[{"scopus_import":"1","month":"03","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"issue":"3","_id":"1029","article_number":"e0174066","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"fulldoi":"https://doi.org/10.1371/journal.pone.0174066","publication":"PLoS One","has_accepted_license":"1","date_published":"2017-03-16T00:00:00Z","publication_status":"published","type":"journal_article","ddc":["570"],"title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","file":[{"content_type":"application/pdf","file_id":"4772","access_level":"open_access","date_updated":"2018-12-12T10:09:47Z","creator":"system","date_created":"2018-12-12T10:09:47Z","file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","relation":"main_file","file_size":3429381}],"abstract":[{"lang":"eng","text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking."}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5556"},{"status":"public","id":"6392","relation":"dissertation_contains"}]},"article_processing_charge":"Yes","citation":{"ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066.","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0174066.","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” PLoS One, vol. 12, no. 3. Public Library of Science, 2017.","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066"},"volume":12,"language":[{"iso":"eng"}],"file_date_updated":"2018-12-12T10:09:47Z","oa_version":"Published Version","publication_identifier":{"issn":["1932-6203"]},"day":"16","intvolume":" 12","department":[{"_id":"ToBo"}],"quality_controlled":"1","doi":"10.1371/journal.pone.0174066","external_id":{"isi":["000396318300121"]},"author":[{"orcid":"0000-0001-6549-4177","last_name":"Lukacisin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin","first_name":"Martin"},{"last_name":"Landon","full_name":"Landon, Matthieu","first_name":"Matthieu"},{"full_name":"Jajoo, Rishi","last_name":"Jajoo","first_name":"Rishi"}],"pubrep_id":"800","date_updated":"2026-11-05T23:30:30Z","date_created":"2018-12-11T11:49:46Z","publist_id":"6361","status":"public","publisher":"Public Library of Science"},{"publication":"Development","has_accepted_license":"1","page":"1798 - 1806","type":"journal_article","ddc":["570"],"publication_status":"published","date_published":"2017-05-15T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"fulldoi":"https://doi.org/10.1242/dev.144964","_id":"676","pmid":1,"issue":"10","year":"2017","isi":1,"month":"05","article_type":"original","scopus_import":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","publist_id":"7047","publisher":"Company of Biologists","external_id":{"pmid":["28512197"],"isi":["000402275900007"]},"doi":"10.1242/dev.144964","quality_controlled":"1","department":[{"_id":"Bio"},{"_id":"CaHe"}],"corr_author":"1","intvolume":" 144","date_created":"2018-12-11T11:47:52Z","author":[{"orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","first_name":"Gabriel"},{"first_name":"Jim","full_name":"Veldhuis, Jim","last_name":"Veldhuis"},{"orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","first_name":"Vanessa"},{"orcid":"0000-0001-5199-9940","first_name":"Daniel","full_name":"Capek, Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","full_name":"Maître, Jean-Léon","first_name":"Jean-Léon","orcid":"0000-0002-3688-1474"},{"full_name":"Brodland, Wayne","last_name":"Brodland","first_name":"Wayne"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"date_updated":"2026-11-05T23:30:34Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:39Z","volume":144,"citation":{"ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","ieee":"G. Krens et al., “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” Development, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.","chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144964.","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 2017;144(10):1798-1806. doi:10.1242/dev.144964","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., & Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.144964","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806.","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:10.1242/dev.144964."},"day":"15","oa_version":"Published Version","publication_identifier":{"issn":["0950-1991"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"},{"relation":"dissertation_contains","id":"50","status":"public"}]},"file":[{"checksum":"bc25125fb664706cdf180e061429f91d","file_id":"6905","content_type":"application/pdf","file_size":8194516,"relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:47:39Z","file_name":"2017_Development_Krens.pdf","date_created":"2019-09-24T06:56:22Z","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation."}],"title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","article_processing_charge":"No"},{"publication":"Nature Cell Biology","type":"journal_article","page":"306 - 317","date_published":"2017-03-27T00:00:00Z","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1038/ncb3492","oa":1,"_id":"661","pmid":1,"year":"2017","month":"03","isi":1,"scopus_import":"1","project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589"},{"grant_number":"I930-B20","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publist_id":"7074","status":"public","main_file_link":[{"open_access":"1","url":"https://europepmc.org/articles/pmc5635970"}],"publisher":"Nature Publishing Group","quality_controlled":"1","doi":"10.1038/ncb3492","external_id":{"pmid":["28346437"],"isi":["000397917000009"]},"acknowledged_ssus":[{"_id":"SSU"}],"intvolume":" 19","corr_author":"1","department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"author":[{"first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael","last_name":"Smutny","orcid":"0000-0002-5920-9090"},{"first_name":"Zsuzsa","last_name":"Ákos","full_name":"Ákos, Zsuzsa"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan"},{"first_name":"Verena","full_name":"Ruprecht, Verena","last_name":"Ruprecht"},{"full_name":"Capek, Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0001-5199-9940"},{"first_name":"Martin","full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Papusheva, Ekaterina","last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina"},{"first_name":"Masazumi","last_name":"Tada","full_name":"Tada, Masazumi"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754"},{"last_name":"Vicsek","full_name":"Vicsek, Tamás","first_name":"Tamás"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-11-05T23:30:34Z","date_created":"2018-12-11T11:47:46Z","ec_funded":1,"language":[{"iso":"eng"}],"citation":{"chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3492.","ieee":"M. Smutny et al., “Friction forces position the neural anlage,” Nature Cell Biology, vol. 19. Nature Publishing Group, pp. 306–317, 2017.","ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. Nature Cell Biology. 2017;19:306-317. doi:10.1038/ncb3492","apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3492","short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317.","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:10.1038/ncb3492.","ista":"Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M, Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction forces position the neural anlage. Nature Cell Biology. 19, 306–317."},"volume":19,"publication_identifier":{"issn":["1465-7392"]},"oa_version":"Submitted Version","day":"27","related_material":{"record":[{"relation":"dissertation_contains","id":"8350","status":"public"},{"relation":"dissertation_contains","status":"public","id":"50"}]},"title":"Friction forces position the neural anlage","abstract":[{"text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo.","lang":"eng"}],"article_processing_charge":"No"},{"intvolume":" 46","department":[{"_id":"MiSi"}],"corr_author":"1","quality_controlled":"1","doi":"10.1016/j.immuni.2017.04.006","external_id":{"isi":["000399451100002"]},"date_created":"2018-12-11T11:47:47Z","date_updated":"2026-11-05T23:30:46Z","author":[{"first_name":"Frank P","last_name":"Assen","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"publist_id":"7065","status":"public","publisher":"Cell Press","title":"The dynamic cytokine niche","abstract":[{"lang":"eng","text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it."}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6947"}]},"article_processing_charge":"No","citation":{"ieee":"F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” Immunity, vol. 46, no. 4. Cell Press, pp. 519–520, 2017.","chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” Immunity. Cell Press, 2017. https://doi.org/10.1016/j.immuni.2017.04.006.","ama":"Assen FP, Sixt MK. The dynamic cytokine niche. Immunity. 2017;46(4):519-520. doi:10.1016/j.immuni.2017.04.006","apa":"Assen, F. P., & Sixt, M. K. (2017). The dynamic cytokine niche. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2017.04.006","mla":"Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” Immunity, vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:10.1016/j.immuni.2017.04.006.","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520."},"volume":46,"language":[{"iso":"eng"}],"oa_version":"None","publication_identifier":{"issn":["1074-7613"]},"day":"18","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1016/j.immuni.2017.04.006","publication":"Immunity","date_published":"2017-04-18T00:00:00Z","publication_status":"published","type":"journal_article","page":"519 - 520","scopus_import":"1","month":"04","isi":1,"issue":"4","_id":"664","year":"2017"},{"editor":[{"first_name":"Deepak","last_name":"D'Souza","full_name":"D'Souza, Deepak"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs."}],"file":[{"content_type":"application/pdf","checksum":"a0d9f5f94dc594c4e71e78525c9942f1","file_id":"4835","access_level":"open_access","date_created":"2018-12-12T10:10:45Z","creator":"system","date_updated":"2020-07-14T12:48:16Z","file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","file_size":948514,"relation":"main_file"}],"title":"JTDec: A tool for tree decompositions in soot","related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"day":"01","publication_identifier":{"issn":["0302-9743"]},"oa_version":"Submitted Version","volume":10482,"citation":{"ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:10.1007/978-3-319-68167-2_4","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66. Springer, 2017. https://doi.org/10.1007/978-3-319-68167-2_4.","mla":"Chatterjee, Krishnendu, et al. JTDec: A Tool for Tree Decompositions in Soot. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:10.1007/978-3-319-68167-2_4.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66.","apa":"Chatterjee, K., Goharshady, A. K., & Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. https://doi.org/10.1007/978-3-319-68167-2_4","ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66."},"conference":{"location":"Pune, India","start_date":"2017-10-03","name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2017-10-06"},"alternative_title":["LNCS"],"file_date_updated":"2020-07-14T12:48:16Z","language":[{"iso":"eng"}],"date_updated":"2026-11-05T23:30:50Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-1702-6584","first_name":"Amir","full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady"},{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722"}],"pubrep_id":"845","ec_funded":1,"date_created":"2018-12-11T11:49:22Z","corr_author":"1","department":[{"_id":"KrCh"}],"intvolume":" 10482","external_id":{"isi":["000723567800004"]},"quality_controlled":"1","doi":"10.1007/978-3-319-68167-2_4","publisher":"Springer","status":"public","publist_id":"6468","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"}],"scopus_import":"1","isi":1,"month":"01","year":"2017","_id":"949","fulldoi":"https://doi.org/10.1007/978-3-319-68167-2_4","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","date_published":"2017-01-01T00:00:00Z","page":"59 - 66","type":"conference","ddc":["005"],"has_accepted_license":"1"},{"isi":1,"month":"01","scopus_import":"1","project":[{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"_id":"639","year":"2017","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"fulldoi":"https://doi.org/10.1007/978-3-319-63390-9_3","arxiv":1,"type":"conference","page":"41 - 63","date_published":"2017-01-01T00:00:00Z","publication_status":"published","related_material":{"record":[{"id":"7014","status":"public","relation":"later_version"},{"relation":"dissertation_contains","id":"8934","status":"public"}]},"title":"Non-polynomial worst case analysis of recursive programs","abstract":[{"text":"We study the problem of developing efficient approaches for proving worst-case bounds of non-deterministic recursive programs. Ranking functions are sound and complete for proving termination and worst-case bounds of non-recursive programs. First, we apply ranking functions to recursion, resulting in measure functions, and show that they provide a sound and complete approach to prove worst-case bounds of non-deterministic recursive programs. Our second contribution is the synthesis of measure functions in non-polynomial forms. We show that non-polynomial measure functions with logarithm and exponentiation can be synthesized through abstraction of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem using linear programming. While previous methods obtain worst-case polynomial bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr) where r is not an integer. We present experimental results to demonstrate that our approach can efficiently obtain worst-case bounds of classical recursive algorithms such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm.","lang":"eng"}],"article_processing_charge":"No","editor":[{"first_name":"Rupak","full_name":"Majumdar, Rupak","last_name":"Majumdar"},{"last_name":"Kunčak","full_name":"Kunčak, Viktor","first_name":"Viktor"}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"conference":{"start_date":"2017-07-24","location":"Heidelberg, Germany","name":"CAV: Computer Aided Verification","end_date":"2017-07-28"},"citation":{"ista":"Chatterjee K, Fu H, Goharshady AK. 2017. Non-polynomial worst case analysis of recursive programs. CAV: Computer Aided Verification, LNCS, vol. 10427, 41–63.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst Case Analysis of Recursive Programs.” edited by Rupak Majumdar and Viktor Kunčak, 10427:41–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_3.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst case analysis of recursive programs,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 41–63.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst case analysis of recursive programs. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:41-63. doi:10.1007/978-3-319-63390-9_3","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2017). Non-polynomial worst case analysis of recursive programs. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_3","mla":"Chatterjee, Krishnendu, et al. Non-Polynomial Worst Case Analysis of Recursive Programs. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 41–63, doi:10.1007/978-3-319-63390-9_3.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 41–63."},"volume":10427,"publication_identifier":{"isbn":["978-331963389-3"]},"oa_version":"Submitted Version","day":"01","quality_controlled":"1","doi":"10.1007/978-3-319-63390-9_3","external_id":{"arxiv":["1705.00317"],"isi":["000431900900003"]},"intvolume":" 10427","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:47:39Z","date_updated":"2026-11-05T23:30:50Z","ec_funded":1,"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir","last_name":"Goharshady","orcid":"0000-0003-1702-6584"}],"publist_id":"7149","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}],"publisher":"Springer"},{"article_number":"176","year":"2017","_id":"960","project":[{"grant_number":"618444","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"T00817-B21","_id":"25985A36-B435-11E9-9278-68D0E5697425","name":"The biochemical basis of PAR polarization","call_identifier":"FWF"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"scopus_import":"1","month":"06","isi":1,"date_published":"2017-06-28T00:00:00Z","publication_status":"published","ddc":["570"],"type":"journal_article","has_accepted_license":"1","publication":"Frontiers in Cellular Neuroscience","fulldoi":"https://doi.org/10.3389/fncel.2017.00176","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1662-5102"]},"oa_version":"Published Version","day":"28","citation":{"apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., & Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncel.2017.00176","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017).","mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience, vol. 11, 176, Frontiers Research Foundation, 2017, doi:10.3389/fncel.2017.00176.","ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” Frontiers in Cellular Neuroscience, vol. 11. Frontiers Research Foundation, 2017.","chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fncel.2017.00176.","ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 2017;11. doi:10.3389/fncel.2017.00176","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176."},"volume":11,"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:16Z","article_processing_charge":"Yes","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","abstract":[{"text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context.","lang":"eng"}],"file":[{"access_level":"open_access","file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf","creator":"system","date_created":"2018-12-12T10:09:40Z","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","file_size":2153858,"content_type":"application/pdf","checksum":"dc1f5a475b918d09a0f9f587400b1626","file_id":"4764"}],"related_material":{"record":[{"id":"9962","status":"public","relation":"dissertation_contains"}]},"publisher":"Frontiers Research Foundation","publist_id":"6445","status":"public","ec_funded":1,"author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"},{"orcid":"0000-0001-6335-9748","first_name":"Christian F","full_name":"Düllberg, Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg"},{"last_name":"Mieck","full_name":"Mieck, Christine","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87","first_name":"Christine","orcid":"0000-0003-1919-7416"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"date_created":"2018-12-11T11:49:25Z","pubrep_id":"830","date_updated":"2026-11-05T23:30:52Z","intvolume":" 11","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"quality_controlled":"1","doi":"10.3389/fncel.2017.00176","external_id":{"isi":["000404486700001"]}},{"publisher":"Public Library of Science","status":"public","publist_id":"7004","ec_funded":1,"date_created":"2018-12-11T11:47:58Z","pubrep_id":"894","date_updated":"2026-11-05T23:30:53Z","author":[{"first_name":"Marta","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","orcid":"0000-0002-2519-8004"},{"orcid":"0000-0002-2519-824X","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tiago","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953"}],"external_id":{"isi":["000406619800014"]},"quality_controlled":"1","doi":"10.1371/journal.pcbi.1005609","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"corr_author":"1","intvolume":" 13","day":"18","oa_version":"Published Version","publication_identifier":{"issn":["1553-734X"]},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:46Z","volume":13,"citation":{"ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017)."},"article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"9849","relation":"research_data"},{"id":"9850","status":"public","relation":"research_data"},{"id":"9851","status":"public","relation":"research_data"},{"status":"public","id":"9852","relation":"research_data"},{"id":"6263","status":"public","relation":"dissertation_contains"}]},"file":[{"relation":"main_file","file_size":3775716,"access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:47:46Z","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","date_created":"2018-12-12T10:15:01Z","checksum":"9143c290fa6458ed2563bff4b295554a","file_id":"5117","content_type":"application/pdf"}],"abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","ddc":["576"],"type":"journal_article","publication_status":"published","date_published":"2017-07-18T00:00:00Z","has_accepted_license":"1","publication":"PLoS Computational Biology","oa":1,"fulldoi":"https://doi.org/10.1371/journal.pcbi.1005609","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2017","article_number":"e1005609","_id":"696","issue":"7","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091"}],"isi":1,"month":"07","scopus_import":"1","article_type":"original"},{"isi":1,"month":"08","scopus_import":"1","article_type":"original","project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"},{"grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"_id":"1027","year":"2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"fulldoi":"https://doi.org/10.1016/j.copbio.2017.02.013","has_accepted_license":"1","publication":"Current Opinion in Biotechnology","type":"journal_article","ddc":["570"],"page":"90 - 97","date_published":"2017-08-01T00:00:00Z","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"6263","status":"public"}]},"title":"Toward a quantitative understanding of antibiotic resistance evolution","abstract":[{"lang":"eng","text":"The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance."}],"file":[{"access_level":"open_access","creator":"dernst","date_updated":"2019-01-18T09:57:57Z","date_created":"2019-01-18T09:57:57Z","file_name":"2017_CurrentOpinion_Lukaciinova.pdf","relation":"main_file","file_size":858338,"content_type":"application/pdf","success":1,"file_id":"5846"}],"article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2019-01-18T09:57:57Z","language":[{"iso":"eng"}],"citation":{"ieee":"M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding of antibiotic resistance evolution,” Current Opinion in Biotechnology, vol. 46. Elsevier, pp. 90–97, 2017.","chicago":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013.","ama":"Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97. doi:10.1016/j.copbio.2017.02.013","apa":"Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.013","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97.","mla":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology, vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97."},"volume":46,"oa_version":"Published Version","day":"01","quality_controlled":"1","doi":"10.1016/j.copbio.2017.02.013","external_id":{"isi":["000408077400015"]},"intvolume":" 46","department":[{"_id":"ToBo"}],"corr_author":"1","date_updated":"2026-11-05T23:30:53Z","date_created":"2018-12-11T11:49:45Z","ec_funded":1,"pubrep_id":"801","author":[{"first_name":"Marta","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","orcid":"0000-0002-2519-8004"},{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X"}],"publist_id":"6364","status":"public","publisher":"Elsevier"},{"article_processing_charge":"No","title":"PirB regulates asymmetries in hippocampal circuitry","file":[{"checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8","file_id":"4934","content_type":"application/pdf","relation":"main_file","file_size":5798454,"file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","date_created":"2018-12-12T10:12:16Z","creator":"system","date_updated":"2020-07-14T12:47:40Z","access_level":"open_access"}],"abstract":[{"text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"51"}]},"oa_version":"Published Version","publication_identifier":{"issn":["1932-6203"]},"day":"01","citation":{"ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377.","apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0179377","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:10.1371/journal.pone.0179377.","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).","ieee":"H. Ukai et al., “PirB regulates asymmetries in hippocampal circuitry,” PLoS One, vol. 12, no. 6. Public Library of Science, 2017.","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0179377.","ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 2017;12(6). doi:10.1371/journal.pone.0179377"},"volume":12,"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:40Z","pubrep_id":"897","author":[{"first_name":"Hikari","full_name":"Ukai, Hikari","last_name":"Ukai"},{"first_name":"Aiko","full_name":"Kawahara, Aiko","last_name":"Kawahara"},{"last_name":"Hirayama","full_name":"Hirayama, Keiko","first_name":"Keiko"},{"first_name":"Matthew J","last_name":"Case","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Case, Matthew J"},{"first_name":"Shotaro","full_name":"Aino, Shotaro","last_name":"Aino"},{"last_name":"Miyabe","full_name":"Miyabe, Masahiro","first_name":"Masahiro"},{"first_name":"Ken","full_name":"Wakita, Ken","last_name":"Wakita"},{"first_name":"Ryohei","full_name":"Oogi, Ryohei","last_name":"Oogi"},{"full_name":"Kasayuki, Michiyo","last_name":"Kasayuki","first_name":"Michiyo"},{"first_name":"Shihomi","full_name":"Kawashima, Shihomi","last_name":"Kawashima"},{"first_name":"Shunichi","full_name":"Sugimoto, Shunichi","last_name":"Sugimoto"},{"first_name":"Kanako","last_name":"Chikamatsu","full_name":"Chikamatsu, Kanako"},{"full_name":"Nitta, Noritaka","last_name":"Nitta","first_name":"Noritaka"},{"first_name":"Tsuneyuki","last_name":"Koga","full_name":"Koga, Tsuneyuki"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"last_name":"Takai","full_name":"Takai, Toshiyuki","first_name":"Toshiyuki"},{"full_name":"Ito, Isao","last_name":"Ito","first_name":"Isao"}],"date_created":"2018-12-11T11:47:54Z","date_updated":"2026-11-05T23:30:55Z","intvolume":" 12","department":[{"_id":"RySh"}],"quality_controlled":"1","doi":"10.1371/journal.pone.0179377","external_id":{"isi":["000402923200125"]},"publisher":"Public Library of Science","publist_id":"7034","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"scopus_import":"1","article_type":"original","isi":1,"month":"06","article_number":"e0179377","year":"2017","issue":"6","_id":"682","fulldoi":"https://doi.org/10.1371/journal.pone.0179377","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2017-06-01T00:00:00Z","publication_status":"published","ddc":["571"],"type":"journal_article","has_accepted_license":"1","publication":"PLoS One"},{"type":"journal_article","ddc":["575"],"page":"1 - 29","date_published":"2017-03-17T00:00:00Z","publication_status":"published","publication":"Auxins and Cytokinins in Plant Biology","has_accepted_license":"1","oa":1,"fulldoi":"https://doi.org/10.1007/978-1-4939-6831-2_1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","_id":"1024","project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I 1774-B16"}],"month":"03","scopus_import":"1","publisher":"Springer","publist_id":"6369","status":"public","pubrep_id":"1019","date_updated":"2026-11-05T23:30:55Z","date_created":"2018-12-11T11:49:45Z","author":[{"orcid":"0000-0003-3638-1426","first_name":"Andrej","last_name":"Hurny","full_name":"Hurny, Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"quality_controlled":"1","doi":"10.1007/978-1-4939-6831-2_1","intvolume":" 1569","department":[{"_id":"EvBe"}],"corr_author":"1","oa_version":"Submitted Version","publication_identifier":{"issn":["1064-3745"]},"day":"17","language":[{"iso":"eng"}],"file_date_updated":"2019-10-15T07:47:05Z","alternative_title":["Methods in Molecular Biology"],"citation":{"ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29."},"volume":1569,"article_processing_charge":"No","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"539"}]},"title":"Methodological advances in auxin and cytokinin biology","file":[{"file_size":840646,"relation":"main_file","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:14:18Z","date_updated":"2019-10-15T07:47:05Z","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","file_id":"5068","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges."}]},{"status":"public","publist_id":"6362","publisher":"Wiley","corr_author":"1","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"intvolume":" 56","external_id":{"isi":["000398154000038"]},"doi":"10.1002/anie.201611998","quality_controlled":"1","date_updated":"2026-11-05T23:30:57Z","ec_funded":1,"date_created":"2018-12-11T11:49:46Z","author":[{"orcid":"0000-0002-6709-2195","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","full_name":"Kainrath, Stephanie","first_name":"Stephanie"},{"last_name":"Stadler","full_name":"Stadler, Manuela","first_name":"Manuela"},{"first_name":"Eva","full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","orcid":"0000-0002-7218-7738"},{"last_name":"Distel","full_name":"Distel, Martin","first_name":"Martin"},{"first_name":"Harald L","full_name":"Janovjak, Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"volume":56,"citation":{"ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie International Edition, vol. 56, no. 16. Wiley, pp. 4608–4611, 2017.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie International Edition. Wiley, 2017. https://doi.org/10.1002/anie.201611998.","mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie International Edition, vol. 56, no. 16, Wiley, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie International Edition 56 (2017) 4608–4611.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201611998","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie International Edition. 56(16), 4608–4611."},"language":[{"iso":"eng"}],"file_date_updated":"2019-01-18T09:39:55Z","day":"20","publication_identifier":{"issn":["1433-7851"]},"oa_version":"Published Version","file":[{"content_type":"application/pdf","success":1,"file_id":"5845","access_level":"open_access","file_name":"2017_communications_Kainrath.pdf","creator":"dernst","date_created":"2019-01-18T09:39:55Z","date_updated":"2019-01-18T09:39:55Z","file_size":2614942,"relation":"main_file"}],"abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes."}],"title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","acknowledgement":"This work was supported by a grant from the European Union􏰝s Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","related_material":{"record":[{"status":"public","id":"418","relation":"dissertation_contains"},{"status":"public","id":"7680","relation":"part_of_dissertation"}]},"das_tickbox":"1","article_processing_charge":"No","publication":"Angewandte Chemie International Edition","has_accepted_license":"1","publication_status":"published","date_published":"2017-03-20T00:00:00Z","page":"4608-4611","ddc":["540"],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"fulldoi":"https://doi.org/10.1002/anie.201611998","issue":"16","_id":"1028","year":"2017","scopus_import":"1","month":"03","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303564"},{"call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"}]},{"year":"2016","_id":"1082","month":"12","scopus_import":"1","page":"1965-1973","type":"conference","publication_status":"published","date_published":"2016-12-01T00:00:00Z","arxiv":1,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Preprint","conference":{"end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems","location":"Barcelona, Spain","start_date":"2016-12-05"},"alternative_title":["Advances in Neural Information Processing Systems"],"language":[{"iso":"eng"}],"volume":29,"citation":{"ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.","ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems Foundation, 2016.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 1965–1973.","mla":"Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 1965–73.","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation."},"article_processing_charge":"No","related_material":{"link":[{"url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck","relation":"other"}]},"abstract":[{"text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y.","lang":"eng"}],"title":"Relevant sparse codes with variational information bottleneck","publisher":"Neural Information Processing Systems Foundation","status":"public","publist_id":"6298","main_file_link":[{"url":"https://arxiv.org/abs/1605.07332","open_access":"1"}],"date_updated":"2025-06-03T11:33:51Z","date_created":"2018-12-11T11:50:03Z","author":[{"first_name":"Matthew J","full_name":"Chalk, Matthew J","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper"}],"external_id":{"arxiv":["1605.07332"]},"quality_controlled":"1","department":[{"_id":"GaTk"}],"intvolume":" 29"},{"publist_id":"6297","status":"public","publisher":"Oxford University Press","intvolume":" 27","department":[{"_id":"RySh"}],"doi":"10.1093/cercor/bhw090","quality_controlled":"1","external_id":{"isi":["000397636600048"]},"date_updated":"2025-09-22T14:19:11Z","date_created":"2018-12-11T11:50:03Z","author":[{"last_name":"Booker","full_name":"Booker, Sam","first_name":"Sam"},{"first_name":"Daniel","full_name":"Althof, Daniel","last_name":"Althof"},{"first_name":"Anna","full_name":"Gross, Anna","last_name":"Gross"},{"full_name":"Loreth, Desiree","last_name":"Loreth","first_name":"Desiree"},{"first_name":"Johanna","last_name":"Müller","full_name":"Müller, Johanna"},{"last_name":"Unger","full_name":"Unger, Andreas","first_name":"Andreas"},{"full_name":"Fakler, Bernd","last_name":"Fakler","first_name":"Bernd"},{"last_name":"Varro","full_name":"Varro, Andrea","first_name":"Andrea"},{"full_name":"Watanabe, Masahiko","last_name":"Watanabe","first_name":"Masahiko"},{"first_name":"Martin","last_name":"Gassmann","full_name":"Gassmann, Martin"},{"full_name":"Bettler, Bernhard","last_name":"Bettler","first_name":"Bernhard"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"full_name":"Vida, Imre","last_name":"Vida","first_name":"Imre"},{"full_name":"Kulik, Ákos","last_name":"Kulik","first_name":"Ákos"}],"citation":{"ama":"Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 2016;27(3):2318-2334. doi:10.1093/cercor/bhw090","ieee":"S. Booker et al., “KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons,” Cerebral Cortex, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016.","chicago":"Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller, Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex. Oxford University Press, 2016. https://doi.org/10.1093/cercor/bhw090.","short":"S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler, A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik, Cerebral Cortex 27 (2016) 2318–2334.","mla":"Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex, vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:10.1093/cercor/bhw090.","apa":"Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik, Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhw090","ista":"Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334."},"volume":27,"language":[{"iso":"eng"}],"oa_version":"None","day":"12","title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","abstract":[{"text":" Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABABreceptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins. ","lang":"eng"}],"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation (3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland (I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider, Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided by Dr G.V. Ohning, CURE Center, UCLA, CA. ","article_processing_charge":"No","publication":"Cerebral Cortex","date_published":"2016-04-12T00:00:00Z","publication_status":"published","type":"journal_article","page":"2318 - 2334","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1093/cercor/bhw090","issue":"3","_id":"1083","year":"2016","scopus_import":"1","month":"04","isi":1},{"publist_id":"6286","status":"public","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":" 58","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.MFCS.2016.24","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"795","date_created":"2018-12-11T11:50:05Z","date_updated":"2025-07-10T11:50:02Z","ec_funded":1,"citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted limit-average automata of bounded width,” presented at the MFCS: Mathematical Foundations of Computer Science, Krakow; Poland, 2016, vol. 58.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.24.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted limit-average automata of bounded width. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.MFCS.2016.24","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Nested weighted limit-average automata of bounded width (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science, Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2016.24","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Chatterjee, Krishnendu, et al. Nested Weighted Limit-Average Automata of Bounded Width. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.MFCS.2016.24.","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata of bounded width. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 24."},"volume":58,"file_date_updated":"2018-12-12T10:17:31Z","language":[{"iso":"eng"}],"alternative_title":["LIPIcs"],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2016-08-26","location":"Krakow; Poland","start_date":"2016-08-22"},"oa_version":"Published Version","day":"01","title":"Nested weighted limit-average automata of bounded width","file":[{"date_created":"2018-12-12T10:17:31Z","file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf","creator":"system","date_updated":"2018-12-12T10:17:31Z","access_level":"open_access","file_size":564560,"relation":"main_file","content_type":"application/pdf","file_id":"5286"}],"abstract":[{"text":" While weighted automata provide a natural framework to express quantitative properties, many basic properties like average response time cannot be expressed with weighted automata. Nested weighted automata extend weighted automata and consist of a master automaton and a set of slave automata that are invoked by the master automaton. Nested weighted automata are strictly more expressive than weighted automata (e.g., average response time can be expressed with nested weighted automata), but the basic decision questions have higher complexity (e.g., for deterministic automata, the emptiness question for nested weighted automata is PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME). We consider a natural subclass of nested weighted automata where at any point at most a bounded number k of slave automata can be active. We focus on automata whose master value function is the limit average. We show that these nested weighted automata with bounded width are strictly more expressive than weighted automata (e.g., average response time with no overlapping requests can be expressed with bound k=1, but not with non-nested weighted automata). We show that the complexity of the basic decision problems (i.e., emptiness and universality) for the subclass with k constant matches the complexity for weighted automata. Moreover, when k is part of the input given in unary we establish PSPACE-completeness.","lang":"eng"}],"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under grant 2014/15/D/ST6/04543.","article_processing_charge":"No","has_accepted_license":"1","date_published":"2016-08-01T00:00:00Z","publication_status":"published","type":"conference","ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"fulldoi":"https://doi.org/10.4230/LIPIcs.MFCS.2016.24","_id":"1090","article_number":"24","year":"2016","scopus_import":"1","month":"08","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"scopus_import":1,"month":"08","year":"2016","article_number":"20","_id":"1093","oa":1,"fulldoi":"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2016-08-01T00:00:00Z","type":"conference","ddc":["004"],"has_accepted_license":"1","file":[{"file_id":"4895","content_type":"application/pdf","file_size":501827,"relation":"main_file","creator":"system","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","date_created":"2018-12-12T10:11:39Z","date_updated":"2018-12-12T10:11:39Z","access_level":"open_access"}],"abstract":[{"text":"We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results. ","lang":"eng"}],"title":"Linear distances between Markov chains","related_material":{"record":[{"id":"1155","status":"public","relation":"dissertation_contains"}]},"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF) under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award), by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced Postdoc. Mobility Fellowship – grant number P300P2_161067.","day":"01","oa_version":"Published Version","volume":59,"citation":{"ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Linear distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Daca, Przemyslaw, et al. Linear Distances between Markov Chains. Vol. 59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.20.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City; Canada, 2016, vol. 59.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20"},"conference":{"location":"Quebec City; Canada","start_date":"2016-08-23","name":"CONCUR: Concurrency Theory","end_date":"2016-08-26"},"alternative_title":["LIPIcs"],"file_date_updated":"2018-12-12T10:11:39Z","language":[{"iso":"eng"}],"date_updated":"2026-04-15T10:02:12Z","pubrep_id":"794","date_created":"2018-12-11T11:50:06Z","ec_funded":1,"author":[{"first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","full_name":"Daca, Przemyslaw"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881"},{"first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"intvolume":" 59","quality_controlled":"1","doi":"10.4230/LIPIcs.CONCUR.2016.20","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","publist_id":"6283"},{"month":"08","project":[{"call_identifier":"FP7","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","grant_number":"604102"}],"_id":"1094","year":"2016","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","fulldoi":"https://doi.org/10.1007/978-1-4939-6352-2_12","publication":"High-Resolution Imaging of Cellular Proteins","publication_status":"published","date_published":"2016-08-12T00:00:00Z","page":"203 - 216","type":"book_chapter","abstract":[{"text":"Immunogold labeling of freeze-fracture replicas has recently been used for high-resolution visualization of protein localization in electron microscopy. This method has higher labeling efficiency than conventional immunogold methods for membrane molecules allowing precise quantitative measurements. However, one of the limitations of freeze-fracture replica immunolabeling is difficulty in keeping structural orientation and identifying labeled profiles in complex tissues like brain. The difficulty is partly due to fragmentation of freeze-fracture replica preparations during labeling procedures and limited morphological clues on the replica surface. To overcome these issues, we introduce here a grid-glued replica method combined with SEM observation. This method allows histological staining before dissolving the tissue and easy handling of replicas during immunogold labeling, and keeps the whole replica surface intact without fragmentation. The procedure described here is also useful for matched double-replica analysis allowing further identification of labeled profiles in corresponding P-face and E-face.","lang":"eng"}],"title":"Immunogold protein localization on grid-glued freeze-fracture replicas","acknowledgement":"We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron microscope imaging. This work was supported by the European Union (HBP—Project Ref. 604102). ","article_processing_charge":"No","volume":1474,"citation":{"chicago":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” In High-Resolution Imaging of Cellular Proteins, 1474:203–16. Springer, 2016. https://doi.org/10.1007/978-1-4939-6352-2_12.","ieee":"H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued freeze-fracture replicas,” in High-Resolution Imaging of Cellular Proteins, vol. 1474, Springer, 2016, pp. 203–216.","ama":"Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Vol 1474. Springer; 2016:203-216. doi:10.1007/978-1-4939-6352-2_12","apa":"Harada, H., & Shigemoto, R. (2016). Immunogold protein localization on grid-glued freeze-fracture replicas. In High-Resolution Imaging of Cellular Proteins (Vol. 1474, pp. 203–216). Springer. https://doi.org/10.1007/978-1-4939-6352-2_12","short":"H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins, Springer, 2016, pp. 203–216.","mla":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” High-Resolution Imaging of Cellular Proteins, vol. 1474, Springer, 2016, pp. 203–16, doi:10.1007/978-1-4939-6352-2_12.","ista":"Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods in Molecular Biology, vol. 1474, 203–216."},"alternative_title":["Methods in Molecular Biology"],"language":[{"iso":"eng"}],"day":"12","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"]},"oa_version":"None","department":[{"_id":"RySh"}],"intvolume":" 1474","acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1007/978-1-4939-6352-2_12","quality_controlled":"1","date_updated":"2025-04-15T07:12:21Z","date_created":"2018-12-11T11:50:06Z","author":[{"orcid":"0000-0001-7429-7896","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","full_name":"Harada, Harumi"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"}],"ec_funded":1,"status":"public","publist_id":"6281","publisher":"Springer"},{"ec_funded":1,"author":[{"full_name":"Haas, Andreas","last_name":"Haas","first_name":"Andreas"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Holzer","full_name":"Holzer, Andreas"},{"first_name":"Christoph","last_name":"Kirsch","full_name":"Kirsch, Christoph"},{"first_name":"Michael","last_name":"Lippautz","full_name":"Lippautz, Michael"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","full_name":"Sezgin, Ali"},{"first_name":"Ana","full_name":"Sokolova, Ana","last_name":"Sokolova"},{"first_name":"Helmut","full_name":"Veith, Helmut","last_name":"Veith"}],"date_created":"2018-12-11T11:50:07Z","pubrep_id":"793","date_updated":"2025-04-15T06:25:58Z","doi":"10.4230/LIPIcs.CONCUR.2016.6","quality_controlled":"1","department":[{"_id":"ToHe"}],"intvolume":" 59","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","publist_id":"6280","acknowledgement":"This work has been supported by the National Research Network RiSE on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23, S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1, the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","abstract":[{"text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. ","lang":"eng"}],"file":[{"file_id":"4795","content_type":"application/pdf","relation":"main_file","file_size":589747,"access_level":"open_access","file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","creator":"system","date_created":"2018-12-12T10:10:10Z","date_updated":"2018-12-12T10:10:10Z"}],"title":"Local linearizability for concurrent container-type data structures","day":"01","oa_version":"Published Version","alternative_title":["LIPIcs"],"conference":{"end_date":"2016-08-26","name":"CONCUR: Concurrency Theory","location":"Quebec City; Canada","start_date":"2016-08-23"},"file_date_updated":"2018-12-12T10:10:10Z","language":[{"iso":"eng"}],"volume":59,"citation":{"ieee":"A. Haas et al., “Local linearizability for concurrent container-type data structures,” in Leibniz International Proceedings in Informatics, Quebec City; Canada, 2016, vol. 59.","chicago":"Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability for Concurrent Container-Type Data Structures.” In Leibniz International Proceedings in Informatics, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6.","ama":"Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent container-type data structures. In: Leibniz International Proceedings in Informatics. Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.6","apa":"Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H., … Veith, H. (2016). Local linearizability for concurrent container-type data structures. In Leibniz International Proceedings in Informatics (Vol. 59). Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6","short":"A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A. Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type Data Structures.” Leibniz International Proceedings in Informatics, vol. 59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.6.","ista":"Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A, Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 6."},"fulldoi":"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"type":"conference","publication_status":"published","date_published":"2016-08-01T00:00:00Z","has_accepted_license":"1","publication":"Leibniz International Proceedings in Informatics","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"}],"month":"08","scopus_import":1,"year":"2016","article_number":"6","_id":"1095"},{"publication":"Developmental Cell","publication_status":"published","date_published":"2016-06-20T00:00:00Z","page":"493 - 506","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1016/j.devcel.2016.05.024","issue":"6","_id":"1096","year":"2016","scopus_import":"1","isi":1,"month":"06","status":"public","publist_id":"6279","publisher":"Cell Press","department":[{"_id":"CaHe"}],"intvolume":" 37","external_id":{"isi":["000378204200005"]},"quality_controlled":"1","doi":"10.1016/j.devcel.2016.05.024","author":[{"last_name":"Schwayer","id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia","first_name":"Cornelia","orcid":"0000-0001-5130-2226"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K"},{"first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","last_name":"Slovakova","full_name":"Slovakova, Jana"},{"first_name":"Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"date_updated":"2026-04-08T13:55:28Z","date_created":"2018-12-11T11:50:07Z","volume":37,"citation":{"ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","apa":"Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., & Heisenberg, C.-P. J. (2016). Actin rings of power. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.05.024","mla":"Schwayer, Cornelia, et al. “Actin Rings of Power.” Developmental Cell, vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:10.1016/j.devcel.2016.05.024.","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506.","chicago":"Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and Carl-Philipp J Heisenberg. “Actin Rings of Power.” Developmental Cell. Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.05.024.","ieee":"C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg, “Actin rings of power,” Developmental Cell, vol. 37, no. 6. Cell Press, pp. 493–506, 2016.","ama":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings of power. Developmental Cell. 2016;37(6):493-506. doi:10.1016/j.devcel.2016.05.024"},"language":[{"iso":"eng"}],"day":"20","oa_version":"None","title":"Actin rings of power","related_material":{"record":[{"status":"public","id":"7186","relation":"part_of_dissertation"}]},"article_processing_charge":"No"},{"alternative_title":["ACM Transactions on Graphics"],"conference":{"location":"Macao, China","start_date":"2016-12-05","end_date":"2016-12-08","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia"},"language":[{"iso":"eng"}],"file_date_updated":"2018-12-12T10:17:42Z","volume":35,"citation":{"apa":"Du, T., Schulz, A., Zhu, B., Bickel, B., & Matusik, W. (2016). Computational multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982427","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.","mla":"Du, Tao, et al. Computational Multicopter Design. Vol. 35, no. 6, 227, ACM, 2016, doi:10.1145/2980179.2982427.","chicago":"Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational Multicopter Design,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982427.","ieee":"T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982427","ista":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227."},"day":"01","oa_version":"Submitted Version","acknowledgement":"We thank Nobuyuki Umetani for his insightful suggestions in our discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing mechanical parts and providing 3D printing technical support; Charles Blouin from RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis work was partially supported by Air Force Research Laboratory’s sponsorship of Julia: A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2- 0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967, MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 645599. ","file":[{"date_created":"2018-12-12T10:17:42Z","creator":"system","file_name":"IST-2017-759-v1+1_copter.pdf","date_updated":"2018-12-12T10:17:42Z","access_level":"open_access","file_size":33114420,"relation":"main_file","content_type":"application/pdf","file_id":"5298"}],"abstract":[{"lang":"eng","text":"We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics."}],"title":"Computational multicopter design","article_processing_charge":"No","status":"public","publist_id":"6278","publisher":"ACM","external_id":{"isi":["000388446200069"]},"quality_controlled":"1","doi":"10.1145/2980179.2982427","department":[{"_id":"BeBi"}],"intvolume":" 35","ec_funded":1,"date_updated":"2025-09-22T14:17:29Z","date_created":"2018-12-11T11:50:07Z","pubrep_id":"759","author":[{"first_name":"Tao","full_name":"Du, Tao","last_name":"Du"},{"first_name":"Adriana","last_name":"Schulz","full_name":"Schulz, Adriana"},{"first_name":"Bo","last_name":"Zhu","full_name":"Zhu, Bo"},{"last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385"},{"first_name":"Wojciech","full_name":"Matusik, Wojciech","last_name":"Matusik"}],"_id":"1097","issue":"6","year":"2016","article_number":"227","month":"11","isi":1,"scopus_import":"1","project":[{"name":"Soft-bodied intelligence for Manipulation","_id":"25082902-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"645599"}],"has_accepted_license":"1","type":"conference","ddc":["006"],"publication_status":"published","date_published":"2016-11-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"fulldoi":"https://doi.org/10.1145/2980179.2982427"}]