[{"publication_status":"published","publication_identifier":{"issn":["00982202"],"eissn":["1528901X"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"11","related_material":{"record":[{"relation":"dissertation_contains","id":"7258","status":"public"}]},"volume":141,"abstract":[{"lang":"eng","text":"Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow."}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1809.07625","open_access":"1"}],"scopus_import":"1","intvolume":" 141","month":"11","date_updated":"2024-03-27T23:30:35Z","department":[{"_id":"BjHo"}],"_id":"6486","article_type":"original","type":"journal_article","status":"public","year":"2019","isi":1,"publication":"Journal of Fluids Engineering","day":"01","date_created":"2019-05-26T21:59:13Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1115/1.4043494","oa":1,"quality_controlled":"1","publisher":"ASME","citation":{"ama":"Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 2019;141(11). doi:10.1115/1.4043494","apa":"Kühnen, J., Scarselli, D., & Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. ASME. https://doi.org/10.1115/1.4043494","short":"J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019).","ieee":"J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” Journal of Fluids Engineering, vol. 141, no. 11. ASME, 2019.","mla":"Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering, vol. 141, no. 11, 111105, ASME, 2019, doi:10.1115/1.4043494.","ista":"Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.","chicago":"Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering. ASME, 2019. https://doi.org/10.1115/1.4043494."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1809.07625"],"isi":["000487748600005"]},"article_processing_charge":"No","author":[{"last_name":"Kühnen","full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179","first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide","last_name":"Scarselli"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"title":"Relaminarization of pipe flow by means of 3D-printed shaped honeycombs","article_number":"111105","project":[{"grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}]},{"publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"day":"25","publication":"Journal of Fluid Mechanics","isi":1,"year":"2019","date_published":"2019-05-25T00:00:00Z","doi":"10.1017/jfm.2019.191","date_created":"2019-04-07T21:59:14Z","page":"934-948","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Eliminating turbulence in oil pipelines","grant_number":"737549","call_identifier":"H2020","_id":"25104D44-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:10.1017/jfm.2019.191.","ieee":"D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” Journal of Fluid Mechanics, vol. 867. Cambridge University Press, pp. 934–948, 2019.","short":"D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.","apa":"Scarselli, D., Kühnen, J., & Hof, B. (2019). Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2019.191","ama":"Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 2019;867:934-948. doi:10.1017/jfm.2019.191","chicago":"Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2019.191.","ista":"Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948."},"title":"Relaminarising pipe flow by wall movement","author":[{"last_name":"Scarselli","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kühnen","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob","first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000462606100001"],"arxiv":["1807.05357"]},"article_processing_charge":"No","oa_version":"Preprint","abstract":[{"text":"Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number.","lang":"eng"}],"month":"05","intvolume":" 867","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1807.05357","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14697645"],"issn":["00221120"]},"publication_status":"published","volume":867,"related_material":{"link":[{"relation":"supplementary_material","url":"https://doi.org/10.1017/jfm.2019.191"}],"record":[{"id":"7258","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"_id":"6228","status":"public","type":"journal_article","date_updated":"2024-03-27T23:30:35Z","department":[{"_id":"BjHo"}]},{"acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.).","oa":1,"publisher":"ASPB","quality_controlled":"1","publication":"Plant Physiology","day":"01","year":"2019","isi":1,"date_created":"2019-04-09T08:38:20Z","doi":"10.1104/pp.19.00201","date_published":"2019-06-01T00:00:00Z","page":"1152-1165","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201.","ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165.","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:10.1104/pp.19.00201.","ieee":"A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019.","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165.","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201","ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165. doi:10.1104/pp.19.00201"},"title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","article_processing_charge":"No","external_id":{"pmid":["30936248"],"isi":["000470086100045"]},"author":[{"first_name":"A","last_name":"Oochi","full_name":"Oochi, A"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","last_name":"Hajny","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub"},{"first_name":"K","last_name":"Fukui","full_name":"Fukui, K"},{"first_name":"Y","full_name":"Nakao, Y","last_name":"Nakao"},{"last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M","full_name":"Quareshy, M","last_name":"Quareshy"},{"full_name":"Takahashi, K","last_name":"Takahashi","first_name":"K"},{"first_name":"T","full_name":"Kinoshita, T","last_name":"Kinoshita"},{"full_name":"Harborough, SR","last_name":"Harborough","first_name":"SR"},{"first_name":"S","last_name":"Kepinski","full_name":"Kepinski, S"},{"last_name":"Kasahara","full_name":"Kasahara, H","first_name":"H"},{"first_name":"RM","full_name":"Napier, RM","last_name":"Napier"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Hayashi, KI","last_name":"Hayashi","first_name":"KI"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport."}],"intvolume":" 180","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.19.00201"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"ec_funded":1,"volume":180,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"},{"relation":"dissertation_contains","id":"8822","status":"public"}]},"issue":"2","_id":"6260","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-27T23:30:37Z","department":[{"_id":"JiFr"}]},{"ddc":["570"],"date_updated":"2024-03-27T23:30:38Z","file_date_updated":"2020-10-21T07:22:34Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"_id":"6508","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"aea43726d80e35ce3885073a5f05c3e3","file_id":"8686","creator":"dernst","file_size":3356292,"date_updated":"2020-10-21T07:22:34Z","file_name":"2019_Cell_Shamipour_accepted.pdf","date_created":"2020-10-21T07:22:34Z"}],"publication_status":"published","publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"8350"}]},"issue":"6","volume":177,"pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we 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 oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"intvolume":" 177","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.04.030"}],"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 2019;177(6):1463-1479.e18. doi:10.1016/j.cell.2019.04.030","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.030","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” Cell, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:10.1016/j.cell.2019.04.030.","ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.030."},"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","article_processing_charge":"No","external_id":{"pmid":["31080065"],"isi":["000469415100013"]},"author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"full_name":"Kardos, Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland"},{"last_name":"Xue","full_name":"Xue, Shi-lei","first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"}],"publication":"Cell","day":"30","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-06-02T21:59:12Z","doi":"10.1016/j.cell.2019.04.030","date_published":"2019-05-30T00:00:00Z","page":"1463-1479.e18","acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"citation":{"mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:10.1016/j.cell.2019.10.006.","ieee":"C. Schwayer et al., “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18. doi:10.1016/j.cell.2019.10.006","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006.","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["31675500"],"isi":["000493898000012"]},"author":[{"last_name":"Schwayer","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia"},{"last_name":"Shamipour","full_name":"Shamipour, Shayan","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","first_name":"Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schauer","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra"},{"full_name":"Balda, M","last_name":"Balda","first_name":"M"},{"last_name":"Tada","full_name":"Tada, M","first_name":"M"},{"full_name":"Matter, K","last_name":"Matter","first_name":"K"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"year":"2019","has_accepted_license":"1","isi":1,"publication":"Cell","day":"31","page":"937-952.e18","date_created":"2019-11-12T12:51:06Z","doi":"10.1016/j.cell.2019.10.006","date_published":"2019-10-31T00:00:00Z","oa":1,"publisher":"Cell Press","quality_controlled":"1","date_updated":"2024-03-27T23:30:38Z","ddc":["570"],"file_date_updated":"2020-10-21T07:09:45Z","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"_id":"7001","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8684","checksum":"33dac4bb77ee630e2666e936b4d57980","success":1,"creator":"dernst","date_updated":"2020-10-21T07:09:45Z","file_size":8805878,"date_created":"2020-10-21T07:09:45Z","file_name":"2019_Cell_Schwayer_accepted.pdf"}],"ec_funded":1,"issue":"4","related_material":{"link":[{"url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","relation":"press_release","description":"News auf IST Website"}],"record":[{"id":"7186","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"8350"}]},"volume":179,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","intvolume":" 179","month":"10"},{"citation":{"mla":"Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891.","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:10.15479/AT:ISTA:6891","apa":"Kopf, A. (2019). The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6891","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6891.","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","last_name":"Kopf"}],"article_processing_charge":"No","title":"The implication of cytoskeletal dynamics on leukocyte migration","project":[{"grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems","_id":"265E2996-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"has_accepted_license":"1","year":"2019","day":"24","page":"171","doi":"10.15479/AT:ISTA:6891","date_published":"2019-07-24T00:00:00Z","date_created":"2019-09-19T08:19:44Z","publisher":"Institute of Science and Technology Austria","oa":1,"supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-10-18T08:49:17Z","ddc":["570"],"file_date_updated":"2020-10-17T22:30:03Z","department":[{"_id":"MiSi"}],"_id":"6891","type":"dissertation","status":"public","keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_size":74735267,"date_updated":"2020-10-17T22:30:03Z","creator":"akopf","file_name":"Kopf_PhD_Thesis.docx","date_created":"2019-10-15T05:28:42Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"6950","checksum":"00d100d6468e31e583051e0a006b640c"},{"creator":"akopf","date_updated":"2020-10-17T22:30:03Z","file_size":52787224,"date_created":"2019-10-15T05:28:47Z","file_name":"Kopf_PhD_Thesis1.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6951","checksum":"5d1baa899993ae6ca81aebebe1797000","embargo":"2020-10-16"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"6328","status":"public"},{"status":"public","id":"15","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6877","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/feeling-like-a-cell/"}]},"abstract":[{"text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07"},{"citation":{"apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 2019;568:546-550. doi:10.1038/s41586-019-1087-5","ieee":"J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” Nature, vol. 568. Springer Nature, pp. 546–550, 2019.","short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.","mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature, vol. 568, Springer Nature, 2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.","ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550.","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["30944468"],"isi":["000465594200050"]},"author":[{"orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"},{"first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656"},{"full_name":"Stopp, Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"de Vries","full_name":"de Vries, Ingrid"},{"first_name":"Meghan K.","full_name":"Driscoll, Meghan K.","last_name":"Driscoll"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"full_name":"Welf, Erik S.","last_name":"Welf","first_name":"Erik S."},{"first_name":"Gaudenz","full_name":"Danuser, Gaudenz","last_name":"Danuser"},{"last_name":"Fiolka","full_name":"Fiolka, Reto","first_name":"Reto"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"},{"name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20","call_identifier":"FWF","_id":"265FAEBA-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1396-2014","name":"Molecular and system level view of immune cell migration"}],"year":"2019","isi":1,"publication":"Nature","day":"25","page":"546-550","date_created":"2019-04-17T06:52:28Z","doi":"10.1038/s41586-019-1087-5","date_published":"2019-04-25T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_updated":"2024-03-27T23:30:39Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"_id":"6328","type":"journal_article","article_type":"letter_note","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":568,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/","relation":"press_release"}],"record":[{"id":"14697","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"6891","status":"public"}]},"abstract":[{"text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion.","lang":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/","open_access":"1"}],"scopus_import":"1","intvolume":" 568","month":"04"},{"date_created":"2019-09-15T22:00:46Z","doi":"10.1016/j.cell.2019.08.047","date_published":"2019-09-19T00:00:00Z","page":"51-53","publication":"Cell","day":"19","year":"2019","isi":1,"quality_controlled":"1","publisher":"Elsevier","title":"The neural crest pitches in to remove apoptotic debris","article_processing_charge":"No","external_id":{"isi":["000486618500011"],"pmid":["31539498"]},"author":[{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047.","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","apa":"Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047","ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell. 2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047.","ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53."},"volume":179,"issue":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"6891","status":"public"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"intvolume":" 179","month":"09","scopus_import":"1","pmid":1,"oa_version":"None","department":[{"_id":"MiSi"}],"date_updated":"2024-03-27T23:30:40Z","status":"public","type":"journal_article","article_type":"original","_id":"6877"},{"date_updated":"2024-03-27T23:30:41Z","department":[{"_id":"SiHi"}],"_id":"6830","article_type":"letter_note","type":"journal_article","status":"public","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"5","related_material":{"record":[{"relation":"part_of_dissertation","id":"7902","status":"public"}]},"volume":103,"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.021"}],"month":"09","intvolume":" 103","citation":{"chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","apa":"Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"article_processing_charge":"No","external_id":{"isi":["000484400200002"],"pmid":["31487522"]},"title":"Memo1 tiles the radial glial cell grid","isi":1,"year":"2019","day":"04","publication":"Neuron","page":"750-752","date_published":"2019-09-04T00:00:00Z","doi":"10.1016/j.neuron.2019.08.021","date_created":"2019-08-25T22:00:50Z","publisher":"Elsevier","quality_controlled":"1","oa":1},{"abstract":[{"text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 20","month":"07","publication_status":"published","publication_identifier":{"eissn":["1422-0067"]},"language":[{"iso":"eng"}],"file":[{"checksum":"dd9d1cbb933a72ceb666c9667890ac51","file_id":"6645","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-07-17T06:17:15Z","file_name":"2019_JournalMolecularScience_Adamowski.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:34Z","file_size":3330291}],"ec_funded":1,"issue":"13","related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"volume":20,"_id":"6627","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-27T23:30:43Z","ddc":["580"],"file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"JiFr"}],"oa":1,"publisher":"MDPI","quality_controlled":"1","year":"2019","has_accepted_license":"1","isi":1,"publication":"International Journal of Molecular Sciences","day":"07","date_created":"2019-07-11T12:00:32Z","doi":"10.3390/ijms20133337","date_published":"2019-07-07T00:00:00Z","article_number":"3337","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"citation":{"ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337","mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337.","chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","external_id":{"pmid":["31284661"],"isi":["000477041100221"]},"author":[{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling"},{"oa":1,"quality_controlled":"1","publisher":"ACM","date_created":"2019-11-26T14:22:09Z","date_published":"2019-11-06T00:00:00Z","doi":"10.1145/3355089.3356576","year":"2019","has_accepted_license":"1","isi":1,"publication":"ACM Transactions on Graphics","day":"06","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"article_number":"157","article_processing_charge":"No","external_id":{"isi":["000498397300007"]},"author":[{"last_name":"Hafner","full_name":"Hafner, Christian","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schumacher","full_name":"Schumacher, Christian","first_name":"Christian"},{"first_name":"Espen","last_name":"Knoop","full_name":"Knoop, Espen"},{"last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"full_name":"Bächer, Moritz","last_name":"Bächer","first_name":"Moritz"}],"title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","citation":{"ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576.","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":" 38","month":"11","abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"volume":38,"related_material":{"record":[{"id":"12897","status":"public","relation":"dissertation_contains"}]},"issue":"6","publication_status":"published","publication_identifier":{"issn":["0730-0301"]},"language":[{"iso":"eng"}],"file":[{"creator":"bbickel","date_updated":"2020-07-14T12:47:49Z","file_size":1673176,"title":"X-CAD Supplemental Material","date_created":"2019-11-26T14:24:26Z","file_name":"xcad_sup_mat_siga19.pdf","access_level":"open_access","relation":"supplementary_material","content_type":"application/pdf","checksum":"56a2fb019adcb556d2b022f5e5acb68c","file_id":"7119"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","description":"This is the author's version of the work.","checksum":"5f29d76aceb5102e766cbab9b17d776e","file_id":"7120","creator":"bbickel","date_updated":"2020-07-14T12:47:49Z","file_size":14563618,"date_created":"2019-11-26T14:24:27Z","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file_name":"XCAD_authors_version.pdf"},{"file_name":"XCAD_video.mp4","date_created":"2019-11-26T14:27:37Z","creator":"bbickel","file_size":259979129,"date_updated":"2020-07-14T12:47:49Z","checksum":"0d31e123286cbec9e28b2001c2bb0d55","file_id":"7121","relation":"main_file","access_level":"open_access","content_type":"video/mp4"}],"article_type":"original","type":"journal_article","status":"public","_id":"7117","file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"BeBi"}],"date_updated":"2024-03-27T23:30:46Z","ddc":["000"]},{"date_published":"2019-03-22T00:00:00Z","doi":"10.1103/PhysRevLett.122.114502","date_created":"2019-03-31T21:59:12Z","day":"22","publication":"Physical Review Letters","isi":1,"year":"2019","publisher":"American Physical Society","quality_controlled":"1","oa":1,"title":"Transition to turbulence in particle laden flows","author":[{"full_name":"Agrawal, Nishchal","last_name":"Agrawal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H","last_name":"Choueiri"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"article_processing_charge":"No","external_id":{"arxiv":["1809.06358"],"isi":["000461922000006"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502.","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502"},"article_number":"114502","issue":"11","related_material":{"record":[{"status":"public","id":"9728","relation":"dissertation_contains"}]},"volume":122,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"publication_status":"published","month":"03","intvolume":" 122","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.06358"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations."}],"department":[{"_id":"BjHo"}],"date_updated":"2024-03-27T23:30:47Z","status":"public","type":"journal_article","_id":"6189"},{"has_accepted_license":"1","year":"2019","day":"03","page":"152","date_published":"2019-05-03T00:00:00Z","doi":"10.15479/AT:ISTA:6371","date_created":"2019-05-03T11:55:51Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Igler","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"}],"article_processing_charge":"No","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"embargo":"2020-05-02","checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_id":"6373","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","date_created":"2019-05-03T11:54:52Z","file_size":12597663,"date_updated":"2021-02-11T11:17:13Z","creator":"cigler"},{"checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","file_id":"6374","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","date_created":"2019-05-03T11:54:54Z","creator":"cigler","file_size":34644426,"date_updated":"2020-07-14T12:47:28Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"67"},{"status":"public","id":"5585","relation":"popular_science"}]},"abstract":[{"text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"date_updated":"2024-02-21T13:45:52Z","ddc":["576","579"],"file_date_updated":"2021-02-11T11:17:13Z","department":[{"_id":"CaGu"}],"_id":"6371","type":"dissertation","status":"public","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"]},{"title":"Evaluation and monitoring of free running oscillators serving as source of randomness","article_processing_charge":"No","author":[{"first_name":"Elie Noumon","last_name":"Allini","full_name":"Allini, Elie Noumon"},{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","full_name":"Skórski, Maciej","last_name":"Skórski"},{"first_name":"Oto","last_name":"Petura","full_name":"Petura, Oto"},{"last_name":"Bernard","full_name":"Bernard, Florent","first_name":"Florent"},{"last_name":"Laban","full_name":"Laban, Marek","first_name":"Marek"},{"first_name":"Viktor","full_name":"Fischer, Viktor","last_name":"Fischer"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242.","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242","ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018."},"oa":1,"publisher":"International Association for Cryptologic Research","quality_controlled":"1","date_created":"2021-11-14T23:01:25Z","date_published":"2018-01-01T00:00:00Z","doi":"10.13154/tches.v2018.i3.214-242","page":"214-242","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","day":"01","year":"2018","has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"10286","department":[{"_id":"KrPi"}],"file_date_updated":"2021-11-15T10:27:29Z","ddc":["000"],"date_updated":"2021-11-15T10:48:49Z","intvolume":" 2018","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied.","lang":"eng"}],"volume":2018,"issue":"3","language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2021-11-15T10:27:29Z","file_size":955755,"date_created":"2021-11-15T10:27:29Z","file_name":"2018_IACR_Allini.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10289","checksum":"b816b848f046c48a8357700d9305dce5","success":1}],"publication_status":"published","publication_identifier":{"eissn":["2569-2925"]}},{"project":[{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k."},"title":"Quasipolynomial set-based symbolic algorithms for parity games","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wolfgang","last_name":"Dvořák","full_name":"Dvořák, Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"first_name":"Alexander","full_name":"Svozil, Alexander","last_name":"Svozil"}],"external_id":{"arxiv":["1909.04983"]},"article_processing_charge":"No","acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","publisher":"EasyChair","quality_controlled":"1","oa":1,"day":"23","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","has_accepted_license":"1","year":"2018","doi":"10.29007/5z5k","date_published":"2018-10-23T00:00:00Z","date_created":"2022-03-18T12:46:32Z","page":"233-253","_id":"10883","status":"public","type":"conference","conference":{"end_date":"2018-11-21","location":"Awassa, Ethiopia","start_date":"2018-11-17","name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning"},"ddc":["000"],"date_updated":"2022-07-29T09:24:31Z","file_date_updated":"2022-05-17T07:51:08Z","department":[{"_id":"KrCh"}],"oa_version":"Published Version","abstract":[{"text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.","lang":"eng"}],"month":"10","intvolume":" 57","alternative_title":["EPiC Series in Computing"],"scopus_import":"1","file":[{"success":1,"checksum":"1229aa8640bd6db610c85decf2265480","file_id":"11392","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_EPiCs_Chatterjee.pdf","date_created":"2022-05-17T07:51:08Z","file_size":720893,"date_updated":"2022-05-17T07:51:08Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2398-7340"]},"publication_status":"published","volume":57,"ec_funded":1},{"status":"public","type":"conference","conference":{"start_date":"2017-03-30","end_date":"2017-04-01","location":"Munich, Germany","name":"MaLiQS: Macroscopic Limits of Quantum Systems"},"_id":"11","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:48:16Z","month":"10","intvolume":" 270","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10843"}],"oa_version":"Preprint","abstract":[{"text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm.","lang":"eng"}],"volume":270,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"title":"Mean-field limits of particles in interaction with quantised radiation fields","publist_id":"8045","author":[{"first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","last_name":"Leopold"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"}],"external_id":{"arxiv":["1806.10843"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214."},"quality_controlled":"1","publisher":"Springer","oa":1,"date_published":"2018-10-27T00:00:00Z","doi":"10.1007/978-3-030-01602-9_9","date_created":"2018-12-11T11:44:08Z","page":"185 - 214","day":"27","year":"2018"},{"publist_id":"6119","author":[{"first_name":"Franco","last_name":"Flandoli","full_name":"Flandoli, Franco"},{"first_name":"Francesco","full_name":"Russo, Francesco","last_name":"Russo"},{"first_name":"Giovanni A","id":"47491882-F248-11E8-B48F-1D18A9856A87","last_name":"Zanco","full_name":"Zanco, Giovanni A"}],"article_processing_charge":"Yes (via OA deal)","title":"Infinite-dimensional calculus under weak spatial regularity of the processes","citation":{"ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826.","chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2.","apa":"Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. Springer. https://doi.org/10.1007/s10959-016-0724-2","ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826. doi:10.1007/s10959-016-0724-2","ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” Journal of Theoretical Probability, vol. 31, no. 2. Springer, pp. 789–826, 2018.","short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826.","mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"page":"789-826","date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s10959-016-0724-2","date_created":"2018-12-11T11:50:45Z","has_accepted_license":"1","year":"2018","day":"01","publication":"Journal of Theoretical Probability","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA.","file_date_updated":"2020-07-14T12:44:39Z","department":[{"_id":"JaMa"}],"date_updated":"2021-01-12T06:49:09Z","ddc":["519"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"712","_id":"1215","volume":31,"issue":"2","publication_status":"published","file":[{"creator":"system","file_size":671125,"date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","date_created":"2018-12-12T10:17:13Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5266","checksum":"47686d58ec21c164540f1a980ff2163f"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"06","intvolume":" 31","abstract":[{"lang":"eng","text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus."}],"oa_version":"Published Version"},{"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"doi":"10.4230/LIPIcs.SoCG.2018.39","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:45:04Z","has_accepted_license":"1","year":"2018","day":"01","project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"article_number":"39","publist_id":"7735","author":[{"last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"}],"title":"Hanani-Tutte for approximating maps of graphs","citation":{"ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39","apa":"Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.39","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39.","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"month":"01","intvolume":" 99","abstract":[{"text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint "pipes" corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.","lang":"eng"}],"oa_version":"Published Version","volume":99,"publication_identifier":{"isbn":["978-3-95977-066-8"]},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:19Z","file_size":718857,"creator":"dernst","date_created":"2018-12-17T12:33:52Z","file_name":"2018_LIPIcs_Fulek.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5701","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c"}],"language":[{"iso":"eng"}],"type":"conference","conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"185","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T06:53:36Z","ddc":["510"]},{"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","page":"35:1 - 35:13","date_created":"2018-12-11T11:45:05Z","doi":"10.4230/LIPIcs.SoCG.2018.35","date_published":"2018-06-11T00:00:00Z","year":"2018","has_accepted_license":"1","day":"11","project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"publist_id":"7733","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"first_name":"Ziga","full_name":"Virk, Ziga","last_name":"Virk"},{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","citation":{"mla":"Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35.","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"intvolume":" 99","month":"06","abstract":[{"lang":"eng","text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex."}],"oa_version":"Published Version","volume":99,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7509403803b3ac1aee94bbc2ad293d21","file_id":"5724","creator":"dernst","date_updated":"2020-07-14T12:45:20Z","file_size":489080,"date_created":"2018-12-17T16:31:31Z","file_name":"2018_LIPIcs_Edelsbrunner.pdf"}],"conference":{"start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","_id":"188","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:20Z","date_updated":"2021-01-12T06:53:48Z","ddc":["000"]},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"01","publication":"Heliyon","has_accepted_license":"1","year":"2018","date_published":"2018-04-01T00:00:00Z","doi":"10.1016/j.heliyon.2018.e00596","date_created":"2018-12-11T11:45:44Z","article_number":"e00596","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018.","apa":"De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596","ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596","chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.","ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596."},"title":"An introduction to the maximum entropy approach and its application to inference problems in biology","author":[{"full_name":"De Martino, Andrea","last_name":"De Martino","first_name":"Andrea"},{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data."}],"month":"04","intvolume":" 4","scopus_import":1,"file":[{"file_name":"2018_Heliyon_DeMartino.pdf","date_created":"2019-02-06T07:36:24Z","creator":"dernst","file_size":994490,"date_updated":"2020-07-14T12:45:59Z","checksum":"67010cf5e3b3e0637c659371714a715a","file_id":"5929","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":4,"ec_funded":1,"_id":"306","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_updated":"2021-01-12T07:40:46Z","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:59Z"}]