’s reputation, previous research has highlighted eight crucial moral systems. These “leading-eight” strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems.","lang":"eng"}],"external_id":{"isi":["000451351000063"],"pmid":["30429320"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30429320"}],"oa":1,"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1810565115","language":[{"iso":"eng"}],"month":"11","pmid":1,"year":"2018","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10293"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/no-cooperation-without-open-communication/"}]},"author":[{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","first_name":"Laura","last_name":"Schmid"},{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"volume":115,"date_created":"2018-12-11T11:44:05Z","date_updated":"2024-03-28T23:30:45Z","ec_funded":1},{"month":"09","isi":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"},{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000447947600021"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41559-018-0651-y","file_date_updated":"2020-07-14T12:47:37Z","ec_funded":1,"publist_id":"7987","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"JoBo"}],"year":"2018","date_updated":"2024-03-28T23:30:49Z","date_created":"2018-12-11T11:44:27Z","volume":2,"author":[{"full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler","first_name":"Claudia"},{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"related_material":{"record":[{"id":"5585","status":"public","relation":"popular_science"},{"relation":"dissertation_contains","status":"public","id":"6371"}]},"scopus_import":"1","day":"10","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"1633 - 1643","publication":"Nature Ecology and Evolution","citation":{"mla":"Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution. Nature Publishing Group, 2018. https://doi.org/10.1038/s41559-018-0651-y.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643.","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. Nature Publishing Group. https://doi.org/10.1038/s41559-018-0651-y","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018."},"date_published":"2018-09-10T00:00:00Z","type":"journal_article","abstract":[{"text":"Gene regulatory networks evolve through rewiring of individual components—that is, through changes in regulatory connections. However, the mechanistic basis of regulatory rewiring is poorly understood. Using a canonical gene regulatory system, we quantify the properties of transcription factors that determine the evolutionary potential for rewiring of regulatory connections: robustness, tunability and evolvability. In vivo repression measurements of two repressors at mutated operator sites reveal their contrasting evolutionary potential: while robustness and evolvability were positively correlated, both were in trade-off with tunability. Epistatic interactions between adjacent operators alleviated this trade-off. A thermodynamic model explains how the differences in robustness, tunability and evolvability arise from biophysical characteristics of repressor–DNA binding. The model also uncovers that the energy matrix, which describes how mutations affect repressor–DNA binding, encodes crucial information about the evolutionary potential of a repressor. The biophysical determinants of evolutionary potential for regulatory rewiring constitute a mechanistic framework for understanding network evolution.","lang":"eng"}],"issue":"10","title":"Evolutionary potential of transcription factors for gene regulatory rewiring","ddc":["570"],"status":"public","intvolume":" 2","_id":"67","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","file":[{"file_name":"2018_NatureEcology_Igler.pdf","access_level":"open_access","file_size":1135973,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7830","date_created":"2020-05-14T11:28:52Z","date_updated":"2020-07-14T12:47:37Z","checksum":"383a2e2c944a856e2e821ec8e7bf71b6"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"20","month":"07","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"},{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","mla":"Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:108.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 10.15479/AT:ISTA:108."},"tmp":{"short":"CC0 (1.0)","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)"},"oa":1,"date_published":"2018-07-20T00:00:00Z","doi":"10.15479/AT:ISTA:108","type":"research_data","datarep_id":"108","license":"https://creativecommons.org/publicdomain/zero/1.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:07Z","abstract":[{"text":"Mean repression values and standard error of the mean are given for all operator mutant libraries.","lang":"eng"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","status":"public","title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5585","year":"2018","file":[{"creator":"system","file_size":16507,"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","access_level":"open_access","file_name":"IST-2018-108-v1+1_data_figures.xlsx","checksum":"1435781526c77413802adee0d4583cce","date_created":"2018-12-12T13:02:45Z","date_updated":"2020-07-14T12:47:07Z","file_id":"5611","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2024-03-28T23:30:49Z","date_created":"2018-12-12T12:31:40Z","related_material":{"record":[{"id":"67","relation":"research_paper","status":"public"},{"id":"6371","relation":"research_paper","status":"public"}]},"author":[{"last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"},{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}]},{"author":[{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"volume":10,"date_updated":"2022-06-07T10:58:31Z","date_created":"2018-12-11T11:49:41Z","year":"2017","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","publication_status":"published","publist_id":"6382","file_date_updated":"2019-10-24T11:38:14Z","doi":"10.1103/Physics.10.32","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"03","file":[{"file_size":193622,"content_type":"application/pdf","creator":"dernst","file_name":"2017_Physics_Fink.pdf","access_level":"open_access","date_updated":"2019-10-24T11:38:14Z","date_created":"2019-10-24T11:38:14Z","success":1,"relation":"main_file","file_id":"6968"}],"oa_version":"Published Version","_id":"1013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10","status":"public","ddc":["530"],"title":"Viewpoint: Microwave quantum states beat the heat","issue":"32","abstract":[{"text":"From microwave ovens to satellite television to the GPS and data services on our mobile phones, microwave technology is everywhere today. But one technology that has so far failed to prove its worth in this wavelength regime is quantum communication that uses the states of single photons as information carriers. This is because single microwave photons, as opposed to classical microwave signals, are extremely vulnerable to noise from thermal excitations in the channels through which they travel. Two new independent studies, one by Ze-Liang Xiang at Technische Universität Wien (Vienna), Austria, and colleagues [1] and another by Benoît Vermersch at the University of Innsbruck, also in Austria, and colleagues [2] now describe a theoretical protocol for microwave quantum communication that is resilient to thermal and other types of noise. Their approach could become a powerful technique to establish fast links between superconducting data processors in a future all-microwave quantum network.","lang":"eng"}],"type":"journal_article","date_published":"2017-03-27T00:00:00Z","citation":{"ama":"Fink JM. Viewpoint: Microwave quantum states beat the heat. Physics. 2017;10(32). doi:10.1103/Physics.10.32","apa":"Fink, J. M. (2017). Viewpoint: Microwave quantum states beat the heat. Physics. American Physical Society. https://doi.org/10.1103/Physics.10.32","ieee":"J. M. Fink, “Viewpoint: Microwave quantum states beat the heat,” Physics, vol. 10, no. 32. American Physical Society, 2017.","ista":"Fink JM. 2017. Viewpoint: Microwave quantum states beat the heat. Physics. 10(32).","short":"J.M. Fink, Physics 10 (2017).","mla":"Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics, vol. 10, no. 32, American Physical Society, 2017, doi:10.1103/Physics.10.32.","chicago":"Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics. American Physical Society, 2017. https://doi.org/10.1103/Physics.10.32."},"publication":"Physics","article_type":"review","has_accepted_license":"1","article_processing_charge":"No","day":"27"},{"article_number":"33","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Association for Computing Machinery","publication_status":"published","acknowledgement":"McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4.","year":"2017","volume":2,"date_created":"2021-12-05T23:01:49Z","date_updated":"2021-12-07T08:04:14Z","author":[{"full_name":"Mciver, Annabelle","last_name":"Mciver","first_name":"Annabelle"},{"last_name":"Morgan","first_name":"Carroll","full_name":"Morgan, Carroll"},{"full_name":"Kaminski, Benjamin Lucien","last_name":"Kaminski","first_name":"Benjamin Lucien"},{"full_name":"Katoen, Joost P","first_name":"Joost P","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"eissn":["2475-1421"]},"month":"12","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3158121"}],"external_id":{"arxiv":["1711.03588"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3158121","conference":{"name":"POPL: Programming Languages","location":"Los Angeles, CA, United States","start_date":"2018-01-07","end_date":"2018-01-13"},"type":"journal_article","issue":"POPL","abstract":[{"text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains.","lang":"eng"}],"intvolume":" 2","title":"A new proof rule for almost-sure termination","status":"public","_id":"10418","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"07","article_type":"original","citation":{"short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:10.1145/3158121.","chicago":"Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121.","ama":"Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158121","apa":"Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158121","ieee":"A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ista":"Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33."},"publication":"Proceedings of the ACM on Programming Languages","date_published":"2017-12-07T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1112","year":"2017","status":"public","publication_status":"published","title":"An application of stochastic differential equations to evolutionary algorithms","department":[{"_id":"NiBa"}],"publisher":"ACM","author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"},{"full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia","first_name":"Jorge"}],"date_created":"2018-12-11T11:50:12Z","date_updated":"2021-01-12T06:48:22Z","oa_version":"None","type":"conference","abstract":[{"lang":"eng","text":"There has been renewed interest in modelling the behaviour of evolutionary algorithms by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogs of the additive and multiplicative drift theorems for SDEs. We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS) on two canonical problems(OneMax and LeadingOnes)."}],"publist_id":"6255","publication":"Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms","citation":{"ama":"Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729","ista":"Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.","ieee":"T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.","apa":"Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729","mla":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.","short":"T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.","chicago":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729."},"quality_controlled":"1","page":"3 - 11","conference":{"start_date":"2017-01-12","location":"Copenhagen, Denmark","end_date":"2017-01-15","name":"FOGA: Foundations of Genetic Algorithms"},"date_published":"2017-01-12T00:00:00Z","doi":"10.1145/3040718.3040729","language":[{"iso":"eng"}],"scopus_import":1,"day":"12","month":"01","publication_identifier":{"isbn":["978-145034651-1"]}},{"publist_id":"6179","file_date_updated":"2020-07-14T12:44:37Z","editor":[{"full_name":"Papadimitriou, Christos","first_name":"Christos","last_name":"Papadimitriou"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2017","volume":67,"date_updated":"2021-01-12T06:48:51Z","date_created":"2018-12-11T11:50:33Z","author":[{"last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"last_name":"De Rezende","first_name":"Susanna","full_name":"De Rezende, Susanna"},{"full_name":"Nordstrom, Jakob","first_name":"Jakob","last_name":"Nordstrom"},{"full_name":"Vinyals, Marc","first_name":"Marc","last_name":"Vinyals"}],"publication_identifier":{"issn":["18688969"]},"month":"01","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.ITCS.2017.38","conference":{"end_date":"2017-01-11","location":"Berkeley, CA, United States","start_date":"2017-01-09","name":"ITCS: Innovations in Theoretical Computer Science"},"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"We study space complexity and time-space trade-offs with a focus not on peak memory usage but on overall memory consumption throughout the computation. Such a cumulative space measure was introduced for the computational model of parallel black pebbling by [Alwen and Serbinenko ’15] as a tool for obtaining results in cryptography. We consider instead the non- deterministic black-white pebble game and prove optimal cumulative space lower bounds and trade-offs, where in order to minimize pebbling time the space has to remain large during a significant fraction of the pebbling. We also initiate the study of cumulative space in proof complexity, an area where other space complexity measures have been extensively studied during the last 10–15 years. Using and extending the connection between proof complexity and pebble games in [Ben-Sasson and Nordström ’08, ’11] we obtain several strong cumulative space results for (even parallel versions of) the resolution proof system, and outline some possible future directions of study of this, in our opinion, natural and interesting space measure.","lang":"eng"}],"intvolume":" 67","status":"public","title":"Cumulative space in black-white pebbling and resolution","ddc":["005","600"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1175","file":[{"date_updated":"2020-07-14T12:44:37Z","date_created":"2018-12-12T10:17:11Z","checksum":"dbc94810be07c2fb1945d5c2a6130e6c","relation":"main_file","file_id":"5263","file_size":557769,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-927-v1+1_LIPIcs-ITCS-2017-38.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"927","scopus_import":1,"has_accepted_license":"1","day":"01","page":"38:1-38-21","citation":{"chicago":"Alwen, Joel F, Susanna De Rezende, Jakob Nordstrom, and Marc Vinyals. “Cumulative Space in Black-White Pebbling and Resolution.” edited by Christos Papadimitriou, 67:38:1-38-21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ITCS.2017.38.","mla":"Alwen, Joel F., et al. Cumulative Space in Black-White Pebbling and Resolution. Edited by Christos Papadimitriou, vol. 67, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21, doi:10.4230/LIPIcs.ITCS.2017.38.","short":"J.F. Alwen, S. De Rezende, J. Nordstrom, M. Vinyals, in:, C. Papadimitriou (Ed.), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21.","ista":"Alwen JF, De Rezende S, Nordstrom J, Vinyals M. 2017. Cumulative space in black-white pebbling and resolution. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 67, 38:1-38-21.","ieee":"J. F. Alwen, S. De Rezende, J. Nordstrom, and M. Vinyals, “Cumulative space in black-white pebbling and resolution,” presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States, 2017, vol. 67, p. 38:1-38-21.","apa":"Alwen, J. F., De Rezende, S., Nordstrom, J., & Vinyals, M. (2017). Cumulative space in black-white pebbling and resolution. In C. Papadimitriou (Ed.) (Vol. 67, p. 38:1-38-21). Presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2017.38","ama":"Alwen JF, De Rezende S, Nordstrom J, Vinyals M. Cumulative space in black-white pebbling and resolution. In: Papadimitriou C, ed. Vol 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:38:1-38-21. doi:10.4230/LIPIcs.ITCS.2017.38"},"date_published":"2017-01-01T00:00:00Z"},{"page":"525-559","citation":{"apa":"Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3","ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017.","ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.","ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3","chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3.","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.","mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3."},"publication":"Bulletin of Mathematical Biology","date_published":"2017-03-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 79","status":"public","title":"Existence of traveling waves for the generalized F–KPP equation","_id":"1191","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed.","lang":"eng"}],"project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00944"}],"language":[{"iso":"eng"}],"doi":"10.1007/s11538-016-0244-3","month":"03","department":[{"_id":"NiBa"}],"publisher":"Springer","publication_status":"published","acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project.","year":"2017","volume":79,"date_created":"2018-12-11T11:50:38Z","date_updated":"2021-01-12T06:48:58Z","author":[{"full_name":"Kollár, Richard","last_name":"Kollár","first_name":"Richard"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian"}],"publist_id":"6160","ec_funded":1},{"page":"636-655","citation":{"chicago":"Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics. Springer, 2017. https://doi.org/10.1007/s10955-016-1672-z.","short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655.","mla":"Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:10.1007/s10955-016-1672-z.","apa":"Budanur, N. B., & Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1672-z","ieee":"N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer, pp. 636–655, 2017.","ista":"Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655.","ama":"Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 2017;167(3-4):636-655. doi:10.1007/s10955-016-1672-z"},"publication":"Journal of Statistical Physics","date_published":"2017-05-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 167","title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","status":"public","ddc":["530"],"_id":"1211","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":2820207,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-782-v1+1_BudCvi15.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:18:01Z","checksum":"3e971d09eb167761aa0888ed415b0056","relation":"main_file","file_id":"5319"}],"oa_version":"Submitted Version","pubrep_id":"782","type":"journal_article","issue":"3-4","abstract":[{"lang":"eng","text":"Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here."}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s10955-016-1672-z","month":"05","publisher":"Springer","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2017","acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","volume":167,"date_created":"2018-12-11T11:50:44Z","date_updated":"2021-01-12T06:49:07Z","author":[{"full_name":"Budanur, Nazmi B","first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010"},{"first_name":"Predrag","last_name":"Cvitanović","full_name":"Cvitanović, Predrag"}],"publist_id":"6136","file_date_updated":"2020-07-14T12:44:39Z"},{"publist_id":"6254","ec_funded":1,"file_date_updated":"2019-10-24T10:54:37Z","year":"2017","publisher":"Brown University","department":[{"_id":"UlWa"}],"publication_status":"published","related_material":{"record":[{"id":"1164","status":"public","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"1595"}]},"author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"},{"last_name":"Pelsmajer","first_name":"Michael","full_name":"Pelsmajer, Michael"},{"first_name":"Marcus","last_name":"Schaefer","full_name":"Schaefer, Marcus"}],"volume":21,"date_updated":"2023-02-23T10:05:57Z","date_created":"2018-12-11T11:50:13Z","month":"01","external_id":{"arxiv":["1608.08662"]},"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.7155/jgaa.00408","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C 1 , . . . , C k with common center c , and edges are drawn radially : every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Toth."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1113","intvolume":" 21","title":"Hanani-Tutte for radial planarity","ddc":["510"],"status":"public","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":573623,"file_name":"2017_JournalGraphAlgorithms_Fulek.pdf","access_level":"open_access","date_created":"2019-10-24T10:54:37Z","date_updated":"2019-10-24T10:54:37Z","success":1,"file_id":"6967","relation":"main_file"}],"scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"ista":"Fulek R, Pelsmajer M, Schaefer M. 2017. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 21(1), 135–154.","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” Journal of Graph Algorithms and Applications, vol. 21, no. 1. Brown University, pp. 135–154, 2017.","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2017). Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00408","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 2017;21(1):135-154. doi:10.7155/jgaa.00408","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications. Brown University, 2017. https://doi.org/10.7155/jgaa.00408.","mla":"Fulek, Radoslav, et al. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications, vol. 21, no. 1, Brown University, 2017, pp. 135–54, doi:10.7155/jgaa.00408.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, Journal of Graph Algorithms and Applications 21 (2017) 135–154."},"publication":"Journal of Graph Algorithms and Applications","page":"135 - 154","article_type":"original","date_published":"2017-01-01T00:00:00Z"},{"language":[{"iso":"eng"}],"date_published":"2017-11-29T00:00:00Z","doi":"10.1039/9781788010405-00025","quality_controlled":"1","page":"25 - 59","publication":"Mechanisms of primary energy transduction in biology ","citation":{"apa":"Sazanov, L. A. (2017). Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In M. Wikström (Ed.), Mechanisms of primary energy transduction in biology (pp. 25–59). Royal Society of Chemistry. https://doi.org/10.1039/9781788010405-00025","ieee":"L. A. Sazanov, “Structure of respiratory complex I: ‘Minimal’ bacterial and ‘de luxe’ mammalian versions,” in Mechanisms of primary energy transduction in biology , M. Wikström, Ed. Royal Society of Chemistry, 2017, pp. 25–59.","ista":"Sazanov LA. 2017.Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Mechanisms of primary energy transduction in biology . , 25–59.","ama":"Sazanov LA. Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Wikström M, ed. Mechanisms of Primary Energy Transduction in Biology . Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry; 2017:25-59. doi:10.1039/9781788010405-00025","chicago":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” In Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, 25–59. Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781788010405-00025.","short":"L.A. Sazanov, in:, M. Wikström (Ed.), Mechanisms of Primary Energy Transduction in Biology , Royal Society of Chemistry, 2017, pp. 25–59.","mla":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, Royal Society of Chemistry, 2017, pp. 25–59, doi:10.1039/9781788010405-00025."},"day":"29","month":"11","publication_identifier":{"isbn":["978-1-78262-865-1"]},"series_title":"Mechanisms of Primary Energy Transduction in Biology ","date_created":"2018-12-11T11:46:30Z","date_updated":"2021-01-12T07:56:59Z","oa_version":"None","author":[{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"status":"public","publication_status":"published","title":"Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions","department":[{"_id":"LeSa"}],"publisher":"Royal Society of Chemistry","editor":[{"first_name":"Mårten","last_name":"Wikström","full_name":"Wikström, Mårten"}],"_id":"444","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations.","lang":"eng"}],"publist_id":"7379","type":"book_chapter"}]