[{"month":"04","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"oa":1,"external_id":{"pmid":[" 32094266"],"isi":["000534387800005"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Protein structure and function in filopodia across scales"}],"doi":"10.1242/jcs.239020","language":[{"iso":"eng"}],"article_number":"jcs239020","file_date_updated":"2020-10-11T22:30:02Z","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","year":"2020","pmid":1,"publication_status":"published","publisher":"The Company of Biologists","department":[{"_id":"FlSc"}],"author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","first_name":"Georgi A","last_name":"Dimchev","full_name":"Dimchev, Georgi A"},{"first_name":"Behnam","last_name":"Amiri","full_name":"Amiri, Behnam"},{"full_name":"Humphries, Ashley C.","first_name":"Ashley C.","last_name":"Humphries"},{"full_name":"Schaks, Matthias","first_name":"Matthias","last_name":"Schaks"},{"full_name":"Dimchev, Vanessa","first_name":"Vanessa","last_name":"Dimchev"},{"first_name":"Theresia E. B.","last_name":"Stradal","full_name":"Stradal, Theresia E. B."},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"last_name":"Krause","first_name":"Matthias","full_name":"Krause, Matthias"},{"full_name":"Way, Michael","first_name":"Michael","last_name":"Way"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"}],"date_updated":"2023-09-05T15:41:48Z","date_created":"2020-09-17T14:00:33Z","volume":133,"keyword":["Cell Biology"],"day":"09","article_processing_charge":"No","has_accepted_license":"1","publication":"Journal of Cell Science","citation":{"ieee":"G. A. Dimchev et al., “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” Journal of Cell Science, vol. 133, no. 7. The Company of Biologists, 2020.","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.239020","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 2020;133(7). doi:10.1242/jcs.239020","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.239020.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:10.1242/jcs.239020."},"article_type":"original","date_published":"2020-04-09T00:00:00Z","type":"journal_article","abstract":[{"text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. ","lang":"eng"}],"issue":"7","_id":"8434","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["570"],"title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","intvolume":" 133","file":[{"file_name":"2020_JournalCellScience_Dimchev.pdf","access_level":"open_access","creator":"dernst","file_size":13493302,"content_type":"application/pdf","embargo":"2020-10-10","file_id":"8435","relation":"main_file","date_updated":"2020-10-11T22:30:02Z","date_created":"2020-09-17T14:07:51Z","checksum":"ba917e551acc4ece2884b751434df9ae"}],"oa_version":"Published Version"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"27","citation":{"mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9.","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946.","chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology. Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9.","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9","ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9","ieee":"T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020."},"publication":"Nature Biotechnology","page":"944-946","article_type":"original","date_published":"2020-04-27T00:00:00Z","type":"journal_article","abstract":[{"text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7889","intvolume":" 38","title":"Plants with genetically encoded autoluminescence","status":"public","ddc":["570"],"oa_version":"Submitted Version","file":[{"checksum":"1b30467500ec6277229a875b06e196d0","date_created":"2020-08-28T08:57:07Z","date_updated":"2021-03-02T23:30:03Z","file_id":"8316","embargo":"2021-03-01","relation":"main_file","creator":"dernst","file_size":1180086,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_NatureBiotech_Mitiouchkina.pdf"}],"publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"month":"04","external_id":{"isi":["000529298800003"],"pmid":["32341562"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41587-020-0500-9","language":[{"iso":"eng"}],"ec_funded":1,"file_date_updated":"2021-03-02T23:30:03Z","pmid":1,"year":"2020","acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1038/s41587-020-0578-0","relation":"erratum"}]},"author":[{"full_name":"Mitiouchkina, Tatiana","last_name":"Mitiouchkina","first_name":"Tatiana"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383","first_name":"Louisa","last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa"},{"full_name":"Markina, Nadezhda M.","last_name":"Markina","first_name":"Nadezhda M."},{"full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V.","last_name":"Chepurnyh"},{"first_name":"Elena B.","last_name":"Guglya","full_name":"Guglya, Elena B."},{"full_name":"Karataeva, Tatiana A.","last_name":"Karataeva","first_name":"Tatiana A."},{"full_name":"Palkina, Kseniia A.","last_name":"Palkina","first_name":"Kseniia A."},{"full_name":"Shakhova, Ekaterina S.","last_name":"Shakhova","first_name":"Ekaterina S."},{"last_name":"Fakhranurova","first_name":"Liliia I.","full_name":"Fakhranurova, Liliia I."},{"last_name":"Chekova","first_name":"Sofia V.","full_name":"Chekova, Sofia V."},{"last_name":"Tsarkova","first_name":"Aleksandra S.","full_name":"Tsarkova, Aleksandra S."},{"full_name":"Golubev, Yaroslav V.","last_name":"Golubev","first_name":"Yaroslav V."},{"first_name":"Vadim V.","last_name":"Negrebetsky","full_name":"Negrebetsky, Vadim V."},{"full_name":"Dolgushin, Sergey A.","last_name":"Dolgushin","first_name":"Sergey A."},{"full_name":"Shalaev, Pavel V.","last_name":"Shalaev","first_name":"Pavel V."},{"first_name":"Dmitry","last_name":"Shlykov","full_name":"Shlykov, Dmitry"},{"first_name":"Olesya A.","last_name":"Melnik","full_name":"Melnik, Olesya A."},{"full_name":"Shipunova, Victoria O.","last_name":"Shipunova","first_name":"Victoria O."},{"full_name":"Deyev, Sergey M.","last_name":"Deyev","first_name":"Sergey M."},{"first_name":"Andrey I.","last_name":"Bubyrev","full_name":"Bubyrev, Andrey I."},{"first_name":"Alexander S.","last_name":"Pushin","full_name":"Pushin, Alexander S."},{"full_name":"Choob, Vladimir V.","last_name":"Choob","first_name":"Vladimir V."},{"first_name":"Sergey V.","last_name":"Dolgov","full_name":"Dolgov, Sergey V."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."},{"full_name":"Sarkisyan, Karen S.","first_name":"Karen S.","last_name":"Sarkisyan"}],"volume":38,"date_created":"2020-05-25T15:02:00Z","date_updated":"2023-09-05T15:30:34Z"},{"date_created":"2021-07-29T11:29:50Z","date_updated":"2024-03-28T23:30:19Z","oa_version":"Preprint","author":[{"full_name":"Slovakova, Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","last_name":"Slovakova"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"full_name":"Huljev, Karla","first_name":"Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"10766"},{"id":"9623","relation":"dissertation_contains","status":"public"}]},"title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion","status":"public","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publisher":"Cold Spring Harbor Laboratory","acknowledgement":"We would like to thank Edouard Hannezo for discussions, Shayan Shami Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript. We also thank Jack Merrin for preparing the microwells, and the Scientific Service Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC) to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie COFUND No. P_IST_EU01 to J.S.","_id":"9750","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2020","abstract":[{"lang":"eng","text":"Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact."}],"ec_funded":1,"type":"preprint","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"SSU"}],"language":[{"iso":"eng"}],"date_published":"2020-11-20T00:00:00Z","doi":"10.1101/2020.11.20.391284","page":"41","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"187-2013","_id":"2521E28E-B435-11E9-9278-68D0E5697425","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension"}],"publication":"bioRxiv","oa":1,"citation":{"ieee":"J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","apa":"Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., & Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.20.391284","ista":"Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K, Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv, 10.1101/2020.11.20.391284.","ama":"Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. 2020. doi:10.1101/2020.11.20.391284","chicago":"Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.11.20.391284.","short":"J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020).","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.11.20.391284."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.11.20.391284"}],"month":"11","day":"20","article_processing_charge":"No"},{"year":"2020","acknowledgement":"We thank A. Leithner and J. Renkawitz for discussion and critical reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic setups; the Bioimaging Facility of IST Austria for excellent support, as well as the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan, L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687.","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"MiSi"}],"author":[{"full_name":"Reversat, Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928","first_name":"Anne","last_name":"Reversat"},{"full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723"},{"full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A"},{"full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan"},{"full_name":"Aguilera Servin, Juan L","first_name":"Juan L","last_name":"Aguilera Servin","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2862-8372"},{"full_name":"De Vries, Ingrid","first_name":"Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","first_name":"Miroslav","full_name":"Hons, Miroslav"},{"last_name":"Piel","first_name":"Matthieu","full_name":"Piel, Matthieu"},{"first_name":"Andrew","last_name":"Callan-Jones","full_name":"Callan-Jones, Andrew"},{"first_name":"Raphael","last_name":"Voituriez","full_name":"Voituriez, Raphael"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/off-road-mode-enables-mobile-cells-to-move-freely/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"14697","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"12401"}]},"date_updated":"2024-03-28T23:30:24Z","date_created":"2020-05-24T22:01:01Z","volume":582,"ec_funded":1,"external_id":{"isi":["000532688300008"]},"quality_controlled":"1","isi":1,"project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911","_id":"26018E70-B435-11E9-9278-68D0E5697425"},{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"doi":"10.1038/s41586-020-2283-z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"_id":"7885","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Cellular locomotion using environmental topography","intvolume":" 582","oa_version":"None","type":"journal_article","abstract":[{"text":"Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour.","lang":"eng"}],"publication":"Nature","citation":{"chicago":"Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan, Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental Topography.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2283-z.","mla":"Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.” Nature, vol. 582, Springer Nature, 2020, pp. 582–585, doi:10.1038/s41586-020-2283-z.","short":"A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez, M.K. Sixt, Nature 582 (2020) 582–585.","ista":"Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL, de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK. 2020. Cellular locomotion using environmental topography. Nature. 582, 582–585.","apa":"Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2283-z","ieee":"A. Reversat et al., “Cellular locomotion using environmental topography,” Nature, vol. 582. Springer Nature, pp. 582–585, 2020.","ama":"Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental topography. Nature. 2020;582:582–585. doi:10.1038/s41586-020-2283-z"},"article_type":"original","page":"582–585","date_published":"2020-06-25T00:00:00Z","scopus_import":"1","day":"25","article_processing_charge":"No"},{"article_type":"original","citation":{"chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2020. https://doi.org/10.1016/j.nahs.2020.100856.","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5, 100856, Elsevier, 2020, doi:10.1016/j.nahs.2020.100856.","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","apa":"Garcia Soto, M., & Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2020.100856","ieee":"M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5. Elsevier, 2020.","ama":"Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 2020;36(5). doi:10.1016/j.nahs.2020.100856"},"publication":"Nonlinear Analysis: Hybrid Systems","date_published":"2020-05-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","intvolume":" 36","title":"Abstraction based verification of stability of polyhedral switched systems","ddc":["000"],"status":"public","_id":"7426","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2020-10-21T13:16:45Z","date_updated":"2022-05-16T22:30:04Z","checksum":"560abfddb53f9fe921b6744f59f2cfaa","file_id":"8688","embargo":"2022-05-15","relation":"main_file","creator":"dernst","file_size":818774,"content_type":"application/pdf","file_name":"2020_NAHS_GarciaSoto.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","type":"journal_article","issue":"5","abstract":[{"text":"This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method.","lang":"eng"}],"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000528828600003"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.nahs.2020.100856","publication_identifier":{"issn":["1751-570X"]},"month":"05","publisher":"Elsevier","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2020","volume":36,"date_created":"2020-02-02T23:00:59Z","date_updated":"2023-08-17T14:32:54Z","author":[{"first_name":"Miriam","last_name":"Garcia Soto","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0003−2936−5719","full_name":"Garcia Soto, Miriam"},{"full_name":"Prabhakar, Pavithra","last_name":"Prabhakar","first_name":"Pavithra"}],"article_number":"100856","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2022-05-16T22:30:04Z"},{"oa_version":"Published Version","file":[{"file_size":10848175,"content_type":"application/pdf","creator":"semtenan","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","access_level":"open_access","date_created":"2020-12-30T15:34:01Z","date_updated":"2021-12-31T23:30:04Z","checksum":"ec2797ab7a6f253b35df0572b36d1b43","relation":"main_file","embargo":"2021-12-30","file_id":"8984"},{"relation":"source_file","file_id":"8985","date_created":"2020-12-30T15:37:36Z","date_updated":"2021-12-31T23:30:04Z","checksum":"cc30e6608a9815414024cf548dff3b3a","embargo_to":"open_access","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","access_level":"closed","file_size":10073648,"content_type":"application/pdf","creator":"semtenan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8983","ddc":["570"],"status":"public","title":"Metabolic regulation of Drosophila macrophage tissue invasion","abstract":[{"text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-12-30T00:00:00Z","citation":{"chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983.","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","mla":"Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983.","apa":"Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:10.15479/AT:ISTA:8983"},"page":"141","has_accepted_license":"1","article_processing_charge":"No","day":"30","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8557"},{"id":"6187","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Emtenani, Shamsi","last_name":"Emtenani","first_name":"Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:24:17Z","date_created":"2020-12-30T15:41:26Z","acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","year":"2020","department":[{"_id":"DaSi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2021-12-31T23:30:04Z","doi":"10.15479/AT:ISTA:8983","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"12"},{"department":[{"_id":"DaSi"},{"_id":"JoCs"}],"title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","publication_status":"submitted","status":"public","_id":"8557","acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_created":"2020-09-23T09:36:47Z","date_updated":"2024-03-28T23:30:25Z","related_material":{"record":[{"id":"10614","relation":"later_version","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8983"}]},"author":[{"full_name":"Belyaeva, Vera","first_name":"Vera","last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stephanie","last_name":"Wachner","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","full_name":"Wachner, Stephanie"},{"orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn","first_name":"Igor","full_name":"Gridchyn, Igor"},{"first_name":"Markus","last_name":"Linder","full_name":"Linder, Markus"},{"full_name":"Emtenani, Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87","last_name":"Emtenani","first_name":"Shamsi"},{"full_name":"György, Attila","last_name":"György","first_name":"Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sibilia, Maria","last_name":"Sibilia","first_name":"Maria"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"}],"type":"preprint","ec_funded":1,"abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues."}],"project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7"},{"name":"Tissue barrier penetration is crucial for immunity and metastasis","grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://doi.org/10.1101/2020.09.18.301481","open_access":"1"}],"citation":{"ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. doi:10.1101/2020.09.18.301481","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, 10.1101/2020.09.18.301481.","apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. https://doi.org/10.1101/2020.09.18.301481","ieee":"V. Belyaeva et al., “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” bioRxiv. .","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, doi:10.1101/2020.09.18.301481.","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, n.d. https://doi.org/10.1101/2020.09.18.301481."},"oa":1,"publication":"bioRxiv","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2020-09-18T00:00:00Z","doi":"10.1101/2020.09.18.301481","article_processing_charge":"No","day":"18","month":"09"},{"month":"12","project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"external_id":{"arxiv":["2012.00322"]},"oa":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"article_number":"2012.00322","file_date_updated":"2020-12-02T10:42:31Z","ec_funded":1,"publication_status":"submitted","department":[{"_id":"GeKa"}],"acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. GS and MV acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO).","year":"2020","date_updated":"2024-03-28T23:30:27Z","date_created":"2020-12-02T10:42:53Z","author":[{"full_name":"Aggarwal, Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","orcid":"0000-0001-9985-9293","first_name":"Kushagra","last_name":"Aggarwal"},{"last_name":"Hofmann","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C"},{"orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","first_name":"Daniel","full_name":"Jirovec, Daniel"},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","first_name":"Ivan","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan"},{"full_name":"Sammak, Amir","last_name":"Sammak","first_name":"Amir"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"},{"first_name":"Sara","last_name":"Marti-Sanchez","full_name":"Marti-Sanchez, Sara"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Giordano","last_name":"Scappucci","full_name":"Scappucci, Giordano"},{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10559"},{"relation":"research_data","status":"public","id":"8834"},{"relation":"dissertation_contains","status":"public","id":"10058"}]},"day":"02","article_processing_charge":"No","has_accepted_license":"1","publication":"arXiv","citation":{"ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. arXiv, 2012.00322.","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity in planar Germanium. arXiv.","ieee":"K. Aggarwal et al., “Enhancement of proximity induced superconductivity in planar Germanium,” arXiv. .","ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced superconductivity in planar Germanium. arXiv.","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, n.d.","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, 2012.00322.","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros, ArXiv (n.d.)."},"date_published":"2020-12-02T00:00:00Z","type":"preprint","abstract":[{"lang":"eng","text":"Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip."}],"status":"public","ddc":["530"],"title":"Enhancement of proximity induced superconductivity in planar Germanium","_id":"8831","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"8832","relation":"main_file","date_updated":"2020-12-02T10:42:31Z","date_created":"2020-12-02T10:42:31Z","checksum":"22a612e206232fa94b138b2c2f957582","file_name":"Superconducting_2D_Ge.pdf","access_level":"open_access","creator":"gkatsaro","content_type":"application/pdf","file_size":1697939}],"oa_version":"Submitted Version"},{"month":"09","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"doi":"10.3390/ijms21186737","language":[{"iso":"eng"}],"external_id":{"isi":["000579945300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"},{"_id":"25D32BC0-B435-11E9-9278-68D0E5697425","name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus"},{"grant_number":"785907","_id":"26436750-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","call_identifier":"H2020"}],"file_date_updated":"2020-09-21T14:08:58Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","article_number":"6737","author":[{"full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"full_name":"Bhandari, Pradeep","last_name":"Bhandari","first_name":"Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","last_name":"Case"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]},"date_created":"2020-09-20T22:01:35Z","date_updated":"2024-03-28T23:30:31Z","volume":21,"acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","year":"2020","publication_status":"published","publisher":"MDPI","department":[{"_id":"RySh"}],"day":"14","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-09-14T00:00:00Z","publication":"International Journal of Molecular Sciences","citation":{"mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences, vol. 21, no. 18, 6737, MDPI, 2020, doi:10.3390/ijms21186737.","short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21186737.","ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 2020;21(18). doi:10.3390/ijms21186737","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” International Journal of Molecular Sciences, vol. 21, no. 18. MDPI, 2020.","apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., & Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21186737"},"article_type":"original","abstract":[{"lang":"eng","text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography."}],"issue":"18","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"8551","relation":"main_file","success":1,"checksum":"2e4f62f3cfe945b7391fc3070e5a289f","date_created":"2020-09-21T14:08:58Z","date_updated":"2020-09-21T14:08:58Z","access_level":"open_access","file_name":"2020_JournMolecSciences_Kleindienst.pdf","creator":"dernst","file_size":5748456,"content_type":"application/pdf"}],"_id":"8532","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","intvolume":" 21"},{"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"date_created":"2020-05-10T22:00:50Z","date_updated":"2024-03-28T23:30:34Z","volume":12075,"year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:48:03Z","conference":{"name":"ESOP: Programming Languages and Systems","location":"Dublin, Ireland","start_date":"2020-04-25","end_date":"2020-04-30"},"doi":"10.1007/978-3-030-44914-8_5","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000681656800005"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030449131"]},"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7895","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-26T13:34:48Z","checksum":"8618b80f4cf7b39a60e61a6445ad9807","file_name":"2020_LNCS_Chatterjee.pdf","access_level":"open_access","file_size":651250,"content_type":"application/pdf","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7810","ddc":["000"],"title":"Optimal and perfectly parallel algorithms for on-demand data-flow analysis","status":"public","intvolume":" 12075","abstract":[{"text":"Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries.\r\nIn this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2020-04-18T00:00:00Z","publication":"European Symposium on Programming","citation":{"ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In: European Symposium on Programming. Vol 12075. Springer Nature; 2020:112-140. doi:10.1007/978-3-030-44914-8_5","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A. (2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In European Symposium on Programming (Vol. 12075, pp. 112–140). Dublin, Ireland: Springer Nature. https://doi.org/10.1007/978-3-030-44914-8_5","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal and perfectly parallel algorithms for on-demand data-flow analysis,” in European Symposium on Programming, Dublin, Ireland, 2020, vol. 12075, pp. 112–140.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European Symposium on Programming, Springer Nature, 2020, pp. 112–140.","mla":"Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” European Symposium on Programming, vol. 12075, Springer Nature, 2020, pp. 112–40, doi:10.1007/978-3-030-44914-8_5.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” In European Symposium on Programming, 12075:112–40. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-44914-8_5."},"page":"112-140","day":"18","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"month":"10","publication_identifier":{"eisbn":["9783030591526"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030591519"]},"external_id":{"isi":["000723555700014"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"conference":{"name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2020-10-19","location":"Hanoi, Vietnam","end_date":"2020-10-23"},"doi":"10.1007/978-3-030-59152-6_14","language":[{"iso":"eng"}],"file_date_updated":"2020-11-06T07:41:03Z","year":"2020","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","author":[{"first_name":"Ali","last_name":"Asadi","full_name":"Asadi, Ali"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"},{"first_name":"Kiarash","last_name":"Mohammadi","full_name":"Mohammadi, Kiarash"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"date_updated":"2024-03-28T23:30:34Z","date_created":"2020-11-06T07:30:05Z","volume":12302,"scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"No","publication":"Automated Technology for Verification and Analysis","citation":{"apa":"Asadi, A., Chatterjee, K., Goharshady, A. K., Mohammadi, K., & Pavlogiannis, A. (2020). Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In Automated Technology for Verification and Analysis (Vol. 12302, pp. 253–270). Hanoi, Vietnam: Springer Nature. https://doi.org/10.1007/978-3-030-59152-6_14","ieee":"A. Asadi, K. Chatterjee, A. K. Goharshady, K. Mohammadi, and A. Pavlogiannis, “Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth,” in Automated Technology for Verification and Analysis, Hanoi, Vietnam, 2020, vol. 12302, pp. 253–270.","ista":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. 2020. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 12302, 253–270.","ama":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In: Automated Technology for Verification and Analysis. Vol 12302. Springer Nature; 2020:253-270. doi:10.1007/978-3-030-59152-6_14","chicago":"Asadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Kiarash Mohammadi, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” In Automated Technology for Verification and Analysis, 12302:253–70. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-59152-6_14.","short":"A. Asadi, K. Chatterjee, A.K. Goharshady, K. Mohammadi, A. Pavlogiannis, in:, Automated Technology for Verification and Analysis, Springer Nature, 2020, pp. 253–270.","mla":"Asadi, Ali, et al. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” Automated Technology for Verification and Analysis, vol. 12302, Springer Nature, 2020, pp. 253–70, doi:10.1007/978-3-030-59152-6_14."},"page":"253-270","date_published":"2020-10-12T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improvements. In this work, we show that treewidth can also be used to obtain faster algorithms for the quantitative problems. For an MC with n states and m transitions, we show that each of the classical quantitative objectives can be computed in O((n+m)⋅t2) time, given a tree decomposition of the MC with width t. Our results also imply a bound of O(κ⋅(n+m)⋅t2) for each objective on MDPs, where κ is the number of strategy-iteration refinements required for the given input and objective. Finally, we make an experimental evaluation of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms outperform existing well-established methods by one or more orders of magnitude.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8728","ddc":["000"],"status":"public","title":"Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth","intvolume":" 12302","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"8729","date_updated":"2020-11-06T07:41:03Z","date_created":"2020-11-06T07:41:03Z","checksum":"ae83f27e5b189d5abc2e7514f1b7e1b5","success":1,"file_name":"2020_LNCS_ATVA_Asadi_accepted.pdf","access_level":"open_access","file_size":726648,"content_type":"application/pdf","creator":"dernst"}]},{"scopus_import":"1","day":"11","article_processing_charge":"No","page":"672-687","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 672–87. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385969.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–687.","mla":"Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–87, doi:10.1145/3385412.3385969.","apa":"Chatterjee, K., Fu, H., Goharshady, A. K., & Goharshady, E. K. (2020). Polynomial invariant generation for non-deterministic recursive programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 672–687). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385969","ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial invariant generation for non-deterministic recursive programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 672–687.","ista":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant generation for non-deterministic recursive programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 672–687.","ama":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation for non-deterministic recursive programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:672-687. doi:10.1145/3385412.3385969"},"date_published":"2020-06-11T00:00:00Z","type":"conference","abstract":[{"text":"We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example.","lang":"eng"}],"status":"public","title":"Polynomial invariant generation for non-deterministic recursive programs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8089","oa_version":"Preprint","month":"06","publication_identifier":{"isbn":["9781450376136"]},"isi":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1902.04373","open_access":"1"}],"external_id":{"isi":["000614622300045"],"arxiv":["1902.04373"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2020-06-20","start_date":"2020-06-15","location":"London, United Kingdom","name":"PLDI: Programming Language Design and Implementation"},"doi":"10.1145/3385412.3385969","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","year":"2020","date_updated":"2024-03-28T23:30:34Z","date_created":"2020-07-05T22:00:45Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","first_name":"Hongfei"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady"},{"full_name":"Goharshady, Ehsan Kafshdar","first_name":"Ehsan Kafshdar","last_name":"Goharshady"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]}},{"isi":1,"quality_controlled":"1","project":[{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000501641400050"],"arxiv":["1712.09692"]},"main_file_link":[{"url":"https://arxiv.org/abs/1712.09692","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.ress.2019.106665","month":"01","publication_identifier":{"issn":["09518320"]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Elsevier","year":"2020","acknowledgement":"We are grateful to the anonymous reviewers for their comments, which significantly improved the present work. The research was partially supported by the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian Academy of Sciences (ÖAW).","date_created":"2019-09-29T22:00:44Z","date_updated":"2024-03-28T23:30:34Z","volume":193,"author":[{"last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi","first_name":"Fatemeh"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"article_number":"106665","article_type":"original","publication":"Reliability Engineering and System Safety","citation":{"mla":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety, vol. 193, 106665, Elsevier, 2020, doi:10.1016/j.ress.2019.106665.","short":"A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (2020).","chicago":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety. Elsevier, 2020. https://doi.org/10.1016/j.ress.2019.106665.","ama":"Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 2020;193. doi:10.1016/j.ress.2019.106665","ista":"Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665.","ieee":"A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network reliability in small treewidth,” Reliability Engineering and System Safety, vol. 193. Elsevier, 2020.","apa":"Goharshady, A. K., & Mohammadi, F. (2020). An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. Elsevier. https://doi.org/10.1016/j.ress.2019.106665"},"date_published":"2020-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"An efficient algorithm for computing network reliability in small treewidth","intvolume":" 193","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6918","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem.","lang":"eng"}]},{"month":"03","publication_identifier":{"issn":["0022-3239"],"eissn":["1573-2878"]},"external_id":{"isi":["000511805200009"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s10957-019-01616-6","language":[{"iso":"eng"}],"file_date_updated":"2021-03-16T23:30:04Z","ec_funded":1,"acknowledgement":"We are grateful to the anonymous referees and editor whose insightful comments helped to considerably improve an earlier version of this paper. The research of the first author is supported by an ERC Grant from the Institute of Science and Technology (IST).","year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"VlKo"}],"author":[{"first_name":"Yekini","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini"},{"full_name":"Gibali, Aviv","last_name":"Gibali","first_name":"Aviv"},{"full_name":"Sagratella, Simone","last_name":"Sagratella","first_name":"Simone"}],"date_updated":"2023-09-06T11:27:15Z","date_created":"2019-12-09T21:33:44Z","volume":184,"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Journal of Optimization Theory and Applications","citation":{"ista":"Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 184, 877–894.","apa":"Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6","ieee":"Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces,” Journal of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894, 2020.","ama":"Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6","chicago":"Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6.","mla":"Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications, vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6.","short":"Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications 184 (2020) 877–894."},"article_type":"original","page":"877–894","date_published":"2020-03-01T00:00:00Z","type":"journal_article","abstract":[{"text":"In this paper, we introduce an inertial projection-type method with different updating strategies for solving quasi-variational inequalities with strongly monotone and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions, we establish different strong convergence results for the proposed algorithm. Primary numerical experiments demonstrate the potential applicability of our scheme compared with some related methods in the literature.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7161","status":"public","title":"Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces","ddc":["518","510","515"],"intvolume":" 184","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2020_JourOptimizationTheoryApplic_Shehu.pdf","content_type":"application/pdf","file_size":332641,"creator":"dernst","relation":"main_file","embargo":"2021-03-15","file_id":"8647","checksum":"9f6dc6c6bf2b48cb3a2091a9ed5feaf2","date_updated":"2021-03-16T23:30:04Z","date_created":"2020-10-12T10:40:27Z"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7652","ddc":["570"],"status":"public","title":"Gene amplification as a form of population-level gene expression regulation","intvolume":" 4","file":[{"relation":"main_file","file_id":"8640","checksum":"ef3bbf42023e30b2c24a6278025d2040","success":1,"date_updated":"2020-10-09T09:56:01Z","date_created":"2020-10-09T09:56:01Z","access_level":"open_access","file_name":"2020_NatureEcolEvo_Tomanek.pdf","content_type":"application/pdf","file_size":745242,"creator":"dernst"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature."}],"issue":"4","publication":"Nature Ecology & Evolution","citation":{"chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7.","short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.","mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.","apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7","ieee":"I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.","ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 4(4), 612–625.","ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7"},"article_type":"original","page":"612-625","date_published":"2020-04-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.","year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"author":[{"first_name":"Isabella","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X","full_name":"Tomanek, Isabella"},{"full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","first_name":"Rok","last_name":"Grah"},{"first_name":"M.","last_name":"Lagator","full_name":"Lagator, M."},{"last_name":"Andersson","first_name":"A. M. C.","full_name":"Andersson, A. M. C."},{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"related_material":{"record":[{"id":"8155","status":"public","relation":"dissertation_contains"},{"id":"7383","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"7016"},{"id":"8653","status":"public","relation":"used_in_publication"}],"link":[{"url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","description":"News on IST Homepage","relation":"press_release"}]},"date_updated":"2024-03-28T23:30:37Z","date_created":"2020-04-08T15:20:53Z","volume":4,"file_date_updated":"2020-10-09T09:56:01Z","oa":1,"external_id":{"isi":["000519008300005"]},"quality_controlled":"1","isi":1,"project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41559-020-1132-7","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["2397-334X"]}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7258","status":"public","title":"New approaches to reduce friction in turbulent pipe flow","ddc":["532"],"file":[{"creator":"dscarsel","file_size":26640830,"content_type":"application/zip","file_name":"2020_Scarselli_Thesis.zip","embargo_to":"open_access","access_level":"closed","date_updated":"2021-01-13T23:30:05Z","date_created":"2020-01-12T15:57:14Z","checksum":"4df1ab24e9896635106adde5a54615bf","file_id":"7259","relation":"source_file"},{"content_type":"application/pdf","file_size":8515844,"creator":"dscarsel","access_level":"open_access","file_name":"2020_Scarselli_Thesis.pdf","checksum":"48659ab98e3414293c7a721385c2fd1c","date_updated":"2021-01-13T23:30:05Z","date_created":"2020-01-12T15:56:14Z","relation":"main_file","embargo":"2021-01-12","file_id":"7260"}],"oa_version":"None","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings.","lang":"eng"}],"citation":{"short":"D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020.","mla":"Scarselli, Davide. New Approaches to Reduce Friction in Turbulent Pipe Flow. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7258.","chicago":"Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe Flow.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7258.","ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:10.15479/AT:ISTA:7258","apa":"Scarselli, D. (2020). New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7258","ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020.","ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria."},"page":"174","date_published":"2020-01-13T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"13","year":"2020","department":[{"_id":"BjHo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"6228","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6486"},{"id":"461","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"422"}]},"author":[{"orcid":"0000-0001-5227-4271","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","first_name":"Davide","full_name":"Scarselli, Davide"}],"date_updated":"2023-09-15T12:20:08Z","date_created":"2020-01-12T16:07:26Z","ec_funded":1,"file_date_updated":"2021-01-13T23:30:05Z","oa":1,"project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Eliminating turbulence in oil pipelines","grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425"},{"name":"Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents","grant_number":"HO 4393/1-2","_id":"25136C54-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:7258","language":[{"iso":"eng"}],"supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"01"},{"date_published":"2020-10-13T00:00:00Z","page":"117","citation":{"ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","apa":"Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653","chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.","mla":"Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020."},"day":"13","has_accepted_license":"1","article_processing_charge":"No","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"oa_version":"Published Version","file":[{"file_id":"8666","relation":"source_file","checksum":"c01d9f59794b4b70528f37637c17ad02","date_updated":"2021-10-20T22:30:03Z","date_created":"2020-10-16T12:14:21Z","access_level":"closed","file_name":"Thesis_ITomanek_final_201016.docx","embargo_to":"open_access","creator":"itomanek","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25131884},{"creator":"itomanek","file_size":15405675,"content_type":"application/pdf","file_name":"Thesis_ITomanek_final_201016.pdf","access_level":"open_access","date_updated":"2021-10-20T22:30:03Z","date_created":"2020-10-16T12:14:21Z","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","file_id":"8667","embargo":"2021-10-19","relation":"main_file"}],"ddc":["576"],"status":"public","title":"The evolution of gene expression by copy number and point mutations","_id":"8653","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","degree_awarded":"PhD","supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8653","oa":1,"month":"10","publication_identifier":{"issn":["2663-337X"]},"date_created":"2020-10-13T13:02:33Z","date_updated":"2023-09-07T13:22:42Z","author":[{"full_name":"Tomanek, Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X","first_name":"Isabella","last_name":"Tomanek"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"7652"}]},"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","year":"2020","file_date_updated":"2021-10-20T22:30:03Z"},{"oa_version":"Published Version","file":[{"date_created":"2020-09-22T09:51:28Z","date_updated":"2020-09-22T09:51:28Z","checksum":"16f7d51fe28f91c21e4896a2028df40b","success":1,"relation":"main_file","file_id":"8555","file_size":5360135,"content_type":"application/pdf","creator":"dernst","file_name":"2020_CurrentBiology_Tan.pdf","access_level":"open_access"}],"intvolume":" 30","ddc":["580"],"title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","status":"public","_id":"7427","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","abstract":[{"text":"Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense.","lang":"eng"}],"type":"journal_article","date_published":"2020-02-03T00:00:00Z","page":"381-395.e8","article_type":"original","citation":{"ama":"Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 2020;30(3):381-395.e8. doi:10.1016/j.cub.2019.11.058","ista":"Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8.","ieee":"S. Tan et al., “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” Current Biology, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020.","apa":"Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.11.058","mla":"Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:10.1016/j.cub.2019.11.058.","short":"S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8.","chicago":"Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology. Cell Press, 2020. https://doi.org/10.1016/j.cub.2019.11.058."},"publication":"Current Biology","article_processing_charge":"No","has_accepted_license":"1","day":"03","scopus_import":"1","volume":30,"date_created":"2020-02-02T23:01:00Z","date_updated":"2024-03-28T23:30:38Z","related_material":{"record":[{"id":"8822","relation":"dissertation_contains","status":"public"}]},"author":[{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang"},{"full_name":"Abas, Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abas","first_name":"Melinda F"},{"last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783"},{"full_name":"Molnar, Gergely","last_name":"Molnar","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub","full_name":"Hajny, Jakub"},{"last_name":"Lasák","first_name":"Pavel","full_name":"Lasák, Pavel"},{"full_name":"Petřík, Ivan","first_name":"Ivan","last_name":"Petřík"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"full_name":"Pospíšil, Jiří","first_name":"Jiří","last_name":"Pospíšil"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Cell Press","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). ","ec_funded":1,"file_date_updated":"2020-09-22T09:51:28Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1016/j.cub.2019.11.058","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000511287900018"],"pmid":["31956021"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["09609822"]},"month":"02"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000514939700001"],"pmid":["31971254"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development","grant_number":"25239","_id":"2699E3D2-B435-11E9-9278-68D0E5697425"}],"doi":"10.1111/nph.16446","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"acknowledgement":"We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests.","year":"2020","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"}],"author":[{"full_name":"Mazur, E","last_name":"Mazur","first_name":"E"},{"full_name":"Kulik, Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","last_name":"Kulik","first_name":"Ivan"},{"first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"related_material":{"record":[{"id":"8822","relation":"dissertation_contains","status":"public"}]},"date_updated":"2024-03-28T23:30:38Z","date_created":"2020-02-18T10:03:47Z","volume":226,"file_date_updated":"2020-11-20T09:32:10Z","ec_funded":1,"publication":"New Phytologist","citation":{"chicago":"Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16446.","mla":"Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:10.1111/nph.16446.","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383.","ista":"Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383.","apa":"Mazur, E., Kulik, I., Hajny, J., & Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. Wiley. https://doi.org/10.1111/nph.16446","ieee":"E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” New Phytologist, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020.","ama":"Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 2020;226(5):1375-1383. doi:10.1111/nph.16446"},"article_type":"original","page":"1375-1383","date_published":"2020-06-01T00:00:00Z","day":"01","article_processing_charge":"No","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7500","status":"public","title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","ddc":["580"],"intvolume":" 226","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_NewPhytologist_Mazur.pdf","content_type":"application/pdf","file_size":2106888,"creator":"dernst","relation":"main_file","file_id":"8781","checksum":"17de728b0205979feb95ce663ba918c2","success":1,"date_updated":"2020-11-20T09:32:10Z","date_created":"2020-11-20T09:32:10Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts."}],"issue":"5"},{"oa":1,"doi":"10.15479/AT:ISTA:8822","degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["2663-337X"]},"year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"author":[{"orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub","full_name":"Hajny, Jakub"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7427"},{"relation":"part_of_dissertation","status":"public","id":"6260"},{"id":"7500","status":"public","relation":"part_of_dissertation"},{"id":"191","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"449"}]},"date_updated":"2023-09-19T10:39:33Z","date_created":"2020-12-01T12:38:18Z","file_date_updated":"2021-12-08T23:30:03Z","citation":{"chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822.","mla":"Hajny, Jakub. Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822.","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020.","ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria.","apa":"Hajny, J. (2020). Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822","ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020.","ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:10.15479/AT:ISTA:8822"},"page":"249","date_published":"2020-12-01T00:00:00Z","day":"01","article_processing_charge":"No","has_accepted_license":"1","_id":"8822","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","ddc":["580"],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":91279806,"creator":"jhajny","access_level":"closed","embargo_to":"open_access","file_name":"Jakub Hajný IST Austria final_JH.docx","checksum":"210a9675af5e4c78b0b56d920ac82866","date_created":"2020-12-04T07:27:52Z","date_updated":"2021-07-16T22:30:03Z","relation":"source_file","file_id":"8919"},{"file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","access_level":"open_access","content_type":"application/pdf","file_size":68707697,"creator":"jhajny","relation":"main_file","embargo":"2021-12-07","file_id":"8933","date_created":"2020-12-09T15:04:41Z","date_updated":"2021-12-08T23:30:03Z","checksum":"1781385b4aa73eba89cc76c6172f71d2"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization."}]},{"publication_identifier":{"issn":["2663-337X"]},"month":"09","oa":1,"doi":"10.15479/AT:ISTA:8350","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"file_date_updated":"2021-09-11T22:30:05Z","acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"publication_status":"published","related_material":{"record":[{"id":"661","relation":"part_of_dissertation","status":"public"},{"id":"6508","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7001"},{"id":"735","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"}],"date_created":"2020-09-09T11:12:10Z","date_updated":"2023-09-27T14:16:45Z","has_accepted_license":"1","article_processing_charge":"No","day":"09","citation":{"chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","mla":"Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.","apa":"Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350"},"page":"107","date_published":"2020-09-09T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8350","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","ddc":["570"],"status":"public","oa_version":"None","file":[{"file_name":"Shayan-Thesis-Final.docx","embargo_to":"open_access","access_level":"closed","creator":"sshamip","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":65194814,"file_id":"8351","relation":"source_file","date_updated":"2021-09-11T22:30:05Z","date_created":"2020-09-09T11:06:27Z","checksum":"6e47871c74f85008b9876112eb3fcfa1"},{"access_level":"open_access","file_name":"Shayan-Thesis-Final.pdf","content_type":"application/pdf","file_size":23729605,"creator":"sshamip","relation":"main_file","embargo":"2021-09-10","file_id":"8352","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","date_created":"2020-09-09T11:06:13Z","date_updated":"2021-09-11T22:30:05Z"}]},{"pmid":1,"acknowledgement":"AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.","year":"2020","department":[{"_id":"SiHi"}],"publisher":"Frontiers","publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9962"}]},"author":[{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","last_name":"Hansen","full_name":"Hansen, Andi H"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"volume":8,"date_updated":"2024-03-28T23:30:41Z","date_created":"2020-09-26T06:11:07Z","article_number":"574382","ec_funded":1,"file_date_updated":"2020-09-28T13:11:17Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33102480"],"isi":["000577915900001"]},"oa":1,"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development"}],"quality_controlled":"1","isi":1,"doi":"10.3389/fcell.2020.574382","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2296-634X"]},"month":"09","_id":"8569","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 8","ddc":["570"],"status":"public","title":"Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex","oa_version":"Published Version","file":[{"file_name":"2020_Frontiers_Hansen.pdf","access_level":"open_access","file_size":5527139,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8584","date_created":"2020-09-28T13:11:17Z","date_updated":"2020-09-28T13:11:17Z","checksum":"01f731824194c94c81a5da360d997073","success":1}],"type":"journal_article","issue":"9","abstract":[{"text":"Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future.","lang":"eng"}],"citation":{"apa":"Hansen, A. H., & Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2020.574382","ieee":"A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex,” Frontiers in Cell and Developmental Biology, vol. 8, no. 9. Frontiers, 2020.","ista":"Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 8(9), 574382.","ama":"Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 2020;8(9). doi:10.3389/fcell.2020.574382","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology. Frontiers, 2020. https://doi.org/10.3389/fcell.2020.574382.","short":"A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology 8 (2020).","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology, vol. 8, no. 9, 574382, Frontiers, 2020, doi:10.3389/fcell.2020.574382."},"publication":"Frontiers in Cell and Developmental Biology","article_type":"original","date_published":"2020-09-25T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"25"},{"publication_identifier":{"issn":["1940-087X"]},"month":"05","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"doi":"10.3791/61147","project":[{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"},{"name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000546406600043"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:48:03Z","article_number":"e61147","date_created":"2020-05-11T08:31:20Z","date_updated":"2024-03-28T23:30:42Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7902"}]},"author":[{"first_name":"Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung"},{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","first_name":"Ximena"},{"full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"publisher":"MyJove Corporation","department":[{"_id":"SiHi"}],"publication_status":"published","year":"2020","has_accepted_license":"1","article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2020-05-08T00:00:00Z","article_type":"original","citation":{"chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments. MyJove Corporation, 2020. https://doi.org/10.3791/61147.","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments, no. 159, e61147, MyJove Corporation, 2020, doi:10.3791/61147.","ieee":"R. J. Beattie et al., “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” Journal of Visual Experiments, no. 159. MyJove Corporation, 2020.","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., & Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. MyJove Corporation. https://doi.org/10.3791/61147","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. 2020;(159). doi:10.3791/61147"},"publication":"Journal of Visual Experiments","issue":"159","abstract":[{"text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf","creator":"rbeattie","content_type":"application/pdf","file_size":1352186,"file_id":"7816","relation":"main_file","checksum":"3154ea7f90b9fb45e084cd1c2770597d","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-11T08:28:38Z"}],"oa_version":"Published Version","title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7815"},{"ec_funded":1,"file_date_updated":"2021-06-07T22:30:03Z","year":"2020","department":[{"_id":"SiHi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6830"},{"status":"public","relation":"dissertation_contains","id":"28"},{"relation":"dissertation_contains","status":"public","id":"7815"}]},"author":[{"full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-05-29T08:27:32Z","date_updated":"2023-10-18T08:45:16Z","publication_identifier":{"issn":["2663-337X"]},"month":"06","oa":1,"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"doi":"10.15479/AT:ISTA:7902","language":[{"iso":"eng"}],"supervisor":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation.","lang":"eng"}],"_id":"7902","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Genetic dissection of neural development in health and disease at single cell resolution","status":"public","file":[{"date_updated":"2021-06-07T22:30:03Z","date_created":"2020-06-05T08:18:08Z","checksum":"43c172bf006c95b65992d473c7240d13","file_id":"7927","relation":"source_file","creator":"xcontreras","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":53134142,"file_name":"PhDThesis_Contreras.docx","embargo_to":"open_access","access_level":"closed"},{"embargo":"2021-06-06","file_id":"7928","relation":"main_file","date_created":"2020-06-05T08:18:07Z","date_updated":"2021-06-07T22:30:03Z","checksum":"addfed9128271be05cae3608e03a6ec0","file_name":"PhDThesis_Contreras.pdf","access_level":"open_access","creator":"xcontreras","content_type":"application/pdf","file_size":35117191}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"05","citation":{"ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","apa":"Contreras, X. (2020). Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7902","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7902.","mla":"Contreras, Ximena. Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7902.","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020."},"page":"214","date_published":"2020-06-05T00:00:00Z"},{"issue":"8","type":"journal_article","file":[{"relation":"main_file","file_id":"8200","embargo":"2021-02-01","date_created":"2020-08-04T13:11:52Z","date_updated":"2021-02-02T23:30:03Z","checksum":"30016d778d266b8e17d01094917873b8","file_name":"2020_JCB_Sixt.pdf","access_level":"open_access","content_type":"application/pdf","file_size":830725,"creator":"dernst"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Zena Werb (1945-2020): Cell biology in context","intvolume":" 219","_id":"8190","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-22T00:00:00Z","article_type":"letter_note","publication":"The Journal of Cell Biology","citation":{"chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.202007029.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:10.1083/jcb.202007029.","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” The Journal of Cell Biology, vol. 219, no. 8. Rockefeller University Press, 2020.","apa":"Sixt, M. K., & Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202007029","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 2020;219(8). doi:10.1083/jcb.202007029"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2021-02-02T23:30:03Z","article_number":"e202007029","date_updated":"2023-10-17T10:04:49Z","date_created":"2020-08-02T22:00:57Z","volume":219,"author":[{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"last_name":"Huttenlocher","first_name":"Anna","full_name":"Huttenlocher, Anna"}],"publication_status":"published","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"}],"year":"2020","month":"07","publication_identifier":{"eissn":["1540-8140"]},"language":[{"iso":"eng"}],"doi":"10.1083/jcb.202007029","isi":1,"external_id":{"isi":["000573631000004"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1},{"date_published":"2020-12-11T00:00:00Z","publication":"Science Advances","citation":{"mla":"Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:10.1126/sciadv.abc8895.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020).","chicago":"Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances. AAAS, 2020. https://doi.org/10.1126/sciadv.abc8895.","ama":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 2020;6(50). doi:10.1126/sciadv.abc8895","ista":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895.","apa":"Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., & Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abc8895","ieee":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” Science Advances, vol. 6, no. 50. AAAS, 2020."},"article_type":"original","day":"11","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2020_ScienceAdvances_Zhang.pdf","file_size":10578145,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8994","checksum":"5ac2500b191c08ef6dab5327f40ff663","success":1,"date_created":"2021-01-07T12:44:33Z","date_updated":"2021-01-07T12:44:33Z"}],"oa_version":"Published Version","_id":"8986","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["580"],"title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","status":"public","intvolume":" 6","abstract":[{"text":"Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants.","lang":"eng"}],"issue":"50","type":"journal_article","doi":"10.1126/sciadv.abc8895","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000599903600014"],"pmid":["33310852"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"month":"12","publication_identifier":{"eissn":["2375-2548"]},"author":[{"first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia"},{"first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:44Z","date_created":"2021-01-03T23:01:23Z","volume":6,"year":"2020","acknowledgement":"We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"AAAS","file_date_updated":"2021-01-07T12:44:33Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","article_number":"eabc8895"},{"volume":21,"date_created":"2020-08-24T06:24:03Z","date_updated":"2024-03-28T23:30:44Z","related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Chen, Huihuang","first_name":"Huihuang","last_name":"Chen"},{"full_name":"Lai, Linyi","first_name":"Linyi","last_name":"Lai"},{"full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"first_name":"Liping","last_name":"Liu","full_name":"Liu, Liping"},{"first_name":"Bello Hassan","last_name":"Jakada","full_name":"Jakada, Bello Hassan"},{"first_name":"Youmei","last_name":"Huang","full_name":"Huang, Youmei"},{"first_name":"Qing","last_name":"He","full_name":"He, Qing"},{"full_name":"Chai, Mengnan","last_name":"Chai","first_name":"Mengnan"},{"full_name":"Niu, Xiaoping","last_name":"Niu","first_name":"Xiaoping"},{"full_name":"Qin, Yuan","first_name":"Yuan","last_name":"Qin"}],"publisher":"MDPI","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","file_date_updated":"2020-08-25T09:53:50Z","article_number":"5272","language":[{"iso":"eng"}],"doi":"10.3390/ijms21165727","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000565090300001"],"pmid":["32785037"]},"publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"month":"08","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8292","date_created":"2020-08-25T09:53:50Z","date_updated":"2020-08-25T09:53:50Z","checksum":"03b039244e6ae80580385fd9f577e2b2","success":1,"file_name":"2020_IntMolecSciences_Chen.pdf","access_level":"open_access","content_type":"application/pdf","file_size":5718755,"creator":"cziletti"}],"intvolume":" 21","title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","ddc":["570"],"status":"public","_id":"8283","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"16","abstract":[{"text":"Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. ","lang":"eng"}],"type":"journal_article","date_published":"2020-08-10T00:00:00Z","article_type":"original","citation":{"ama":"Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727","ista":"Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272.","apa":"Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165727","ieee":"H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020.","mla":"Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727.","short":"H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020).","chicago":"Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165727."},"publication":"International Journal of Molecular Sciences","article_processing_charge":"No","has_accepted_license":"1","day":"10","scopus_import":"1"},{"article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","date_published":"2020-08-06T00:00:00Z","article_type":"original","citation":{"ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062.","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062","ieee":"A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.","ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062.","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062.","short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020)."},"publication":"Journal of Cell Science","issue":"15","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"ajohnson","file_size":15150403,"content_type":"application/pdf","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","access_level":"open_access","date_updated":"2021-08-08T22:30:03Z","date_created":"2020-11-26T17:12:51Z","checksum":"2d11f79a0b4e0a380fb002b933da331a","embargo":"2021-08-07","file_id":"8815","relation":"main_file"}],"intvolume":" 133","ddc":["575"],"title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","status":"public","_id":"8139","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"month":"08","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"doi":"10.1242/jcs.248062","project":[{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000561047900021"],"pmid":["32616560"]},"oa":1,"ec_funded":1,"file_date_updated":"2021-08-08T22:30:03Z","article_number":"jcs248062","volume":133,"date_updated":"2023-12-01T13:51:07Z","date_created":"2020-07-21T08:58:19Z","related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia"},{"full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"first_name":"Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha"},{"full_name":"Vert, G","first_name":"G","last_name":"Vert"},{"last_name":"Bednarek","first_name":"SY","full_name":"Bednarek, SY"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publisher":"The Company of Biologists","publication_status":"published","pmid":1,"year":"2020","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. "},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"11","citation":{"ieee":"H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” Plant Communications, vol. 1, no. 3. Elsevier, 2020.","apa":"Semerádová, H., Montesinos López, J. C., & Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2020.100048","ista":"Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048.","ama":"Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 2020;1(3). doi:10.1016/j.xplc.2020.100048","chicago":"Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications. Elsevier, 2020. https://doi.org/10.1016/j.xplc.2020.100048.","short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020).","mla":"Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications, vol. 1, no. 3, 100048, Elsevier, 2020, doi:10.1016/j.xplc.2020.100048."},"publication":"Plant Communications","article_type":"original","date_published":"2020-05-11T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development."}],"_id":"9160","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 1","title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","status":"public","ddc":["580"],"file":[{"content_type":"application/pdf","file_size":840289,"creator":"dernst","access_level":"open_access","file_name":"2020_PlantComm_Semeradova.pdf","checksum":"785b266d82a94b007cf40dbbe7c4847e","success":1,"date_created":"2021-02-18T10:23:59Z","date_updated":"2021-02-18T10:23:59Z","relation":"main_file","file_id":"9161"}],"oa_version":"Published Version","publication_identifier":{"issn":["2590-3462"]},"month":"05","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["33367243"],"isi":["000654052800010"]},"project":[{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.xplc.2020.100048","language":[{"iso":"eng"}],"article_number":"100048","file_date_updated":"2021-02-18T10:23:59Z","pmid":1,"acknowledgement":"H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared.","year":"2020","publisher":"Elsevier","department":[{"_id":"EvBe"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10135"}]},"author":[{"full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova","first_name":"Hana"},{"full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","first_name":"Juan C"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"volume":1,"date_created":"2021-02-18T10:18:43Z","date_updated":"2024-03-28T23:30:47Z"},{"abstract":[{"text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with piecewise constant dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this third edition, six tools have been applied to solve five different benchmark problems in the category for piecewise constant dynamics: BACH, Lyse, Hy- COMP, PHAVer/SX, PHAVerLite, and VeriSiMPL. Compared to last year, a new tool has participated (HyCOMP) and PHAVerLite has replaced PHAVer-lite. The result is a snap- shot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results probably provide the most complete assessment of tools for the safety verification of continuous and hybrid systems with piecewise constant dynamics up to this date.","lang":"eng"}],"alternative_title":["EPiC Series in Computing"],"type":"conference","file":[{"content_type":"application/pdf","file_size":346415,"creator":"dernst","file_name":"2019_EPiCs_Frehse.pdf","access_level":"open_access","date_updated":"2022-05-17T06:55:49Z","date_created":"2022-05-17T06:55:49Z","checksum":"4b92e333db7b4e2349501a804dfede69","success":1,"relation":"main_file","file_id":"11391"}],"oa_version":"Published Version","intvolume":" 61","ddc":["000"],"status":"public","title":"ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10877","article_processing_charge":"No","has_accepted_license":"1","day":"25","scopus_import":"1","date_published":"2019-05-25T00:00:00Z","page":"1-13","citation":{"ama":"Frehse G, Abate A, Adzkiya D, et al. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In: Frehse G, Althoff M, eds. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. Vol 61. EasyChair; 2019:1-13. doi:10.29007/rjwn","ista":"Frehse G, Abate A, Adzkiya D, Becchi A, Bu L, Cimatti A, Giacobbe M, Griggio A, Mover S, Mufid MS, Riouak I, Tonetta S, Zaffanella E. 2019. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems, EPiC Series in Computing, vol. 61, 1–13.","apa":"Frehse, G., Abate, A., Adzkiya, D., Becchi, A., Bu, L., Cimatti, A., … Zaffanella, E. (2019). ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In G. Frehse & M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems (Vol. 61, pp. 1–13). Montreal, Canada: EasyChair. https://doi.org/10.29007/rjwn","ieee":"G. Frehse et al., “ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics,” in ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, Montreal, Canada, 2019, vol. 61, pp. 1–13.","mla":"Frehse, Goran, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, vol. 61, EasyChair, 2019, pp. 1–13, doi:10.29007/rjwn.","short":"G. Frehse, A. Abate, D. Adzkiya, A. Becchi, L. Bu, A. Cimatti, M. Giacobbe, A. Griggio, S. Mover, M.S. Mufid, I. Riouak, S. Tonetta, E. Zaffanella, in:, G. Frehse, M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, EasyChair, 2019, pp. 1–13.","chicago":"Frehse, Goran, Alessandro Abate, Dieky Adzkiya, Anna Becchi, Lei Bu, Alessandro Cimatti, Mirco Giacobbe, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” In ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, 61:1–13. EasyChair, 2019. https://doi.org/10.29007/rjwn."},"publication":"ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems","file_date_updated":"2022-05-17T06:55:49Z","volume":61,"date_created":"2022-03-18T12:29:23Z","date_updated":"2022-05-17T07:09:47Z","author":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"full_name":"Abate, Alessandro","last_name":"Abate","first_name":"Alessandro"},{"last_name":"Adzkiya","first_name":"Dieky","full_name":"Adzkiya, Dieky"},{"full_name":"Becchi, Anna","first_name":"Anna","last_name":"Becchi"},{"full_name":"Bu, Lei","last_name":"Bu","first_name":"Lei"},{"full_name":"Cimatti, Alessandro","last_name":"Cimatti","first_name":"Alessandro"},{"last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco"},{"full_name":"Griggio, Alberto","first_name":"Alberto","last_name":"Griggio"},{"last_name":"Mover","first_name":"Sergio","full_name":"Mover, Sergio"},{"last_name":"Mufid","first_name":"Muhammad Syifa'ul","full_name":"Mufid, Muhammad Syifa'ul"},{"last_name":"Riouak","first_name":"Idriss","full_name":"Riouak, Idriss"},{"full_name":"Tonetta, Stefano","last_name":"Tonetta","first_name":"Stefano"},{"first_name":"Enea","last_name":"Zaffanella","full_name":"Zaffanella, Enea"}],"editor":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"full_name":"Althoff, Matthias","first_name":"Matthias","last_name":"Althoff"}],"publisher":"EasyChair","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2019","acknowledgement":"The authors gratefully acknowledge \fnancial support by the European Commission project\r\nUnCoVerCPS under grant number 643921. Lei Bu is supported by the National Natural Science\r\nFoundation of China (No.61572249).","publication_identifier":{"issn":["2398-7340"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.29007/rjwn","conference":{"end_date":"2019-04-15","location":"Montreal, Canada","start_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"quality_controlled":"1","oa":1},{"article_processing_charge":"No","day":"15","scopus_import":1,"date_published":"2019-09-15T00:00:00Z","page":"909–928","article_type":"original","citation":{"mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics, vol. 5, no. 3, Springer Nature, 2019, pp. 909–928, doi:10.1007/s40879-018-0218-0.","short":"N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40879-018-0218-0.","ama":"Kalinin N, Shkolnikov M. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 2019;5(3):909–928. doi:10.1007/s40879-018-0218-0","ista":"Kalinin N, Shkolnikov M. 2019. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 5(3), 909–928.","apa":"Kalinin, N., & Shkolnikov, M. (2019). Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-018-0218-0","ieee":"N. Kalinin and M. Shkolnikov, “Tropical formulae for summation over a part of SL(2,Z),” European Journal of Mathematics, vol. 5, no. 3. Springer Nature, pp. 909–928, 2019."},"publication":"European Journal of Mathematics","issue":"3","type":"journal_article","oa_version":"Preprint","intvolume":" 5","status":"public","title":"Tropical formulae for summation over a part of SL(2,Z)","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"441","publication_identifier":{"eissn":["2199-6768"],"issn":["2199-675X"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/s40879-018-0218-0","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.02089"}],"oa":1,"external_id":{"arxiv":["1711.02089"]},"ec_funded":1,"publist_id":"7382","volume":5,"date_updated":"2021-01-12T07:56:46Z","date_created":"2018-12-11T11:46:29Z","author":[{"first_name":"Nikita","last_name":"Kalinin","full_name":"Kalinin, Nikita"},{"full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov","first_name":"Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"TaHa"}],"publisher":"Springer Nature","publication_status":"published","year":"2019"},{"citation":{"ieee":"Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki, “Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,” in The hippo pathway, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp. 167–181.","apa":"Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., & Furutani-Seiki, M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In A. Hergovich (Ed.), The hippo pathway (Vol. 1893, pp. 167–181). Springer. https://doi.org/10.1007/978-1-4939-8910-2_14","ista":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The hippo pathway. MIMB, vol. 1893, 167–181.","ama":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich A, ed. The Hippo Pathway. Vol 1893. Methods in Molecular Biology. Springer; 2019:167-181. doi:10.1007/978-1-4939-8910-2_14","chicago":"Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg, and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” In The Hippo Pathway, edited by Alexander Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. https://doi.org/10.1007/978-1-4939-8910-2_14.","short":"Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki, in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181.","mla":"Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” The Hippo Pathway, edited by Alexander Hergovich, vol. 1893, Springer, 2019, pp. 167–81, doi:10.1007/978-1-4939-8910-2_14."},"publication":"The hippo pathway","page":"167-181","quality_controlled":"1","doi":"10.1007/978-1-4939-8910-2_14","date_published":"2019-01-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"series_title":"Methods in Molecular Biology","publication_identifier":{"isbn":["978-1-4939-8909-6"]},"month":"01","day":"01","_id":"5793","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","editor":[{"last_name":"Hergovich","first_name":"Alexander","full_name":"Hergovich, Alexander"}],"intvolume":" 1893","department":[{"_id":"CaHe"}],"publisher":"Springer","status":"public","publication_status":"published","title":"Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids","author":[{"full_name":"Asaoka, Yoichi","last_name":"Asaoka","first_name":"Yoichi"},{"first_name":"Hitoshi","last_name":"Morita","full_name":"Morita, Hitoshi"},{"full_name":"Furumoto, Hiroko","last_name":"Furumoto","first_name":"Hiroko"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"full_name":"Furutani-Seiki, Makoto","last_name":"Furutani-Seiki","first_name":"Makoto"}],"oa_version":"None","volume":1893,"date_created":"2019-01-06T22:59:11Z","date_updated":"2021-01-12T08:03:30Z","type":"book_chapter","alternative_title":["MIMB"],"abstract":[{"lang":"eng","text":"The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis."}]},{"citation":{"chicago":"Demay, Gregory, Peter Gazi, Ueli Maurer, and Bjorn Tackmann. “Per-Session Security: Password-Based Cryptography Revisited.” Journal of Computer Security. IOS Press, 2019. https://doi.org/10.3233/JCS-181131.","mla":"Demay, Gregory, et al. “Per-Session Security: Password-Based Cryptography Revisited.” Journal of Computer Security, vol. 27, no. 1, IOS Press, 2019, pp. 75–111, doi:10.3233/JCS-181131.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, Journal of Computer Security 27 (2019) 75–111.","ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2019. Per-session security: Password-based cryptography revisited. Journal of Computer Security. 27(1), 75–111.","apa":"Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2019). Per-session security: Password-based cryptography revisited. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-181131","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Per-session security: Password-based cryptography revisited,” Journal of Computer Security, vol. 27, no. 1. IOS Press, pp. 75–111, 2019.","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Per-session security: Password-based cryptography revisited. Journal of Computer Security. 2019;27(1):75-111. doi:10.3233/JCS-181131"},"publication":"Journal of Computer Security","page":"75-111","article_type":"original","date_published":"2019-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"1","_id":"5887","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 27","status":"public","title":"Per-session security: Password-based cryptography revisited","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"text":"Cryptographic security is usually defined as a guarantee that holds except when a bad event with negligible probability occurs, and nothing is guaranteed in that bad case. However, in settings where such failure can happen with substantial probability, one needs to provide guarantees even for the bad case. A typical example is where a (possibly weak) password is used instead of a secure cryptographic key to protect a session, the bad event being that the adversary correctly guesses the password. In a situation with multiple such sessions, a per-session guarantee is desired: any session for which the password has not been guessed remains secure, independently of whether other sessions have been compromised. A new formalism for stating such gracefully degrading security guarantees is introduced and applied to analyze the examples of password-based message authentication and password-based encryption. While a natural per-message guarantee is achieved for authentication, the situation of password-based encryption is more delicate: a per-session confidentiality guarantee only holds against attackers for which the distribution of password-guessing effort over the sessions is known in advance. In contrast, for more general attackers without such a restriction, a strong, composable notion of security cannot be achieved.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/166"}],"oa":1,"project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","doi":"10.3233/JCS-181131","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0926227X"]},"month":"01","year":"2019","publisher":"IOS Press","department":[{"_id":"KrPi"}],"publication_status":"published","author":[{"last_name":"Demay","first_name":"Gregory","full_name":"Demay, Gregory"},{"id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Gazi","full_name":"Gazi, Peter"},{"last_name":"Maurer","first_name":"Ueli","full_name":"Maurer, Ueli"},{"full_name":"Tackmann, Bjorn","last_name":"Tackmann","first_name":"Bjorn"}],"volume":27,"date_updated":"2021-01-12T08:05:08Z","date_created":"2019-01-27T22:59:10Z","ec_funded":1},{"abstract":[{"lang":"eng","text":"We give non-degeneracy criteria for Riemannian simplices based on simplices in spaces of constant sectional curvature. It extends previous work on Riemannian simplices, where we developed Riemannian simplices with respect to Euclidean reference simplices. The criteria we give in this article are in terms of quality measures for spaces of constant curvature that we develop here. We see that simplices in spaces that have nearly constant curvature, are already non-degenerate under very weak quality demands. This is of importance because it allows for sampling of Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature."}],"issue":"1","type":"journal_article","file":[{"creator":"mwintrae","content_type":"application/pdf","file_size":2170882,"access_level":"open_access","file_name":"mainJournalFinal.pdf","checksum":"57b4df2f16a74eb499734ec8ee240178","date_updated":"2020-07-14T12:47:32Z","date_created":"2019-06-03T09:30:01Z","file_id":"6516","relation":"main_file"}],"oa_version":"Published Version","ddc":["510"],"title":"Simplices modelled on spaces of constant curvature","status":"public","intvolume":" 10","_id":"6515","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2019-07-01T00:00:00Z","page":"223–256","publication":"Journal of Computational Geometry ","citation":{"ista":"Dyer R, Vegter G, Wintraecken M. 2019. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 10(1), 223–256.","apa":"Dyer, R., Vegter, G., & Wintraecken, M. (2019). Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . Carleton University. https://doi.org/10.20382/jocg.v10i1a9","ieee":"R. Dyer, G. Vegter, and M. Wintraecken, “Simplices modelled on spaces of constant curvature,” Journal of Computational Geometry , vol. 10, no. 1. Carleton University, pp. 223–256, 2019.","ama":"Dyer R, Vegter G, Wintraecken M. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 2019;10(1):223–256. doi:10.20382/jocg.v10i1a9","chicago":"Dyer, Ramsay, Gert Vegter, and Mathijs Wintraecken. “Simplices Modelled on Spaces of Constant Curvature.” Journal of Computational Geometry . Carleton University, 2019. https://doi.org/10.20382/jocg.v10i1a9.","mla":"Dyer, Ramsay, et al. “Simplices Modelled on Spaces of Constant Curvature.” Journal of Computational Geometry , vol. 10, no. 1, Carleton University, 2019, pp. 223–256, doi:10.20382/jocg.v10i1a9.","short":"R. Dyer, G. Vegter, M. Wintraecken, Journal of Computational Geometry 10 (2019) 223–256."},"file_date_updated":"2020-07-14T12:47:32Z","ec_funded":1,"date_updated":"2021-01-12T08:07:50Z","date_created":"2019-06-03T09:35:33Z","volume":10,"author":[{"first_name":"Ramsay","last_name":"Dyer","full_name":"Dyer, Ramsay"},{"full_name":"Vegter, Gert","last_name":"Vegter","first_name":"Gert"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Carleton University","year":"2019","month":"07","publication_identifier":{"issn":["1920-180X"]},"language":[{"iso":"eng"}],"doi":"10.20382/jocg.v10i1a9","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"We construct a verifiable delay function (VDF) by showing how the Rivest-Shamir-Wagner time-lock puzzle can be made publicly verifiable. Concretely, we give a statistically sound public-coin protocol to prove that a tuple (N,x,T,y) satisfies y=x2T (mod N) where the prover doesn’t know the factorization of N and its running time is dominated by solving the puzzle, that is, compute x2T, which is conjectured to require T sequential squarings. To get a VDF we make this protocol non-interactive using the Fiat-Shamir heuristic.The motivation for this work comes from the Chia blockchain design, which uses a VDF as akey ingredient. For typical parameters (T≤2 40, N= 2048), our proofs are of size around 10K B, verification cost around three RSA exponentiations and computing the proof is 8000 times faster than solving the puzzle even without any parallelism."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6528","status":"public","title":"Simple verifiable delay functions","ddc":["000"],"intvolume":" 124","file":[{"access_level":"open_access","file_name":"2019_LIPIcs_Pietrzak.pdf","creator":"dernst","file_size":558770,"content_type":"application/pdf","file_id":"6529","relation":"main_file","checksum":"f0ae1bb161431d9db3dea5ace082bfb5","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-06T14:22:04Z"}],"oa_version":"Published Version","scopus_import":1,"day":"10","article_processing_charge":"No","has_accepted_license":"1","publication":"10th Innovations in Theoretical Computer Science Conference","citation":{"ama":"Pietrzak KZ. Simple verifiable delay functions. In: 10th Innovations in Theoretical Computer Science Conference. Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.ITCS.2019.60","ista":"Pietrzak KZ. 2019. Simple verifiable delay functions. 10th Innovations in Theoretical Computer Science Conference. ITCS 2019: Innovations in Theoretical Computer Science, LIPIcs, vol. 124, 60.","apa":"Pietrzak, K. Z. (2019). Simple verifiable delay functions. In 10th Innovations in Theoretical Computer Science Conference (Vol. 124). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.60","ieee":"K. Z. Pietrzak, “Simple verifiable delay functions,” in 10th Innovations in Theoretical Computer Science Conference, San Diego, CA, United States, 2019, vol. 124.","mla":"Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” 10th Innovations in Theoretical Computer Science Conference, vol. 124, 60, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.ITCS.2019.60.","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” In 10th Innovations in Theoretical Computer Science Conference, Vol. 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ITCS.2019.60."},"date_published":"2019-01-10T00:00:00Z","article_number":"60","file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"year":"2019","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"author":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-06-06T14:12:36Z","date_updated":"2021-01-12T08:07:53Z","volume":124,"month":"01","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-095-8"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://eprint.iacr.org/2018/627","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"conference":{"end_date":"2019-01-12","start_date":"2019-01-10","location":"San Diego, CA, United States","name":"ITCS 2019: Innovations in Theoretical Computer Science"},"doi":"10.4230/LIPICS.ITCS.2019.60","language":[{"iso":"eng"}]},{"date_published":"2019-05-16T00:00:00Z","citation":{"short":"A. Kundu, M. Garcia Soto, P. Prabhakar, in:, 5th Indian Control Conference Proceedings, IEEE, 2019.","mla":"Kundu, Atreyee, et al. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” 5th Indian Control Conference Proceedings, 8715598, IEEE, 2019, doi:10.1109/INDIANCC.2019.8715598.","chicago":"Kundu, Atreyee, Miriam Garcia Soto, and Pavithra Prabhakar. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” In 5th Indian Control Conference Proceedings. IEEE, 2019. https://doi.org/10.1109/INDIANCC.2019.8715598.","ama":"Kundu A, Garcia Soto M, Prabhakar P. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In: 5th Indian Control Conference Proceedings. IEEE; 2019. doi:10.1109/INDIANCC.2019.8715598","ieee":"A. Kundu, M. Garcia Soto, and P. Prabhakar, “Formal synthesis of stabilizing controllers for periodically controlled linear switched systems,” in 5th Indian Control Conference Proceedings, Delhi, India, 2019.","apa":"Kundu, A., Garcia Soto, M., & Prabhakar, P. (2019). Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In 5th Indian Control Conference Proceedings. Delhi, India: IEEE. https://doi.org/10.1109/INDIANCC.2019.8715598","ista":"Kundu A, Garcia Soto M, Prabhakar P. 2019. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. 5th Indian Control Conference Proceedings. ICC 2019 - Indian Control Conference, 8715598."},"publication":"5th Indian Control Conference Proceedings","has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":"1","oa_version":"Submitted Version","file":[{"file_id":"8687","relation":"main_file","success":1,"checksum":"d622a91af1e427f6b1e0ba8e18a2b767","date_updated":"2020-10-21T13:13:49Z","date_created":"2020-10-21T13:13:49Z","access_level":"open_access","file_name":"2019_ICC_Kundu.pdf","creator":"dernst","file_size":396031,"content_type":"application/pdf"}],"title":"Formal synthesis of stabilizing controllers for periodically controlled linear switched systems","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6565","abstract":[{"lang":"eng","text":"In this paper, we address the problem of synthesizing periodic switching controllers for stabilizing a family of linear systems. Our broad approach consists of constructing a finite game graph based on the family of linear systems such that every winning strategy on the game graph corresponds to a stabilizing switching controller for the family of linear systems. The construction of a (finite) game graph, the synthesis of a winning strategy and the extraction of a stabilizing controller are all computationally feasible. We illustrate our method on an example."}],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1109/INDIANCC.2019.8715598","conference":{"location":"Delhi, India","start_date":"2019-01-09","end_date":"2019-01-11","name":"ICC 2019 - Indian Control Conference"},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"publication_identifier":{"isbn":["978-153866246-5"]},"month":"05","date_created":"2019-06-17T06:57:33Z","date_updated":"2021-01-12T08:08:01Z","author":[{"first_name":"Atreyee","last_name":"Kundu","full_name":"Kundu, Atreyee"},{"full_name":"Garcia Soto, Miriam","orcid":"0000−0003−2936−5719","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","last_name":"Garcia Soto","first_name":"Miriam"},{"last_name":"Prabhakar","first_name":"Pavithra","full_name":"Prabhakar, Pavithra"}],"publisher":"IEEE","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2019","file_date_updated":"2020-10-21T13:13:49Z","article_number":"8715598"},{"date_updated":"2021-01-12T08:08:16Z","date_created":"2019-07-12T08:34:57Z","file":[{"date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-12T08:32:46Z","checksum":"ceabd152cfa55170d57763f9c6c60a53","file_id":"6629","relation":"main_file","creator":"mwintrae","content_type":"application/pdf","file_size":321176,"file_name":"IntrinsicExtrinsicCCCG2019.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","author":[{"first_name":"Gert","last_name":"Vegter","full_name":"Vegter, Gert"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs"}],"publication_status":"published","title":"The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds","ddc":["004"],"status":"public","department":[{"_id":"HeEd"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6628","year":"2019","file_date_updated":"2020-07-14T12:47:34Z","abstract":[{"lang":"eng","text":"Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces in Euclidean space by piecewise flat triangular meshes with a given number of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and d is the dimension of Euclidean space. Moreover the pro-portionality constant can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In this short note, we prove the extrinsic nature of this constant for manifolds of sufficiently high codimension. We do so by constructing an family of isometric embeddings of the flat torus in Euclidean space."}],"ec_funded":1,"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"CCCG: Canadian Conference in Computational Geometry","end_date":"2019-08-10","location":"Edmonton, Canada","start_date":"2019-08-08"},"date_published":"2019-08-01T00:00:00Z","quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"page":"275-279","publication":"The 31st Canadian Conference in Computational Geometry","oa":1,"citation":{"short":"G. Vegter, M. Wintraecken, in:, The 31st Canadian Conference in Computational Geometry, 2019, pp. 275–279.","mla":"Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff Distance of Optimal Triangulations of Manifolds.” The 31st Canadian Conference in Computational Geometry, 2019, pp. 275–79.","chicago":"Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff Distance of Optimal Triangulations of Manifolds.” In The 31st Canadian Conference in Computational Geometry, 275–79, 2019.","ama":"Vegter G, Wintraecken M. The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. In: The 31st Canadian Conference in Computational Geometry. ; 2019:275-279.","ieee":"G. Vegter and M. Wintraecken, “The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds,” in The 31st Canadian Conference in Computational Geometry, Edmonton, Canada, 2019, pp. 275–279.","apa":"Vegter, G., & Wintraecken, M. (2019). The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. In The 31st Canadian Conference in Computational Geometry (pp. 275–279). Edmonton, Canada.","ista":"Vegter G, Wintraecken M. 2019. The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. The 31st Canadian Conference in Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 275–279."},"month":"08","day":"01","has_accepted_license":"1","scopus_import":1},{"intvolume":" 129","status":"public","title":"Topological data analysis in information space","ddc":["510"],"_id":"6648","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"2019_LIPICS_Edelsbrunner.pdf","creator":"dernst","content_type":"application/pdf","file_size":1355179,"file_id":"6666","relation":"main_file","checksum":"8ec8720730d4c789bf7b06540f1c29f4","date_updated":"2020-07-14T12:47:35Z","date_created":"2019-07-24T06:40:01Z"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory\r\nneeded for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context."}],"page":"31:1-31:14","citation":{"ama":"Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information space. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:31:1-31:14. doi:10.4230/LIPICS.SOCG.2019.31","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information space,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 31:1-31:14.","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2019). Topological data analysis in information space. In 35th International Symposium on Computational Geometry (Vol. 129, p. 31:1-31:14). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.31","ista":"Edelsbrunner H, Virk Z, Wagner H. 2019. Topological data analysis in information space. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 31:1-31:14.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14.","mla":"Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14, doi:10.4230/LIPICS.SOCG.2019.31.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data Analysis in Information Space.” In 35th International Symposium on Computational Geometry, 129:31:1-31:14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.31."},"publication":"35th International Symposium on Computational Geometry","date_published":"2019-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2019","volume":129,"date_updated":"2021-01-12T08:08:23Z","date_created":"2019-07-17T10:36:09Z","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Virk, Ziga","last_name":"Virk","first_name":"Ziga"},{"full_name":"Wagner, Hubert","first_name":"Hubert","last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:35Z","project":[{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1903.08510"]},"language":[{"iso":"eng"}],"doi":"10.4230/LIPICS.SOCG.2019.31","conference":{"end_date":"2019-06-21","start_date":"2019-06-18","location":"Portland, OR, United States","name":"SoCG 2019: Symposium on Computational Geometry"},"publication_identifier":{"isbn":["9783959771047"]},"month":"06"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"15","page":"995-1000","article_type":"original","citation":{"ista":"Zenmyo N, Tokumaru H, Uchinomiya S, Fuchida H, Tabata S, Hamachi I, Shigemoto R, Ojida A. 2019. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 92(5), 995–1000.","ieee":"N. Zenmyo et al., “Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins,” Bulletin of the Chemical Society of Japan, vol. 92, no. 5. Bulletin of the Chemical Society of Japan, pp. 995–1000, 2019.","apa":"Zenmyo, N., Tokumaru, H., Uchinomiya, S., Fuchida, H., Tabata, S., Hamachi, I., … Ojida, A. (2019). Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan. https://doi.org/10.1246/bcsj.20190034","ama":"Zenmyo N, Tokumaru H, Uchinomiya S, et al. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 2019;92(5):995-1000. doi:10.1246/bcsj.20190034","chicago":"Zenmyo, Naoki, Hiroki Tokumaru, Shohei Uchinomiya, Hirokazu Fuchida, Shigekazu Tabata, Itaru Hamachi, Ryuichi Shigemoto, and Akio Ojida. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan, 2019. https://doi.org/10.1246/bcsj.20190034.","mla":"Zenmyo, Naoki, et al. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan, vol. 92, no. 5, Bulletin of the Chemical Society of Japan, 2019, pp. 995–1000, doi:10.1246/bcsj.20190034.","short":"N. Zenmyo, H. Tokumaru, S. Uchinomiya, H. Fuchida, S. Tabata, I. Hamachi, R. Shigemoto, A. Ojida, Bulletin of the Chemical Society of Japan 92 (2019) 995–1000."},"publication":"Bulletin of the Chemical Society of Japan","date_published":"2019-05-15T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"text":"Chemical labeling of proteins with synthetic molecular probes offers the possibility to probe the functions of proteins of interest in living cells. However, the methods for covalently labeling targeted proteins using complementary peptide tag-probe pairs are still limited, irrespective of the versatility of such pairs in biological research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific covalent labeling of proteins. A broad-range evaluation of the reactivity profiles of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized and high labeling selectivity and reactivity. In particular, the labeling specificity of this pair was notably improved compared to the previously reported one. This pair was successfully utilized for the fluorescence imaging of membrane proteins on the surfaces of living cells, demonstrating its potential utility in biological research.","lang":"eng"}],"intvolume":" 92","status":"public","title":"Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6659","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2464903,"access_level":"open_access","file_name":"2019_BCSJ_Zenmyo.pdf","success":1,"checksum":"186de511d6e0ca93f5d981e2443eb8cd","date_updated":"2020-10-02T08:49:58Z","date_created":"2020-10-02T08:49:58Z","file_id":"8594","relation":"main_file"}],"oa_version":"Published Version","publication_identifier":{"issn":["00092673"]},"month":"05","project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1246/bcsj.20190034","ec_funded":1,"file_date_updated":"2020-10-02T08:49:58Z","publisher":"Bulletin of the Chemical Society of Japan","department":[{"_id":"RySh"}],"publication_status":"published","acknowledgement":"his work was supported by the Grant-in-Aid for Scientific Research B (JSPS KAKENHI grant no. JP17H03090 to A. O.); the Scientific Research on Innovative Areas “Chemistry for Multimolecular Crowding Biosystems” (JSPS KAKENHI grant no. JP17H06349 to A. O.); and the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.). A. O. acknowledges the financial support of the Takeda Science Foundation.","year":"2019","volume":92,"date_updated":"2021-01-12T08:08:26Z","date_created":"2019-07-21T21:59:16Z","author":[{"first_name":"Naoki","last_name":"Zenmyo","full_name":"Zenmyo, Naoki"},{"full_name":"Tokumaru, Hiroki","last_name":"Tokumaru","first_name":"Hiroki"},{"full_name":"Uchinomiya, Shohei","first_name":"Shohei","last_name":"Uchinomiya"},{"full_name":"Fuchida, Hirokazu","first_name":"Hirokazu","last_name":"Fuchida"},{"id":"4427179E-F248-11E8-B48F-1D18A9856A87","first_name":"Shigekazu","last_name":"Tabata","full_name":"Tabata, Shigekazu"},{"first_name":"Itaru","last_name":"Hamachi","full_name":"Hamachi, Itaru"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"first_name":"Akio","last_name":"Ojida","full_name":"Ojida, Akio"}]},{"oa_version":"Published Version","file":[{"file_size":575475,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_LIPICS_Kolmogorov.pdf","checksum":"f5ebee8eec6ae09e30365578ee63a492","date_updated":"2020-07-14T12:47:38Z","date_created":"2019-07-31T07:01:45Z","relation":"main_file","file_id":"6738"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6725","intvolume":" 132","title":"Testing the complexity of a valued CSP language","status":"public","ddc":["000"],"abstract":[{"text":"A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language. \r\nRecent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"date_published":"2019-07-01T00:00:00Z","citation":{"ieee":"V. Kolmogorov, “Testing the complexity of a valued CSP language,” in 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, 2019, vol. 132, p. 77:1-77:12.","apa":"Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In 46th International Colloquium on Automata, Languages and Programming (Vol. 132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2019.77","ista":"Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th International Colloquium on Automata, Languages and Programming. ICALP 2019: International Colloquim on Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12.","ama":"Kolmogorov V. Testing the complexity of a valued CSP language. In: 46th International Colloquium on Automata, Languages and Programming. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:10.4230/LIPICS.ICALP.2019.77","chicago":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” In 46th International Colloquium on Automata, Languages and Programming, 132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.77.","short":"V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12.","mla":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” 46th International Colloquium on Automata, Languages and Programming, vol. 132, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:10.4230/LIPICS.ICALP.2019.77."},"publication":"46th International Colloquium on Automata, Languages and Programming","page":"77:1-77:12","has_accepted_license":"1","day":"01","scopus_import":1,"author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"volume":132,"date_updated":"2021-01-12T08:08:40Z","date_created":"2019-07-29T12:23:29Z","year":"2019","department":[{"_id":"VlKo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:38Z","doi":"10.4230/LIPICS.ICALP.2019.77","conference":{"name":"ICALP 2019: International Colloquim on Automata, Languages and Programming","location":"Patras, Greece","start_date":"2019-07-08","end_date":"2019-07-12"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1803.02289"]},"oa":1,"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-3-95977-109-2"],"issn":["1868-8969"]},"month":"07"},{"series_title":"LNCS","scopus_import":"1","day":"29","article_processing_charge":"No","page":"157-180","publication":"Progress in Cryptology – AFRICACRYPT 2019","citation":{"ieee":"M. Walter, “Sampling the integers with low relative error,” in Progress in Cryptology – AFRICACRYPT 2019, vol. 11627, J. Buchmann, A. Nitaj, and T. Rachidi, Eds. Cham: Springer Nature, 2019, pp. 157–180.","apa":"Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann, A. Nitaj, & T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019 (Vol. 11627, pp. 157–180). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-23696-0_9","ista":"Walter M. 2019.Sampling the integers with low relative error. In: Progress in Cryptology – AFRICACRYPT 2019. vol. 11627, 157–180.","ama":"Walter M. Sampling the integers with low relative error. In: Buchmann J, Nitaj A, Rachidi T, eds. Progress in Cryptology – AFRICACRYPT 2019. Vol 11627. LNCS. Cham: Springer Nature; 2019:157-180. doi:10.1007/978-3-030-23696-0_9","chicago":"Walter, Michael. “Sampling the Integers with Low Relative Error.” In Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann, A Nitaj, and T Rachidi, 11627:157–80. LNCS. Cham: Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23696-0_9.","short":"M. Walter, in:, J. Buchmann, A. Nitaj, T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019, Springer Nature, Cham, 2019, pp. 157–180.","mla":"Walter, Michael. “Sampling the Integers with Low Relative Error.” Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann et al., vol. 11627, Springer Nature, 2019, pp. 157–80, doi:10.1007/978-3-030-23696-0_9."},"date_published":"2019-06-29T00:00:00Z","type":"book_chapter","abstract":[{"lang":"eng","text":"Randomness is an essential part of any secure cryptosystem, but many constructions rely on distributions that are not uniform. This is particularly true for lattice based cryptosystems, which more often than not make use of discrete Gaussian distributions over the integers. For practical purposes it is crucial to evaluate the impact that approximation errors have on the security of a scheme to provide the best possible trade-off between security and performance. Recent years have seen surprising results allowing to use relatively low precision while maintaining high levels of security. A key insight in these results is that sampling a distribution with low relative error can provide very strong security guarantees. Since floating point numbers provide guarantees on the relative approximation error, they seem a suitable tool in this setting, but it is not obvious which sampling algorithms can actually profit from them. While previous works have shown that inversion sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES 2014; Prest, ASIACRYPT 2017), other works have called into question if this is possible for other sampling techniques (Zheng et al., Eprint report 2018/309). In this work, we consider all sampling algorithms that are popular in the cryptographic setting and analyze the relationship of floating point precision and the resulting relative error. We show that all of the algorithms either natively achieve a low relative error or can be adapted to do so."}],"status":"public","title":"Sampling the integers with low relative error","intvolume":" 11627","_id":"6726","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","month":"06","publication_identifier":{"isbn":["978-3-0302-3695-3"],"eisbn":["978-3-0302-3696-0"],"issn":["0302-9743","1611-3349"]},"quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"main_file_link":[{"url":"https://eprint.iacr.org/2019/068","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"AFRICACRYPT: International Conference on Cryptology in Africa","end_date":"2019-07-11","location":"Rabat, Morocco","start_date":"2019-07-09"},"doi":"10.1007/978-3-030-23696-0_9","place":"Cham","ec_funded":1,"publication_status":"published","department":[{"_id":"KrPi"}],"editor":[{"last_name":"Buchmann","first_name":"J","full_name":"Buchmann, J"},{"full_name":"Nitaj, A","first_name":"A","last_name":"Nitaj"},{"first_name":"T","last_name":"Rachidi","full_name":"Rachidi, T"}],"publisher":"Springer Nature","year":"2019","date_updated":"2023-02-23T12:50:15Z","date_created":"2019-07-29T12:25:31Z","volume":11627,"author":[{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","first_name":"Michael"}]},{"date_published":"2019-11-15T00:00:00Z","publication":"IEEE Transactions on Signal Processing","citation":{"ama":"Hashemi SA, Condo C, Mondelli M, Gross WJ. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 2019;67(22). doi:10.1109/TSP.2019.2944738","ista":"Hashemi SA, Condo C, Mondelli M, Gross WJ. 2019. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 67(22), 8854897.","ieee":"S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast polar decoders,” IEEE Transactions on Signal Processing, vol. 67, no. 22. IEEE, 2019.","apa":"Hashemi, S. A., Condo, C., Mondelli, M., & Gross, W. J. (2019). Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2019.2944738","mla":"Hashemi, Seyyed Ali, et al. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing, vol. 67, no. 22, 8854897, IEEE, 2019, doi:10.1109/TSP.2019.2944738.","short":"S.A. Hashemi, C. Condo, M. Mondelli, W.J. Gross, IEEE Transactions on Signal Processing 67 (2019).","chicago":"Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing. IEEE, 2019. https://doi.org/10.1109/TSP.2019.2944738."},"article_type":"original","day":"15","article_processing_charge":"No","scopus_import":1,"oa_version":"Preprint","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"6750","title":"Rate-flexible fast polar decoders","status":"public","intvolume":" 67","abstract":[{"lang":"eng","text":"Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported. "}],"issue":"22","type":"journal_article","doi":"10.1109/TSP.2019.2944738","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1903.09203","open_access":"1"}],"external_id":{"arxiv":["1903.09203"]},"quality_controlled":"1","month":"11","publication_identifier":{"issn":["1053587X"]},"author":[{"first_name":"Seyyed Ali","last_name":"Hashemi","full_name":"Hashemi, Seyyed Ali"},{"full_name":"Condo, Carlo","first_name":"Carlo","last_name":"Condo"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"},{"last_name":"Gross","first_name":"Warren J","full_name":"Gross, Warren J"}],"date_created":"2019-07-31T09:51:14Z","date_updated":"2021-01-12T08:08:51Z","volume":67,"year":"2019","publication_status":"published","publisher":"IEEE","department":[{"_id":"MaMo"}],"article_number":"8854897"},{"type":"journal_article","issue":"3","abstract":[{"text":"We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns. \r\nWe also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions.","lang":"eng"}],"intvolume":" 26","ddc":["510"],"status":"public","title":"On grounded L-graphs and their relatives","_id":"6759","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"20fc366fc6683ef0b074a019b73a663a","date_created":"2019-08-05T06:46:55Z","date_updated":"2020-07-14T12:47:39Z","relation":"main_file","file_id":"6764","content_type":"application/pdf","file_size":533697,"creator":"dernst","access_level":"open_access","file_name":"2019_eJourCombinatorics_Jelinek.pdf"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"19","article_type":"original","citation":{"ama":"Jelínek V, Töpfer M. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 2019;26(3). doi:10.37236/8096","apa":"Jelínek, V., & Töpfer, M. (2019). On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/8096","ieee":"V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” Electronic Journal of Combinatorics, vol. 26, no. 3. Electronic Journal of Combinatorics, 2019.","ista":"Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 26(3), P3.17.","short":"V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019).","mla":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics, vol. 26, no. 3, P3.17, Electronic Journal of Combinatorics, 2019, doi:10.37236/8096.","chicago":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2019. https://doi.org/10.37236/8096."},"publication":"Electronic Journal of Combinatorics","date_published":"2019-07-19T00:00:00Z","article_number":"P3.17","ec_funded":1,"file_date_updated":"2020-07-14T12:47:39Z","department":[{"_id":"DaAl"}],"publisher":"Electronic Journal of Combinatorics","publication_status":"published","year":"2019","volume":26,"date_created":"2019-08-04T21:59:20Z","date_updated":"2022-03-18T12:32:02Z","author":[{"last_name":"Jelínek","first_name":"Vít","full_name":"Jelínek, Vít"},{"full_name":"Töpfer, Martin","id":"4B865388-F248-11E8-B48F-1D18A9856A87","last_name":"Töpfer","first_name":"Martin"}],"publication_identifier":{"eissn":["10778926"]},"month":"07","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1808.04148"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.37236/8096"},{"doi":"10.1007/978-3-030-30806-3_1","conference":{"end_date":"2019-09-13","start_date":"2019-09-11","location":"Brussels, Belgium","name":"RP: Reachability Problems"},"language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"isbn":["978-303030805-6"]},"month":"09","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"full_name":"Novotny, Petr","last_name":"Novotny","first_name":"Petr"}],"volume":11674,"date_updated":"2021-01-12T08:09:12Z","date_created":"2019-08-19T07:58:10Z","year":"2019","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","file_date_updated":"2020-07-14T12:47:41Z","date_published":"2019-09-06T00:00:00Z","citation":{"ieee":"G. Avni, T. A. Henzinger, R. Ibsen-Jensen, and P. Novotny, “Bidding games on Markov decision processes,” in Proceedings of the 13th International Conference of Reachability Problems, Brussels, Belgium, 2019, vol. 11674, pp. 1–12.","apa":"Avni, G., Henzinger, T. A., Ibsen-Jensen, R., & Novotny, P. (2019). Bidding games on Markov decision processes. In Proceedings of the 13th International Conference of Reachability Problems (Vol. 11674, pp. 1–12). Brussels, Belgium: Springer. https://doi.org/10.1007/978-3-030-30806-3_1","ista":"Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. 2019. Bidding games on Markov decision processes. Proceedings of the 13th International Conference of Reachability Problems. RP: Reachability Problems, LNCS, vol. 11674, 1–12.","ama":"Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. Bidding games on Markov decision processes. In: Proceedings of the 13th International Conference of Reachability Problems. Vol 11674. Springer; 2019:1-12. doi:10.1007/978-3-030-30806-3_1","chicago":"Avni, Guy, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Petr Novotny. “Bidding Games on Markov Decision Processes.” In Proceedings of the 13th International Conference of Reachability Problems, 11674:1–12. Springer, 2019. https://doi.org/10.1007/978-3-030-30806-3_1.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, P. Novotny, in:, Proceedings of the 13th International Conference of Reachability Problems, Springer, 2019, pp. 1–12.","mla":"Avni, Guy, et al. “Bidding Games on Markov Decision Processes.” Proceedings of the 13th International Conference of Reachability Problems, vol. 11674, Springer, 2019, pp. 1–12, doi:10.1007/978-3-030-30806-3_1."},"publication":" Proceedings of the 13th International Conference of Reachability Problems","page":"1-12","has_accepted_license":"1","day":"06","scopus_import":1,"file":[{"creator":"gavni","content_type":"application/pdf","file_size":436635,"file_name":"prob.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:41Z","date_created":"2019-08-19T07:56:40Z","checksum":"45ebbc709af2b247d28c7c293c01504b","file_id":"6823","relation":"main_file"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6822","intvolume":" 11674","title":"Bidding games on Markov decision processes","ddc":["000"],"status":"public","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the qualitative winner or quantitative payoff of the game. In bidding games, in each turn, we hold an auction between the two players to determine which player moves the token. Bidding games have largely been studied with concrete bidding mechanisms that are variants of a first-price auction: in each turn both players simultaneously submit bids, the higher\r\nbidder moves the token, and pays his bid to the lower bidder in Richman bidding, to the bank in poorman bidding, and in taxman bidding, the bid is split between the other player and the bank according to a predefined constant factor. Bidding games are deterministic games. They have an intriguing connection with a fragment of stochastic games called \r\n randomturn games. We study, for the first time, a combination of bidding games with probabilistic behavior; namely, we study bidding games that are played on Markov decision processes, where the players bid for the right to choose the next action, which determines the probability distribution according to which the next vertex is chosen. We study parity and meanpayoff bidding games on MDPs and extend results from the deterministic bidding setting to the probabilistic one.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"]},{"abstract":[{"lang":"eng","text":"The fundamental model-checking problem, given as input a model and a specification, asks for the algorithmic verification of whether the model satisfies the specification. Two classical models for reactive systems are graphs and Markov decision processes (MDPs). A basic specification formalism in the verification of reactive systems is the strong fairness (aka Streett) objective, where given different types of requests and corresponding grants, the requirement is that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All omega-regular objectives can be expressed as Streett objectives and hence they are canonical in verification. Consider graphs/MDPs with n vertices, m edges, and a Streett objectives with k pairs, and let b denote the size of the description of the Streett objective for the sets of requests and grants. The current best-known algorithm for the problem requires time O(min(n^2, m sqrt{m log n}) + b log n). In this work we present randomized near-linear time algorithms, with expected running time O~(m + b), where the O~ notation hides poly-log factors. Our randomized algorithms are near-linear in the size of the input, and hence optimal up to poly-log factors. "}],"alternative_title":["LIPIcs"],"type":"conference","oa_version":"Published Version","file":[{"checksum":"e1f0e4061212454574f34a1368d018ec","date_created":"2019-10-01T08:20:30Z","date_updated":"2020-07-14T12:47:43Z","file_id":"6922","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":730112,"access_level":"open_access","file_name":"2019_LIPIcs_Chatterjee.pdf"}],"intvolume":" 140","status":"public","ddc":["000"],"title":"Near-linear time algorithms for Streett objectives in graphs and MDPs","_id":"6887","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2019-08-01T00:00:00Z","citation":{"ama":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Near-linear time algorithms for Streett objectives in graphs and MDPs. In: Leibniz International Proceedings in Informatics. Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.7","ista":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2019. Near-linear time algorithms for Streett objectives in graphs and MDPs. Leibniz International Proceedings in Informatics. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 7.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2019). Near-linear time algorithms for Streett objectives in graphs and MDPs. In Leibniz International Proceedings in Informatics (Vol. 140). Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.7","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Near-linear time algorithms for Streett objectives in graphs and MDPs,” in Leibniz International Proceedings in Informatics, Amsterdam, Netherlands, 2019, vol. 140.","mla":"Chatterjee, Krishnendu, et al. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” Leibniz International Proceedings in Informatics, vol. 140, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.7.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” In Leibniz International Proceedings in Informatics, Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.7."},"publication":"Leibniz International Proceedings in Informatics","ec_funded":1,"file_date_updated":"2020-07-14T12:47:43Z","article_number":"7","volume":140,"date_updated":"2022-08-12T10:54:34Z","date_created":"2019-09-18T08:07:58Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Dvorák, Wolfgang","last_name":"Dvorák","first_name":"Wolfgang"},{"full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"first_name":"Alexander","last_name":"Svozil","full_name":"Svozil, Alexander"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2019","month":"08","language":[{"iso":"eng"}],"doi":"10.4230/LIPICS.CONCUR.2019.7","conference":{"name":"CONCUR: International Conference on Concurrency Theory","end_date":"2019-08-30","location":"Amsterdam, Netherlands","start_date":"2019-08-27"},"project":[{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"publication":"Proceedings - IEEE International Conference on Robotics and Automation","citation":{"mla":"Lechner, Mathias, et al. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” Proceedings - IEEE International Conference on Robotics and Automation, vol. 2019–May, 8793840, IEEE, 2019, doi:10.1109/icra.2019.8793840.","short":"M. Lechner, R. Hasani, M. Zimmer, T.A. Henzinger, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2019.","chicago":"Lechner, Mathias, Ramin Hasani, Manuel Zimmer, Thomas A Henzinger, and Radu Grosu. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” In Proceedings - IEEE International Conference on Robotics and Automation, Vol. 2019–May. IEEE, 2019. https://doi.org/10.1109/icra.2019.8793840.","ama":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. Designing worm-inspired neural networks for interpretable robotic control. In: Proceedings - IEEE International Conference on Robotics and Automation. Vol 2019-May. IEEE; 2019. doi:10.1109/icra.2019.8793840","ista":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. 2019. Designing worm-inspired neural networks for interpretable robotic control. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, vol. 2019–May, 8793840.","ieee":"M. Lechner, R. Hasani, M. Zimmer, T. A. Henzinger, and R. Grosu, “Designing worm-inspired neural networks for interpretable robotic control,” in Proceedings - IEEE International Conference on Robotics and Automation, Montreal, QC, Canada, 2019, vol. 2019–May.","apa":"Lechner, M., Hasani, R., Zimmer, M., Henzinger, T. A., & Grosu, R. (2019). Designing worm-inspired neural networks for interpretable robotic control. In Proceedings - IEEE International Conference on Robotics and Automation (Vol. 2019–May). Montreal, QC, Canada: IEEE. https://doi.org/10.1109/icra.2019.8793840"},"date_published":"2019-05-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","_id":"6888","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","status":"public","ddc":["000"],"title":"Designing worm-inspired neural networks for interpretable robotic control","file":[{"access_level":"open_access","file_name":"2019_ICRA_Lechner.pdf","creator":"dernst","file_size":3265107,"content_type":"application/pdf","file_id":"8636","relation":"main_file","success":1,"checksum":"f5545a6b60c3ffd01feb3613f81d03b6","date_created":"2020-10-08T17:30:38Z","date_updated":"2020-10-08T17:30:38Z"}],"oa_version":"Submitted Version","type":"conference","alternative_title":["ICRA"],"abstract":[{"lang":"eng","text":"In this paper, we design novel liquid time-constant recurrent neural networks for robotic control, inspired by the brain of the nematode, C. elegans. In the worm's nervous system, neurons communicate through nonlinear time-varying synaptic links established amongst them by their particular wiring structure. This property enables neurons to express liquid time-constants dynamics and therefore allows the network to originate complex behaviors with a small number of neurons. We identify neuron-pair communication motifs as design operators and use them to configure compact neuronal network structures to govern sequential robotic tasks. The networks are systematically designed to map the environmental observations to motor actions, by their hierarchical topology from sensory neurons, through recurrently-wired interneurons, to motor neurons. The networks are then parametrized in a supervised-learning scheme by a search-based algorithm. We demonstrate that obtained networks realize interpretable dynamics. We evaluate their performance in controlling mobile and arm robots, and compare their attributes to other artificial neural network-based control agents. Finally, we experimentally show their superior resilience to environmental noise, compared to the existing machine learning-based methods."}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"conference":{"name":"ICRA: International Conference on Robotics and Automation","end_date":"2019-05-24","location":"Montreal, QC, Canada","start_date":"2019-05-20"},"doi":"10.1109/icra.2019.8793840","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"isbn":["9781538660270"]},"year":"2019","publication_status":"published","publisher":"IEEE","department":[{"_id":"ToHe"}],"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"},{"last_name":"Hasani","first_name":"Ramin","full_name":"Hasani, Ramin"},{"full_name":"Zimmer, Manuel","last_name":"Zimmer","first_name":"Manuel"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"date_created":"2019-09-18T08:09:51Z","date_updated":"2021-01-12T08:09:28Z","volume":"2019-May","article_number":"8793840","file_date_updated":"2020-10-08T17:30:38Z"},{"doi":"10.4230/LIPICS.CONCUR.2019.20","conference":{"name":"CONCUR: International Conference on Concurrency Theory","end_date":"2019-08-30","location":"Amsterdam, Netherlands","start_date":"2019-08-27"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1905.03588"]},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369"}],"quality_controlled":"1","month":"08","author":[{"first_name":"Milad","last_name":"Aghajohari","full_name":"Aghajohari, Milad"},{"last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"volume":140,"date_created":"2019-09-18T08:06:58Z","date_updated":"2022-01-26T08:27:10Z","year":"2019","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","file_date_updated":"2020-07-14T12:47:43Z","license":"https://creativecommons.org/licenses/by/3.0/","article_number":"20","date_published":"2019-08-01T00:00:00Z","citation":{"ama":"Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.20","ista":"Aghajohari M, Avni G, Henzinger TA. 2019. Determinacy in discrete-bidding infinite-duration games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 20.","ieee":"M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","apa":"Aghajohari, M., Avni, G., & Henzinger, T. A. (2019). Determinacy in discrete-bidding infinite-duration games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.20","mla":"Aghajohari, Milad, et al. Determinacy in Discrete-Bidding Infinite-Duration Games. Vol. 140, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.20.","short":"M. Aghajohari, G. Avni, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.20."},"article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2019_LIPIcs_Aghajohari.pdf","creator":"kschuh","content_type":"application/pdf","file_size":741425,"file_id":"6915","relation":"main_file","checksum":"4df6d3575c506edb17215adada03cc8e","date_updated":"2020-07-14T12:47:43Z","date_created":"2019-09-27T12:21:38Z"}],"oa_version":"Published Version","_id":"6886","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 140","title":"Determinacy in discrete-bidding infinite-duration games","status":"public","ddc":["000"],"abstract":[{"lang":"eng","text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets. "}],"type":"conference","alternative_title":["LIPIcs"]},{"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"A vector addition system with states (VASS) consists of a finite set of states and counters. A configuration is a state and a value for each counter; a transition changes the state and each counter is incremented, decremented, or left unchanged. While qualitative properties such as state and configuration reachability have been studied for VASS, we consider the long-run average cost of infinite computations of VASS. The cost of a configuration is for each state, a linear combination of the counter values. In the special case of uniform cost functions, the linear combination is the same for all states. The (regular) long-run emptiness problem is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped) computation such that the long-run average value of the cost function does not exceed the threshold. For uniform cost functions, we show that the regular long-run emptiness problem is (a) decidable in polynomial time for integer-valued VASS, and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative counters). For general cost functions, we show that the problem is (c) NP-complete for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most interesting result is for (c) integer-valued VASS with general cost functions, where we establish a connection between the regular long-run emptiness problem and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness problem is equally hard as the regular problem in all cases except (c), where it remains open. "}],"_id":"6885","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Long-run average behavior of vector addition systems with states","ddc":["000"],"intvolume":" 140","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":538120,"creator":"kschuh","file_name":"2019_LIPIcs_Chatterjee.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:43Z","date_created":"2019-09-27T12:09:35Z","checksum":"4985e26e1572d1575d64d38acabd71d6","relation":"main_file","file_id":"6914"}],"scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Long-Run Average Behavior of Vector Addition Systems with States,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.27.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","mla":"Chatterjee, Krishnendu, et al. Long-Run Average Behavior of Vector Addition Systems with States. Vol. 140, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.27.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Long-run average behavior of vector addition systems with states,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2019). Long-run average behavior of vector addition systems with states (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.27","ista":"Chatterjee K, Henzinger TA, Otop J. 2019. Long-run average behavior of vector addition systems with states. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 27.","ama":"Chatterjee K, Henzinger TA, Otop J. Long-run average behavior of vector addition systems with states. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.27"},"date_published":"2019-08-01T00:00:00Z","article_number":"27","file_date_updated":"2020-07-14T12:47:43Z","year":"2019","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"date_updated":"2021-01-12T08:09:27Z","date_created":"2019-09-18T08:06:14Z","volume":140,"month":"08","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"}],"conference":{"start_date":"2019-08-27","location":"Amsterdam, Netherlands","end_date":"2019-08-30","name":"CONCUR: International Conference on Concurrency Theory"},"doi":"10.4230/LIPICS.CONCUR.2019.27","language":[{"iso":"eng"}]},{"volume":140,"date_created":"2019-09-18T08:11:43Z","date_updated":"2021-01-12T08:09:28Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Piterman, Nir","first_name":"Nir","last_name":"Piterman"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:47:43Z","article_number":"6","language":[{"iso":"eng"}],"doi":"10.4230/LIPICS.CONCUR.2019.6","conference":{"end_date":"2019-08-30","start_date":"2019-08-27","location":"Amsterdam, Netherlands","name":"CONCUR: International Conference on Concurrency Theory"},"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"08","file":[{"file_name":"2019_LIPIcs_Chatterjee.pdf","access_level":"open_access","file_size":509163,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"6923","date_updated":"2020-07-14T12:47:43Z","date_created":"2019-10-01T08:49:45Z","checksum":"7b2ecfd4d9d02360308c0ca986fc10a7"}],"oa_version":"Published Version","intvolume":" 140","title":"Combinations of Qualitative Winning for Stochastic Parity Games","ddc":["000"],"status":"public","_id":"6889","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. "}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2019-08-01T00:00:00Z","citation":{"short":"K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","mla":"Chatterjee, Krishnendu, and Nir Piterman. Combinations of Qualitative Winning for Stochastic Parity Games. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.6.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.6.","ama":"Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.6","ieee":"K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic Parity Games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","apa":"Chatterjee, K., & Piterman, N. (2019). Combinations of Qualitative Winning for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.6","ista":"Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic Parity Games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 6."},"has_accepted_license":"1","day":"01","scopus_import":1},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6934","checksum":"2d2202f90c6ac991e50876451627c4b5","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-08T12:47:19Z","access_level":"open_access","file_name":"LIPIcs-DISC-2019-29.pdf","file_size":639378,"content_type":"application/pdf","creator":"jrybicki"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6931","intvolume":" 146","status":"public","title":"Byzantine approximate agreement on graphs","ddc":["004"],"abstract":[{"lang":"eng","text":"Consider a distributed system with n processors out of which f can be Byzantine faulty. In the\r\napproximate agreement task, each processor i receives an input value xi and has to decide on an\r\noutput value yi such that\r\n1. the output values are in the convex hull of the non-faulty processors’ input values,\r\n2. the output values are within distance d of each other.\r\n\r\n\r\nClassically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.\r\nIn this work, we study the task in a discrete setting, where input values with some structure\r\nexpressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to\r\noutput vertices that are within distance d of each other in G, but still remain in the graph-induced\r\nconvex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with\r\na deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,\r\nwe show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,\r\nwhere ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a\r\nvariant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact\r\nvariants of these and related tasks over a large class of combinatorial structures."}],"type":"conference","alternative_title":["LIPIcs"],"date_published":"2019-01-01T00:00:00Z","citation":{"chicago":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” In 33rd International Symposium on Distributed Computing, 146:29:1--29:17. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.DISC.2019.29.","mla":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” 33rd International Symposium on Distributed Computing, vol. 146, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17, doi:10.4230/LIPICS.DISC.2019.29.","short":"T. Nowak, J. Rybicki, in:, 33rd International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17.","ista":"Nowak T, Rybicki J. 2019. Byzantine approximate agreement on graphs. 33rd International Symposium on Distributed Computing. DISC: International Symposium on Distributed Computing, LIPIcs, vol. 146, 29:1--29:17.","apa":"Nowak, T., & Rybicki, J. (2019). Byzantine approximate agreement on graphs. In 33rd International Symposium on Distributed Computing (Vol. 146, p. 29:1--29:17). Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.DISC.2019.29","ieee":"T. Nowak and J. Rybicki, “Byzantine approximate agreement on graphs,” in 33rd International Symposium on Distributed Computing, Budapest, Hungary, 2019, vol. 146, p. 29:1--29:17.","ama":"Nowak T, Rybicki J. Byzantine approximate agreement on graphs. In: 33rd International Symposium on Distributed Computing. Vol 146. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:29:1--29:17. doi:10.4230/LIPICS.DISC.2019.29"},"publication":"33rd International Symposium on Distributed Computing","page":"29:1--29:17","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"keyword":["consensus","approximate agreement","Byzantine faults","chordal graphs","lattice agreement"],"author":[{"full_name":"Nowak, Thomas","first_name":"Thomas","last_name":"Nowak"},{"first_name":"Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel"}],"volume":146,"date_created":"2019-10-08T12:41:38Z","date_updated":"2021-01-12T08:09:38Z","year":"2019","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"DaAl"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:44Z","doi":"10.4230/LIPICS.DISC.2019.29","conference":{"name":"DISC: International Symposium on Distributed Computing","end_date":"2019-10-18","start_date":"2019-10-14","location":"Budapest, Hungary"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1908.02743"]},"oa":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","publication_identifier":{"eisbn":["978-3-95977-126-9"]}}]