[{"oa_version":"Preprint","date_updated":"2023-09-19T14:26:52Z","date_created":"2019-02-13T13:32:48Z","author":[{"last_name":"Haller","first_name":"Stefan","full_name":"Haller, Stefan"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul","full_name":"Swoboda, Paul"},{"full_name":"Savchynskyy, Bogdan","first_name":"Bogdan","last_name":"Savchynskyy"}],"department":[{"_id":"VlKo"}],"publisher":"AAAI Press","title":"Exact MAP-inference by confining combinatorial search with LP relaxation","publication_status":"published","status":"public","_id":"5978","year":"2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We consider the MAP-inference problem for graphical models,which is a valued constraint satisfaction problem defined onreal numbers with a natural summation operation. We proposea family of relaxations (different from the famous Sherali-Adams hierarchy), which naturally define lower bounds for itsoptimum. This family always contains a tight relaxation andwe give an algorithm able to find it and therefore, solve theinitial non-relaxed NP-hard problem.The relaxations we consider decompose the original probleminto two non-overlapping parts: an easy LP-tight part and adifficult one. For the latter part a combinatorial solver must beused. As we show in our experiments, in a number of applica-tions the second, difficult part constitutes only a small fractionof the whole problem. This property allows to significantlyreduce the computational time of the combinatorial solver andtherefore solve problems which were out of reach before."}],"type":"conference","language":[{"iso":"eng"}],"date_published":"2018-02-01T00:00:00Z","conference":{"name":"AAAI: Conference on Artificial Intelligence","start_date":"2018-02-02","location":"New Orleans, LU, United States","end_date":"2018-02-07"},"page":"6581-6588","quality_controlled":"1","isi":1,"external_id":{"isi":["000485488906082"],"arxiv":["2004.06370"]},"citation":{"ista":"Haller S, Swoboda P, Savchynskyy B. 2018. Exact MAP-inference by confining combinatorial search with LP relaxation. Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence, 6581–6588.","ieee":"S. Haller, P. Swoboda, and B. Savchynskyy, “Exact MAP-inference by confining combinatorial search with LP relaxation,” in Proceedings of the 32st AAAI Conference on Artificial Intelligence, New Orleans, LU, United States, 2018, pp. 6581–6588.","apa":"Haller, S., Swoboda, P., & Savchynskyy, B. (2018). Exact MAP-inference by confining combinatorial search with LP relaxation. In Proceedings of the 32st AAAI Conference on Artificial Intelligence (pp. 6581–6588). New Orleans, LU, United States: AAAI Press.","ama":"Haller S, Swoboda P, Savchynskyy B. Exact MAP-inference by confining combinatorial search with LP relaxation. In: Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI Press; 2018:6581-6588.","chicago":"Haller, Stefan, Paul Swoboda, and Bogdan Savchynskyy. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” In Proceedings of the 32st AAAI Conference on Artificial Intelligence, 6581–88. AAAI Press, 2018.","mla":"Haller, Stefan, et al. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–88.","short":"S. Haller, P. Swoboda, B. Savchynskyy, in:, Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–6588."},"main_file_link":[{"url":"https://arxiv.org/abs/2004.06370","open_access":"1"}],"oa":1,"publication":"Proceedings of the 32st AAAI Conference on Artificial Intelligence","article_processing_charge":"No","month":"02","day":"01","scopus_import":"1"},{"author":[{"full_name":"Ridderbos, Joost","first_name":"Joost","last_name":"Ridderbos"},{"first_name":"Matthias","last_name":"Brauns","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","full_name":"Brauns, Matthias"},{"full_name":"Shen, Jie","first_name":"Jie","last_name":"Shen"},{"last_name":"de Vries","first_name":"Folkert K.","full_name":"de Vries, Folkert K."},{"full_name":"Li, Ang","last_name":"Li","first_name":"Ang"},{"first_name":"Erik P. A. M.","last_name":"Bakkers","full_name":"Bakkers, Erik P. A. M."},{"full_name":"Brinkman, Alexander","last_name":"Brinkman","first_name":"Alexander"},{"full_name":"Zwanenburg, Floris A.","first_name":"Floris A.","last_name":"Zwanenburg"}],"date_created":"2019-02-14T12:14:26Z","date_updated":"2023-09-19T14:29:58Z","volume":30,"year":"2018","publication_status":"published","publisher":"Wiley","department":[{"_id":"GeKa"}],"article_number":"1802257","doi":"10.1002/adma.201802257","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1809.08487","open_access":"1"}],"external_id":{"isi":["000450232800015"],"arxiv":["1809.08487"]},"oa":1,"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"issn":["0935-9648"]},"oa_version":"Preprint","_id":"5990","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Josephson effect in a few-hole quantum dot","intvolume":" 30","abstract":[{"text":"A Ge–Si core–shell nanowire is used to realize a Josephson field‐effect transistor with highly transparent contacts to superconducting leads. By changing the electric field, access to two distinct regimes, not combined before in a single device, is gained: in the accumulation mode the device is highly transparent and the supercurrent is carried by multiple subbands, while near depletion, the supercurrent is carried by single‐particle levels of a strongly coupled quantum dot operating in the few‐hole regime. These results establish Ge–Si nanowires as an important platform for hybrid superconductor–semiconductor physics and Majorana fermions.","lang":"eng"}],"issue":"44","type":"journal_article","date_published":"2018-11-02T00:00:00Z","publication":"Advanced Materials","citation":{"ista":"Ridderbos J, Brauns M, Shen J, de Vries FK, Li A, Bakkers EPAM, Brinkman A, Zwanenburg FA. 2018. Josephson effect in a few-hole quantum dot. Advanced Materials. 30(44), 1802257.","apa":"Ridderbos, J., Brauns, M., Shen, J., de Vries, F. K., Li, A., Bakkers, E. P. A. M., … Zwanenburg, F. A. (2018). Josephson effect in a few-hole quantum dot. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201802257","ieee":"J. Ridderbos et al., “Josephson effect in a few-hole quantum dot,” Advanced Materials, vol. 30, no. 44. Wiley, 2018.","ama":"Ridderbos J, Brauns M, Shen J, et al. Josephson effect in a few-hole quantum dot. Advanced Materials. 2018;30(44). doi:10.1002/adma.201802257","chicago":"Ridderbos, Joost, Matthias Brauns, Jie Shen, Folkert K. de Vries, Ang Li, Erik P. A. M. Bakkers, Alexander Brinkman, and Floris A. Zwanenburg. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201802257.","mla":"Ridderbos, Joost, et al. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials, vol. 30, no. 44, 1802257, Wiley, 2018, doi:10.1002/adma.201802257.","short":"J. Ridderbos, M. Brauns, J. Shen, F.K. de Vries, A. Li, E.P.A.M. Bakkers, A. Brinkman, F.A. Zwanenburg, Advanced Materials 30 (2018)."},"day":"02","article_processing_charge":"No","scopus_import":"1"},{"publication_identifier":{"issn":["1553-7404"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1007698","isi":1,"quality_controlled":"1","external_id":{"isi":["000449328500025"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:15Z","article_number":"e1007698","volume":14,"date_created":"2019-02-14T13:07:45Z","date_updated":"2023-09-19T14:31:43Z","author":[{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp"},{"full_name":"Meinhardt, Gudrun","first_name":"Gudrun","last_name":"Meinhardt"},{"full_name":"Plessl, Kerstin","last_name":"Plessl","first_name":"Kerstin"},{"full_name":"Vondra, Sigrid","last_name":"Vondra","first_name":"Sigrid"},{"first_name":"Tamara","last_name":"Weiss","full_name":"Weiss, Tamara"},{"last_name":"Haslinger","first_name":"Peter","full_name":"Haslinger, Peter"},{"last_name":"Lendl","first_name":"Thomas","full_name":"Lendl, Thomas"},{"full_name":"Aumayr, Karin","last_name":"Aumayr","first_name":"Karin"},{"first_name":"Mario","last_name":"Mairhofer","full_name":"Mairhofer, Mario"},{"first_name":"Xiaowei","last_name":"Zhu","full_name":"Zhu, Xiaowei"},{"first_name":"Birgit","last_name":"Schütz","full_name":"Schütz, Birgit"},{"last_name":"Hannibal","first_name":"Roberta L.","full_name":"Hannibal, Roberta L."},{"first_name":"Robert","last_name":"Lindau","full_name":"Lindau, Robert"},{"last_name":"Weil","first_name":"Beatrix","full_name":"Weil, Beatrix"},{"first_name":"Jan","last_name":"Ernerudh","full_name":"Ernerudh, Jan"},{"full_name":"Neesen, Jürgen","first_name":"Jürgen","last_name":"Neesen"},{"first_name":"Gerda","last_name":"Egger","full_name":"Egger, Gerda"},{"full_name":"Mikula, Mario","first_name":"Mario","last_name":"Mikula"},{"last_name":"Röhrl","first_name":"Clemens","full_name":"Röhrl, Clemens"},{"full_name":"Urban, Alexander E.","last_name":"Urban","first_name":"Alexander E."},{"full_name":"Baker, Julie","last_name":"Baker","first_name":"Julie"},{"first_name":"Martin","last_name":"Knöfler","full_name":"Knöfler, Martin"},{"full_name":"Pollheimer, Jürgen","last_name":"Pollheimer","first_name":"Jürgen"}],"publisher":"Public Library of Science","department":[{"_id":"JoDa"}],"publication_status":"published","year":"2018","has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1","date_published":"2018-10-12T00:00:00Z","citation":{"chicago":"Velicky, Philipp, Gudrun Meinhardt, Kerstin Plessl, Sigrid Vondra, Tamara Weiss, Peter Haslinger, Thomas Lendl, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007698.","short":"P. Velicky, G. Meinhardt, K. Plessl, S. Vondra, T. Weiss, P. Haslinger, T. Lendl, K. Aumayr, M. Mairhofer, X. Zhu, B. Schütz, R.L. Hannibal, R. Lindau, B. Weil, J. Ernerudh, J. Neesen, G. Egger, M. Mikula, C. Röhrl, A.E. Urban, J. Baker, M. Knöfler, J. Pollheimer, PLOS Genetics 14 (2018).","mla":"Velicky, Philipp, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics, vol. 14, no. 10, e1007698, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007698.","ieee":"P. Velicky et al., “Genome amplification and cellular senescence are hallmarks of human placenta development,” PLOS Genetics, vol. 14, no. 10. Public Library of Science, 2018.","apa":"Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., … Pollheimer, J. (2018). Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007698","ista":"Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. 2018. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 14(10), e1007698.","ama":"Velicky P, Meinhardt G, Plessl K, et al. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 2018;14(10). doi:10.1371/journal.pgen.1007698"},"publication":"PLOS Genetics","issue":"10","abstract":[{"text":"Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2018_PLOS_Velicky.pdf","access_level":"open_access","creator":"kschuh","file_size":4592947,"content_type":"application/pdf","file_id":"6000","relation":"main_file","date_created":"2019-02-14T13:14:35Z","date_updated":"2020-07-14T12:47:15Z","checksum":"34aa9a5972f61889c19f18be8ee787a0"}],"oa_version":"Published Version","intvolume":" 14","ddc":["570"],"status":"public","title":"Genome amplification and cellular senescence are hallmarks of human placenta development","_id":"5998","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_identifier":{"issn":["1367-4803","1460-2059"]},"month":"11","doi":"10.1093/bioinformatics/bty340","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"pmid":["29722803"],"isi":["000450038900008"]},"project":[{"name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:47:15Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"last_name":"Usmanova","first_name":"Dinara R","full_name":"Usmanova, Dinara R"},{"first_name":"Natalya S","last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S"},{"last_name":"Ariño Bernad","first_name":"Joan","full_name":"Ariño Bernad, Joan"},{"full_name":"Eremina, Aleksandra A","last_name":"Eremina","first_name":"Aleksandra A"},{"first_name":"Anastasiya A","last_name":"Gorshkova","full_name":"Gorshkova, Anastasiya A"},{"full_name":"Kanevskiy, German M","first_name":"German M","last_name":"Kanevskiy"},{"first_name":"Lyubov R","last_name":"Lonishin","full_name":"Lonishin, Lyubov R"},{"full_name":"Meister, Alexander V","last_name":"Meister","first_name":"Alexander V"},{"last_name":"Yakupova","first_name":"Alisa G","full_name":"Yakupova, Alisa G"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","full_name":"Ivankov, Dmitry"}],"volume":34,"date_created":"2019-02-14T12:48:00Z","date_updated":"2023-09-19T14:31:13Z","pmid":1,"year":"2018","publisher":"Oxford University Press ","department":[{"_id":"FyKo"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-11-01T00:00:00Z","citation":{"mla":"Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.","short":"D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658.","chicago":"Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340.","ama":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340","ista":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.","ieee":"D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.","apa":"Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340"},"publication":"Bioinformatics","page":"3653-3658","issue":"21","abstract":[{"lang":"eng","text":"Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5997","date_created":"2019-02-14T13:00:55Z","date_updated":"2020-07-14T12:47:15Z","checksum":"7e0495153f44211479674601d7f6ee03","file_name":"2018_Oxford_Usmanova.pdf","access_level":"open_access","content_type":"application/pdf","file_size":291969,"creator":"kschuh"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5995","intvolume":" 34","ddc":["570"],"title":"Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation","status":"public"},{"file_date_updated":"2020-07-14T12:47:15Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","author":[{"full_name":"Dolati, Setareh","last_name":"Dolati","first_name":"Setareh"},{"last_name":"Kage","first_name":"Frieda","full_name":"Kage, Frieda"},{"full_name":"Mueller, Jan","last_name":"Mueller","first_name":"Jan"},{"last_name":"Müsken","first_name":"Mathias","full_name":"Müsken, Mathias"},{"last_name":"Kirchner","first_name":"Marieluise","full_name":"Kirchner, Marieluise"},{"full_name":"Dittmar, Gunnar","first_name":"Gunnar","last_name":"Dittmar"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"},{"first_name":"Martin","last_name":"Falcke","full_name":"Falcke, Martin"}],"volume":29,"date_created":"2019-02-14T12:25:47Z","date_updated":"2023-09-19T14:30:23Z","pmid":1,"year":"2018","department":[{"_id":"MiSi"}],"publisher":"American Society for Cell Biology ","publication_status":"published","publication_identifier":{"eissn":["1939-4586"]},"month":"11","doi":"10.1091/mbc.e18-02-0082","language":[{"iso":"eng"}],"external_id":{"isi":["000455641000011"],"pmid":["30156465"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"isi":1,"quality_controlled":"1","issue":"22","abstract":[{"text":"Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_ASCB_Dolati.pdf","file_size":6668971,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"5994","checksum":"e98465b4416b3e804c47f40086932af2","date_created":"2019-02-14T12:34:29Z","date_updated":"2020-07-14T12:47:15Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5992","intvolume":" 29","title":"On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility","status":"public","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-11-01T00:00:00Z","citation":{"short":"S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K. Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686.","mla":"Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell, vol. 29, no. 22, American Society for Cell Biology , 2018, pp. 2674–86, doi:10.1091/mbc.e18-02-0082.","chicago":"Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner, Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell. American Society for Cell Biology , 2018. https://doi.org/10.1091/mbc.e18-02-0082.","ama":"Dolati S, Kage F, Mueller J, et al. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 2018;29(22):2674-2686. doi:10.1091/mbc.e18-02-0082","apa":"Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., … Falcke, M. (2018). On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. American Society for Cell Biology . https://doi.org/10.1091/mbc.e18-02-0082","ieee":"S. Dolati et al., “On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility,” Molecular Biology of the Cell, vol. 29, no. 22. American Society for Cell Biology , pp. 2674–2686, 2018.","ista":"Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner K, Falcke M. 2018. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 29(22), 2674–2686."},"publication":"Molecular Biology of the Cell","page":"2674-2686"},{"publisher":"National Academy of Sciences","department":[{"_id":"MaJö"}],"publication_status":"published","pmid":1,"year":"2018","volume":115,"date_updated":"2023-09-19T14:35:36Z","date_created":"2019-02-14T14:33:34Z","author":[{"full_name":"Garrido-Charad, Florencia","last_name":"Garrido-Charad","first_name":"Florencia"},{"full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gutiérrez-Ibáñez, Cristián","first_name":"Cristián","last_name":"Gutiérrez-Ibáñez"},{"full_name":"Fernandez, Pedro","first_name":"Pedro","last_name":"Fernandez"},{"full_name":"López-Jury, Luciana","first_name":"Luciana","last_name":"López-Jury"},{"first_name":"Cristian","last_name":"González-Cabrera","full_name":"González-Cabrera, Cristian"},{"full_name":"Karten, Harvey J.","first_name":"Harvey J.","last_name":"Karten"},{"full_name":"Luksch, Harald","first_name":"Harald","last_name":"Luksch"},{"last_name":"Marín","first_name":"Gonzalo J.","full_name":"Marín, Gonzalo J."}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["30026198"],"isi":["000440982000020"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30026198"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1804517115","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"08","intvolume":" 115","status":"public","title":"“Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network","_id":"6010","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","type":"journal_article","issue":"32","abstract":[{"lang":"eng","text":"The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity."}],"page":"E7615-E7623","citation":{"short":"F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L. López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings of the National Academy of Sciences 115 (2018) E7615–E7623.","mla":"Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences, vol. 115, no. 32, National Academy of Sciences, 2018, pp. E7615–23, doi:10.1073/pnas.1804517115.","chicago":"Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez, Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten, Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1804517115.","ama":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 2018;115(32):E7615-E7623. doi:10.1073/pnas.1804517115","apa":"Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P., López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1804517115","ieee":"F. Garrido-Charad et al., ““Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network,” Proceedings of the National Academy of Sciences, vol. 115, no. 32. National Academy of Sciences, pp. E7615–E7623, 2018.","ista":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 115(32), E7615–E7623."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2018-08-07T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"07"},{"page":"325-342","publication":"Computer Graphics Forum","citation":{"ama":"Bickel B, Cignoni P, Malomo L, Pietroni N. State of the art on stylized fabrication. Computer Graphics Forum. 2018;37(6):325-342. doi:10.1111/cgf.13327","apa":"Bickel, B., Cignoni, P., Malomo, L., & Pietroni, N. (2018). State of the art on stylized fabrication. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13327","ieee":"B. Bickel, P. Cignoni, L. Malomo, and N. Pietroni, “State of the art on stylized fabrication,” Computer Graphics Forum, vol. 37, no. 6. Wiley, pp. 325–342, 2018.","ista":"Bickel B, Cignoni P, Malomo L, Pietroni N. 2018. State of the art on stylized fabrication. Computer Graphics Forum. 37(6), 325–342.","short":"B. Bickel, P. Cignoni, L. Malomo, N. Pietroni, Computer Graphics Forum 37 (2018) 325–342.","mla":"Bickel, Bernd, et al. “State of the Art on Stylized Fabrication.” Computer Graphics Forum, vol. 37, no. 6, Wiley, 2018, pp. 325–42, doi:10.1111/cgf.13327.","chicago":"Bickel, Bernd, Paolo Cignoni, Luigi Malomo, and Nico Pietroni. “State of the Art on Stylized Fabrication.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13327."},"date_published":"2018-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","title":"State of the art on stylized fabrication","status":"public","ddc":["004"],"intvolume":" 37","_id":"6003","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","file":[{"checksum":"d2bbe5c658d8159fbe9016a4f5e82b19","date_updated":"2020-07-14T12:47:15Z","date_created":"2019-02-14T14:09:28Z","relation":"main_file","file_id":"6004","content_type":"application/pdf","file_size":6209349,"creator":"kschuh","access_level":"open_access","file_name":"StylizedFabricationSTAR-Personal.pdf"}],"pubrep_id":"1051","type":"journal_article","abstract":[{"text":"Digital fabrication devices are powerful tools for creating tangible reproductions of 3D digital models. Most available printing technologies aim at producing an accurate copy of a tridimensional shape. However, fabrication technologies can also be used to create a stylistic representation of a digital shape. We refer to this class of methods as ‘stylized fabrication methods’. These methods abstract geometric and physical features of a given shape to create an unconventional representation, to produce an optical illusion or to devise a particular interaction with the fabricated model. In this state‐of‐the‐art report, we classify and overview this broad and emerging class of approaches and also propose possible directions for future research.","lang":"eng"}],"issue":"6","isi":1,"quality_controlled":"1","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"oa":1,"external_id":{"isi":["000437272800019"]},"language":[{"iso":"eng"}],"doi":"10.1111/cgf.13327","month":"09","publication_identifier":{"issn":["0167-7055"]},"publication_status":"published","publisher":"Wiley","department":[{"_id":"BeBi"}],"year":"2018","date_created":"2019-02-14T13:52:25Z","date_updated":"2023-09-19T14:33:40Z","volume":37,"author":[{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"}],"file_date_updated":"2020-07-14T12:47:15Z","ec_funded":1},{"date_published":"2018-09-01T00:00:00Z","citation":{"short":"M.M. Napiórkowski, R. Reuvers, J.P. Solovej, Archive for Rational Mechanics and Analysis 229 (2018) 1037–1090.","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis, vol. 229, no. 3, Springer Nature, 2018, pp. 1037–90, doi:10.1007/s00205-018-1232-6.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Philip Solovej. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00205-018-1232-6.","ama":"Napiórkowski MM, Reuvers R, Solovej JP. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 2018;229(3):1037-1090. doi:10.1007/s00205-018-1232-6","ieee":"M. M. Napiórkowski, R. Reuvers, and J. P. Solovej, “The Bogoliubov free energy functional I: Existence of minimizers and phase diagram,” Archive for Rational Mechanics and Analysis, vol. 229, no. 3. Springer Nature, pp. 1037–1090, 2018.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. P. (2018). The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-018-1232-6","ista":"Napiórkowski MM, Reuvers R, Solovej JP. 2018. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 229(3), 1037–1090."},"publication":"Archive for Rational Mechanics and Analysis","page":"1037-1090","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"6002","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 229","status":"public","title":"The Bogoliubov free energy functional I: Existence of minimizers and phase diagram","issue":"3","abstract":[{"lang":"eng","text":"The Bogoliubov free energy functional is analysed. The functional serves as a model of a translation-invariant Bose gas at positive temperature. We prove the existence of minimizers in the case of repulsive interactions given by a sufficiently regular two-body potential. Furthermore, we prove the existence of a phase transition in this model and provide its phase diagram."}],"type":"journal_article","doi":"10.1007/s00205-018-1232-6","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1511.05935","open_access":"1"}],"external_id":{"arxiv":["1511.05935"],"isi":["000435367300003"]},"oa":1,"project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"month":"09","author":[{"full_name":"Napiórkowski, Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M","last_name":"Napiórkowski"},{"full_name":"Reuvers, Robin","last_name":"Reuvers","first_name":"Robin"},{"full_name":"Solovej, Jan Philip","first_name":"Jan Philip","last_name":"Solovej"}],"volume":229,"date_updated":"2023-09-19T14:33:12Z","date_created":"2019-02-14T13:40:53Z","year":"2018","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"publication_status":"published"},{"publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"month":"03","doi":"10.1017/jfm.2017.923","language":[{"iso":"eng"}],"external_id":{"arxiv":["1709.06372"],"isi":["000437858300003"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.06372"}],"project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"}],"quality_controlled":"1","isi":1,"ec_funded":1,"author":[{"id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","last_name":"Vasudevan","first_name":"Mukund","full_name":"Vasudevan, Mukund"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"}],"volume":839,"date_updated":"2023-09-19T14:37:49Z","date_created":"2019-02-14T12:50:50Z","year":"2018","acknowledgement":" We also thank Philipp Maier and the IST Austria workshop for theirdedicated technical support","department":[{"_id":"BjHo"}],"publisher":"Cambridge University Press","publication_status":"published","article_processing_charge":"No","day":"25","scopus_import":"1","date_published":"2018-03-25T00:00:00Z","citation":{"short":"M. Vasudevan, B. Hof, Journal of Fluid Mechanics 839 (2018) 76–94.","mla":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics, vol. 839, Cambridge University Press, 2018, pp. 76–94, doi:10.1017/jfm.2017.923.","chicago":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2018. https://doi.org/10.1017/jfm.2017.923.","ama":"Vasudevan M, Hof B. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 2018;839:76-94. doi:10.1017/jfm.2017.923","apa":"Vasudevan, M., & Hof, B. (2018). The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.923","ieee":"M. Vasudevan and B. Hof, “The critical point of the transition to turbulence in pipe flow,” Journal of Fluid Mechanics, vol. 839. Cambridge University Press, pp. 76–94, 2018.","ista":"Vasudevan M, Hof B. 2018. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 839, 76–94."},"publication":"Journal of Fluid Mechanics","page":"76-94","article_type":"original","abstract":[{"lang":"eng","text":"In pipes, turbulence sets in despite the linear stability of the laminar Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears in a given experiment – the ‘natural transition point’ – depends on imperfections of the set-up, or, more precisely, on the magnitude of finite amplitude perturbations. At onset, turbulence typically only occupies a certain fraction of the flow, and this fraction equally is found to differ from experiment to experiment. Despite these findings, Reynolds proposed that after sufficiently long times, flows may settle to steady conditions: below a critical velocity, flows should (regardless of initial conditions) always return to laminar, while above this velocity, eddying motion should persist. As will be shown, even in pipes several thousand diameters long, the spatio-temporal intermittent flow patterns observed at the end of the pipe strongly depend on the initial conditions, and there is no indication that different flow patterns would eventually settle to a (statistical) steady state. Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless), we continuously recreate the puff sequence exiting the pipe at the pipe entrance, and in doing so introduce periodic boundary conditions for the puff pattern. This procedure allows us to study the evolution of the flow patterns for arbitrary long times, and we find that after times in excess of advective time units, indeed a statistical steady state is reached. Although the resulting flows remain spatio-temporally intermittent, puff splitting and decay rates eventually reach a balance, so that the turbulent fraction fluctuates around a well-defined level which only depends on . In accordance with Reynolds’ proposition, we find that at lower (here 2020), flows eventually always resume to laminar, while for higher ( ), turbulence persists. The critical point for pipe flow hence falls in the interval of $2020 , which is in very good agreement with the recently proposed value of . The latter estimate was based on single-puff statistics and entirely neglected puff interactions. Unlike in typical contact processes where such interactions strongly affect the percolation threshold, in pipe flow, the critical point is only marginally influenced. Interactions, on the other hand, are responsible for the approach to the statistical steady state. As shown, they strongly affect the resulting flow patterns, where they cause ‘puff clustering’, and these regions of large puff densities are observed to travel across the puff pattern in a wave-like fashion."}],"type":"journal_article","oa_version":"Preprint","_id":"5996","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 839","title":"The critical point of the transition to turbulence in pipe flow","status":"public"},{"article_number":"7","ec_funded":1,"department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery (ACM)","publication_status":"published","year":"2018","volume":40,"date_created":"2019-02-14T12:29:10Z","date_updated":"2023-09-19T14:38:42Z","related_material":{"record":[{"id":"1438","relation":"earlier_version","status":"public"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"full_name":"Novotný, Petr","first_name":"Petr","last_name":"Novotný","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hasheminezhad","first_name":"Rouzbeh","full_name":"Hasheminezhad, Rouzbeh"}],"publication_identifier":{"issn":["0164-0925"]},"month":"06","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000434634500003"],"arxiv":["1510.08517"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1510.08517","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1145/3174800","type":"journal_article","issue":"2","abstract":[{"text":"In this article, we consider the termination problem of probabilistic programs with real-valued variables. Thequestions concerned are: qualitative ones that ask (i) whether the program terminates with probability 1(almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); andquantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) tocompute a boundBsuch that the probability not to terminate afterBsteps decreases exponentially (con-centration problem). To solve these questions, we utilize the notion of ranking supermartingales, which isa powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmicsynthesis of linear ranking-supermartingales over affine probabilistic programs (Apps) with both angelic anddemonic non-determinism. An important subclass of Apps is LRApp which is defined as the class of all Appsover which a linear ranking-supermartingale exists.Our main contributions are as follows. Firstly, we show that the membership problem of LRApp (i) canbe decided in polynomial time for Apps with at most demonic non-determinism, and (ii) isNP-hard and inPSPACEfor Apps with angelic non-determinism. Moreover, theNP-hardness result holds already for Appswithout probability and demonic non-determinism. Secondly, we show that the concentration problem overLRApp can be solved in the same complexity as for the membership problem of LRApp. Finally, we show thatthe expectation problem over LRApp can be solved in2EXPTIMEand isPSPACE-hard even for Apps withoutprobability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate theeffectiveness of our approach to answer the qualitative and quantitative questions over Apps with at mostdemonic non-determinism.","lang":"eng"}],"intvolume":" 40","status":"public","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","_id":"5993","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3174800.","mla":"Chatterjee, Krishnendu, et al. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2, 7, Association for Computing Machinery (ACM), 2018, doi:10.1145/3174800.","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, ACM Transactions on Programming Languages and Systems 40 (2018).","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2018. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 40(2), 7.","ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2. Association for Computing Machinery (ACM), 2018.","apa":"Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2018). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3174800","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 2018;40(2). doi:10.1145/3174800"},"publication":"ACM Transactions on Programming Languages and Systems","date_published":"2018-06-01T00:00:00Z"}]