[{"publication":"Proceedings of the British Machine Vision Conference 2016","publication_status":"published","_id":"1102","project":[{"call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"conference":{"start_date":"2016-09-19","end_date":"2016-09-22","location":"York, United Kingdom","name":"BMVC: British Machine Vision Conference"},"abstract":[{"lang":"eng","text":"Weakly-supervised object localization methods tend to fail for object classes that consistently co-occur with the same background elements, e.g. trains on tracks. We propose a method to overcome these failures by adding a very small amount of model-specific additional annotation. The main idea is to cluster a deep network\\'s mid-level representations and assign object or distractor labels to each cluster. Experiments show substantially improved localization results on the challenging ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for semantic segmentation."}],"volume":"2016-September","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":1,"day":"01","date_published":"2016-09-01T00:00:00Z","publist_id":"6273","status":"public","acknowledgement":"This work was funded in parts by the European Research Council\r\nunder the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant\r\nagreement no 308036. We gratefully acknowledge the support of NVIDIA Corporation with\r\nthe donation of the GPUs used for this research.","citation":{"ama":"Kolesnikov A, Lampert C. Improving weakly-supervised object localization by micro-annotation. In: <i>Proceedings of the British Machine Vision Conference 2016</i>. Vol 2016-September. BMVA Press; 2016:92.1-92.12. doi:<a href=\"https://doi.org/10.5244/C.30.92\">10.5244/C.30.92</a>","ieee":"A. Kolesnikov and C. Lampert, “Improving weakly-supervised object localization by micro-annotation,” in <i>Proceedings of the British Machine Vision Conference 2016</i>, York, United Kingdom, 2016, vol. 2016–September, p. 92.1-92.12.","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” In <i>Proceedings of the British Machine Vision Conference 2016</i>, 2016–September:92.1-92.12. BMVA Press, 2016. <a href=\"https://doi.org/10.5244/C.30.92\">https://doi.org/10.5244/C.30.92</a>.","short":"A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2016, BMVA Press, 2016, p. 92.1-92.12.","mla":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” <i>Proceedings of the British Machine Vision Conference 2016</i>, vol. 2016–September, BMVA Press, 2016, p. 92.1-92.12, doi:<a href=\"https://doi.org/10.5244/C.30.92\">10.5244/C.30.92</a>.","apa":"Kolesnikov, A., &#38; Lampert, C. (2016). Improving weakly-supervised object localization by micro-annotation. In <i>Proceedings of the British Machine Vision Conference 2016</i> (Vol. 2016–September, p. 92.1-92.12). York, United Kingdom: BMVA Press. <a href=\"https://doi.org/10.5244/C.30.92\">https://doi.org/10.5244/C.30.92</a>","ista":"Kolesnikov A, Lampert C. 2016. Improving weakly-supervised object localization by micro-annotation. Proceedings of the British Machine Vision Conference 2016. BMVC: British Machine Vision Conference vol. 2016–September, 92.1-92.12."},"main_file_link":[{"url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf","open_access":"1"}],"ec_funded":1,"type":"conference","month":"09","year":"2016","date_updated":"2021-01-12T06:48:18Z","date_created":"2018-12-11T11:50:09Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"92.1-92.12","doi":"10.5244/C.30.92","oa_version":"Published Version","title":"Improving weakly-supervised object localization by micro-annotation","author":[{"first_name":"Alexander","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"oa":1,"publisher":"BMVA Press"},{"department":[{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"We propose two parallel state-space-exploration algorithms for hybrid automaton (HA), with the goal of enhancing performance on multi-core shared-memory systems. The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN model checker, when traversing the discrete modes of the HA, and enhances it with a parallel exploration of the continuous states within each mode. We show that this simple-minded extension of PBFS does not provide the desired load balancing in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS), which uses a cheap precomputation of the cost associated with the post operations (both continuous and discrete) in order to improve load balancing. We illustrate the TP-BFS and the cost precomputation of the post operators on a support-function-based algorithm for state-space exploration. The performance comparison of the two algorithms shows that, in general, TP-BFS provides a better utilization/load-balancing of the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect to SpaceEx LGG scenario. In order to make the comparison fair, we employed an equal number of post operations in both tools. To the best of our knowledge, this paper represents the first attempt to provide parallel, reachability-analysis algorithms for HA."}],"scopus_import":"1","external_id":{"arxiv":["1606.05473"]},"language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","publication_status":"published","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"conference":{"end_date":"2016-11-20","start_date":"2016-11-18","name":"MEMOCODE: Conference on Formal Methods and Models for System Design","location":"Kanpur, India "},"_id":"1103","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1606.05473","open_access":"1"}],"ec_funded":1,"status":"public","arxiv":1,"article_number":"7797741","day":"27","publist_id":"6272","date_published":"2016-12-27T00:00:00Z","citation":{"ama":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability analysis for hybrid systems. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>","ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India , 2016.","chicago":"Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>.","mla":"Gurung, Amit, et al. <i>Parallel Reachability Analysis for Hybrid Systems</i>. 7797741, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>.","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., &#38; Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>","ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: Conference on Formal Methods and Models for System Design, 7797741."},"acknowledgement":"This work was supported in part by DST-SERB, GoI under Project No. YSS/2014/000623 and by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","date_created":"2018-12-11T11:50:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-04T11:52:29Z","month":"12","year":"2016","publisher":"IEEE","oa":1,"doi":"10.1109/MEMCOD.2016.7797741","title":"Parallel reachability analysis for hybrid systems","author":[{"full_name":"Gurung, Amit","first_name":"Amit","last_name":"Gurung"},{"full_name":"Deka, Arup","first_name":"Arup","last_name":"Deka"},{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"first_name":"Sergiy","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365"},{"full_name":"Grosu, Radu","first_name":"Radu","last_name":"Grosu"},{"full_name":"Ray, Rajarshi","first_name":"Rajarshi","last_name":"Ray"}],"oa_version":"Preprint"},{"oa_version":"None","alternative_title":["Advances in Neural Information Processing Systems"],"author":[{"full_name":"Savin, Cristina","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","page":"3610-3618","oa":1,"publisher":"Neural Information Processing Systems Foundation","year":"2016","month":"12","corr_author":"1","date_updated":"2025-06-03T11:36:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:10Z","acknowledgement":"We  thank  Jozsef  Csicsvari  for  kindly  sharing  the  CA1  data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","citation":{"ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3610-3618.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 3610–3618.","mla":"Savin, Cristina, and Gašper Tkačik. <i>Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3610–18.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems Foundation, 2016.","apa":"Savin, C., &#38; Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems Foundation.","ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618."},"date_published":"2016-12-01T00:00:00Z","publist_id":"6265","day":"01","status":"public","ec_funded":1,"main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods","open_access":"1"}],"type":"conference","intvolume":"        29","_id":"1105","conference":{"start_date":"2016-12-05","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems","location":"Barcelona; Spain"},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","volume":29,"abstract":[{"lang":"eng","text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions."}],"department":[{"_id":"GaTk"}]},{"doi":"10.1083/jcb.201603053","page":"27-36","title":"Nuclear envelope rupture is induced by actin-based nucleus confinement","author":[{"last_name":"Hatch","full_name":"Hatch, Emily M.","first_name":"Emily M."},{"full_name":"HETZER, Martin W","first_name":"Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER"}],"oa_version":"Published Version","publisher":"Rockefeller University Press","oa":1,"month":"10","article_type":"original","publication_identifier":{"issn":["0021-9525","1540-8140"]},"year":"2016","keyword":["Cell Biology"],"date_created":"2022-04-07T07:47:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-14T11:20:38Z","status":"public","day":"03","date_published":"2016-10-03T00:00:00Z","citation":{"ama":"Hatch EM, Hetzer M. Nuclear envelope rupture is induced by actin-based nucleus confinement. <i>Journal of Cell Biology</i>. 2016;215(1):27-36. doi:<a href=\"https://doi.org/10.1083/jcb.201603053\">10.1083/jcb.201603053</a>","ieee":"E. M. Hatch and M. Hetzer, “Nuclear envelope rupture is induced by actin-based nucleus confinement,” <i>Journal of Cell Biology</i>, vol. 215, no. 1. Rockefeller University Press, pp. 27–36, 2016.","chicago":"Hatch, Emily M., and Martin Hetzer. “Nuclear Envelope Rupture Is Induced by Actin-Based Nucleus Confinement.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2016. <a href=\"https://doi.org/10.1083/jcb.201603053\">https://doi.org/10.1083/jcb.201603053</a>.","short":"E.M. Hatch, M. Hetzer, Journal of Cell Biology 215 (2016) 27–36.","mla":"Hatch, Emily M., and Martin Hetzer. “Nuclear Envelope Rupture Is Induced by Actin-Based Nucleus Confinement.” <i>Journal of Cell Biology</i>, vol. 215, no. 1, Rockefeller University Press, 2016, pp. 27–36, doi:<a href=\"https://doi.org/10.1083/jcb.201603053\">10.1083/jcb.201603053</a>.","apa":"Hatch, E. M., &#38; Hetzer, M. (2016). Nuclear envelope rupture is induced by actin-based nucleus confinement. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201603053\">https://doi.org/10.1083/jcb.201603053</a>","ista":"Hatch EM, Hetzer M. 2016. Nuclear envelope rupture is induced by actin-based nucleus confinement. Journal of Cell Biology. 215(1), 27–36."},"intvolume":"       215","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1083/jcb.201603053"}],"article_processing_charge":"No","issue":"1","publication_status":"published","publication":"Journal of Cell Biology","_id":"11069","pmid":1,"abstract":[{"text":"Repeated rounds of nuclear envelope (NE) rupture and repair have been observed in laminopathy and cancer cells and result in intermittent loss of nucleus compartmentalization. Currently, the causes of NE rupture are unclear. Here, we show that NE rupture in cancer cells relies on the assembly of contractile actin bundles that interact with the nucleus via the linker of nucleoskeleton and cytoskeleton (LINC) complex. We found that the loss of actin bundles or the LINC complex did not rescue nuclear lamina defects, a previously identified determinant of nuclear membrane stability, but did decrease the number and size of chromatin hernias. Finally, NE rupture inhibition could be rescued in cells treated with actin-depolymerizing drugs by mechanically constraining nucleus height. These data suggest a model of NE rupture where weak membrane areas, caused by defects in lamina organization, rupture because of an increase in intranuclear pressure from actin-based nucleus confinement.","lang":"eng"}],"volume":215,"extern":"1","scopus_import":"1","external_id":{"pmid":["27697922"]},"language":[{"iso":"eng"}],"quality_controlled":"1"},{"publisher":"Cold Spring Harbor Laboratory","oa":1,"title":"Nucleoporin-mediated regulation of cell identity genes","author":[{"last_name":"Ibarra","first_name":"Arkaitz","full_name":"Ibarra, Arkaitz"},{"last_name":"Benner","first_name":"Chris","full_name":"Benner, Chris"},{"last_name":"Tyagi","first_name":"Swati","full_name":"Tyagi, Swati"},{"last_name":"Cool","first_name":"Jonah","full_name":"Cool, Jonah"},{"first_name":"Martin W","full_name":"HETZER, Martin W","last_name":"HETZER","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"oa_version":"Published Version","doi":"10.1101/gad.287417.116","page":"2253-2258","date_created":"2022-04-07T07:48:08Z","keyword":["Developmental Biology","Genetics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-14T11:21:07Z","article_type":"original","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"year":"2016","month":"11","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1101/gad.287417.116","open_access":"1"}],"intvolume":"        30","citation":{"chicago":"Ibarra, Arkaitz, Chris Benner, Swati Tyagi, Jonah Cool, and Martin Hetzer. “Nucleoporin-Mediated Regulation of Cell Identity Genes.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory, 2016. <a href=\"https://doi.org/10.1101/gad.287417.116\">https://doi.org/10.1101/gad.287417.116</a>.","short":"A. Ibarra, C. Benner, S. Tyagi, J. Cool, M. Hetzer, Genes &#38; Development 30 (2016) 2253–2258.","mla":"Ibarra, Arkaitz, et al. “Nucleoporin-Mediated Regulation of Cell Identity Genes.” <i>Genes &#38; Development</i>, vol. 30, no. 20, Cold Spring Harbor Laboratory, 2016, pp. 2253–58, doi:<a href=\"https://doi.org/10.1101/gad.287417.116\">10.1101/gad.287417.116</a>.","ama":"Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. Nucleoporin-mediated regulation of cell identity genes. <i>Genes &#38; Development</i>. 2016;30(20):2253-2258. doi:<a href=\"https://doi.org/10.1101/gad.287417.116\">10.1101/gad.287417.116</a>","ieee":"A. Ibarra, C. Benner, S. Tyagi, J. Cool, and M. Hetzer, “Nucleoporin-mediated regulation of cell identity genes,” <i>Genes &#38; Development</i>, vol. 30, no. 20. Cold Spring Harbor Laboratory, pp. 2253–2258, 2016.","ista":"Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. 2016. Nucleoporin-mediated regulation of cell identity genes. Genes &#38; Development. 30(20), 2253–2258.","apa":"Ibarra, A., Benner, C., Tyagi, S., Cool, J., &#38; Hetzer, M. (2016). Nucleoporin-mediated regulation of cell identity genes. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/gad.287417.116\">https://doi.org/10.1101/gad.287417.116</a>"},"status":"public","day":"02","date_published":"2016-11-02T00:00:00Z","extern":"1","external_id":{"pmid":["27807035"]},"scopus_import":"1","language":[{"iso":"eng"}],"quality_controlled":"1","pmid":1,"abstract":[{"lang":"eng","text":"The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type-specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate."}],"volume":30,"_id":"11070","article_processing_charge":"No","issue":"20","publication":"Genes & Development","publication_status":"published"},{"oa":1,"publisher":"Cold Spring Harbor Laboratory","page":"1155-1171","doi":"10.1101/gad.280941.116","oa_version":"Published Version","author":[{"last_name":"Franks","first_name":"Tobias M.","full_name":"Franks, Tobias M."},{"last_name":"Benner","full_name":"Benner, Chris","first_name":"Chris"},{"first_name":"Iñigo","full_name":"Narvaiza, Iñigo","last_name":"Narvaiza"},{"last_name":"Marchetto","full_name":"Marchetto, Maria C.N.","first_name":"Maria C.N."},{"last_name":"Young","first_name":"Janet M.","full_name":"Young, Janet M."},{"last_name":"Malik","first_name":"Harmit S.","full_name":"Malik, Harmit S."},{"last_name":"Gage","full_name":"Gage, Fred H.","first_name":"Fred H."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER","full_name":"HETZER, Martin W","first_name":"Martin W"}],"title":"Evolution of a transcriptional regulator from a transmembrane nucleoporin","date_updated":"2024-10-14T11:21:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-04-07T07:48:20Z","keyword":["Developmental Biology","Genetics"],"month":"05","year":"2016","article_type":"original","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"intvolume":"        30","main_file_link":[{"url":"https://doi.org/10.1101/gad.280941.116","open_access":"1"}],"type":"journal_article","date_published":"2016-05-19T00:00:00Z","day":"19","status":"public","citation":{"chicago":"Franks, Tobias M., Chris Benner, Iñigo Narvaiza, Maria C.N. Marchetto, Janet M. Young, Harmit S. Malik, Fred H. Gage, and Martin Hetzer. “Evolution of a Transcriptional Regulator from a Transmembrane Nucleoporin.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory, 2016. <a href=\"https://doi.org/10.1101/gad.280941.116\">https://doi.org/10.1101/gad.280941.116</a>.","short":"T.M. Franks, C. Benner, I. Narvaiza, M.C.N. Marchetto, J.M. Young, H.S. Malik, F.H. Gage, M. Hetzer, Genes &#38; Development 30 (2016) 1155–1171.","mla":"Franks, Tobias M., et al. “Evolution of a Transcriptional Regulator from a Transmembrane Nucleoporin.” <i>Genes &#38; Development</i>, vol. 30, no. 10, Cold Spring Harbor Laboratory, 2016, pp. 1155–71, doi:<a href=\"https://doi.org/10.1101/gad.280941.116\">10.1101/gad.280941.116</a>.","ama":"Franks TM, Benner C, Narvaiza I, et al. Evolution of a transcriptional regulator from a transmembrane nucleoporin. <i>Genes &#38; Development</i>. 2016;30(10):1155-1171. doi:<a href=\"https://doi.org/10.1101/gad.280941.116\">10.1101/gad.280941.116</a>","ieee":"T. M. Franks <i>et al.</i>, “Evolution of a transcriptional regulator from a transmembrane nucleoporin,” <i>Genes &#38; Development</i>, vol. 30, no. 10. Cold Spring Harbor Laboratory, pp. 1155–1171, 2016.","ista":"Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH, Hetzer M. 2016. Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes &#38; Development. 30(10), 1155–1171.","apa":"Franks, T. M., Benner, C., Narvaiza, I., Marchetto, M. C. N., Young, J. M., Malik, H. S., … Hetzer, M. (2016). Evolution of a transcriptional regulator from a transmembrane nucleoporin. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/gad.280941.116\">https://doi.org/10.1101/gad.280941.116</a>"},"volume":30,"abstract":[{"text":"Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo–cytoplasmic transport, recent research suggests that certain NPC proteins have additionally acquired the role of affecting gene expression at the nuclear periphery and in the nucleoplasm in metazoans. Here we identify a widely expressed variant of the transmembrane nucleoporin (Nup) Pom121 (named sPom121, for “soluble Pom121”) that arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead, sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified transcriptional regulator, at gene promoters to control transcription of its target genes in human cells. Interestingly, sPom121 transcripts appear independently in several mammalian species, suggesting convergent innovation of Nup-mediated transcription regulation during mammalian evolution. Our findings implicate alternate transcription initiation as a mechanism to increase the functional diversity of NPC components.","lang":"eng"}],"pmid":1,"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["27198230"]},"scopus_import":"1","extern":"1","publication":"Genes & Development","publication_status":"published","issue":"10","article_processing_charge":"No","_id":"11071"},{"oa":1,"publisher":"Springer Nature","author":[{"first_name":"Robert A.H.","full_name":"van de Ven, Robert A.H.","last_name":"van de Ven"},{"first_name":"Jolien S.","full_name":"de Groot, Jolien S.","last_name":"de Groot"},{"first_name":"Danielle","full_name":"Park, Danielle","last_name":"Park"},{"last_name":"van Domselaar","full_name":"van Domselaar, Robert","first_name":"Robert"},{"last_name":"de Jong","full_name":"de Jong, Danielle","first_name":"Danielle"},{"last_name":"Szuhai","first_name":"Karoly","full_name":"Szuhai, Karoly"},{"full_name":"van der Wall, Elsken","first_name":"Elsken","last_name":"van der Wall"},{"full_name":"Rueda, Oscar M.","first_name":"Oscar M.","last_name":"Rueda"},{"first_name":"H. Raza","full_name":"Ali, H. Raza","last_name":"Ali"},{"first_name":"Carlos","full_name":"Caldas, Carlos","last_name":"Caldas"},{"last_name":"van Diest","first_name":"Paul J.","full_name":"van Diest, Paul J."},{"full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER"},{"full_name":"Sahai, Erik","first_name":"Erik","last_name":"Sahai"},{"full_name":"Derksen, Patrick W.B.","first_name":"Patrick W.B.","last_name":"Derksen"}],"title":"p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis","oa_version":"Published Version","doi":"10.1038/ncomms13874","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","date_created":"2022-04-07T07:48:34Z","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"date_updated":"2022-07-18T08:34:32Z","article_type":"original","publication_identifier":{"issn":["2041-1723"]},"year":"2016","month":"12","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms13874"}],"intvolume":"         7","citation":{"ista":"van de Ven RAH, de Groot JS, Park D, van Domselaar R, de Jong D, Szuhai K, van der Wall E, Rueda OM, Ali HR, Caldas C, van Diest PJ, Hetzer M, Sahai E, Derksen PWB. 2016. p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. Nature Communications. 7, 13874.","apa":"van de Ven, R. A. H., de Groot, J. S., Park, D., van Domselaar, R., de Jong, D., Szuhai, K., … Derksen, P. W. B. (2016). p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ncomms13874\">https://doi.org/10.1038/ncomms13874</a>","mla":"van de Ven, Robert A. H., et al. “P120-Catenin Prevents Multinucleation through Control of MKLP1-Dependent RhoA Activity during Cytokinesis.” <i>Nature Communications</i>, vol. 7, 13874, Springer Nature, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms13874\">10.1038/ncomms13874</a>.","short":"R.A.H. van de Ven, J.S. de Groot, D. Park, R. van Domselaar, D. de Jong, K. Szuhai, E. van der Wall, O.M. Rueda, H.R. Ali, C. Caldas, P.J. van Diest, M. Hetzer, E. Sahai, P.W.B. Derksen, Nature Communications 7 (2016).","chicago":"Ven, Robert A.H. van de, Jolien S. de Groot, Danielle Park, Robert van Domselaar, Danielle de Jong, Karoly Szuhai, Elsken van der Wall, et al. “P120-Catenin Prevents Multinucleation through Control of MKLP1-Dependent RhoA Activity during Cytokinesis.” <i>Nature Communications</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/ncomms13874\">https://doi.org/10.1038/ncomms13874</a>.","ieee":"R. A. H. van de Ven <i>et al.</i>, “p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis,” <i>Nature Communications</i>, vol. 7. Springer Nature, 2016.","ama":"van de Ven RAH, de Groot JS, Park D, et al. p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms13874\">10.1038/ncomms13874</a>"},"status":"public","date_published":"2016-12-22T00:00:00Z","day":"22","article_number":"13874","external_id":{"pmid":["28004812"]},"scopus_import":"1","extern":"1","quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"volume":7,"abstract":[{"text":"Spatiotemporal activation of RhoA and actomyosin contraction underpins cellular adhesion and division. Loss of cell–cell adhesion and chromosomal instability are cardinal events that drive tumour progression. Here, we show that p120-catenin (p120) not only controls cell–cell adhesion, but also acts as a critical regulator of cytokinesis. We find that p120 regulates actomyosin contractility through concomitant binding to RhoA and the centralspindlin component MKLP1, independent of cadherin association. In anaphase, p120 is enriched at the cleavage furrow where it binds MKLP1 to spatially control RhoA GTPase cycling. Binding of p120 to MKLP1 during cytokinesis depends on the N-terminal coiled-coil domain of p120 isoform 1A. Importantly, clinical data show that loss of p120 expression is a common event in breast cancer that strongly correlates with multinucleation and adverse patient survival. In summary, our study identifies p120 loss as a driver event of chromosomal instability in cancer.\r\n","lang":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/ncomms16030"}]},"_id":"11072","article_processing_charge":"No","publication_status":"published","publication":"Nature Communications"},{"citation":{"apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. Presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA: IEEE. <a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">https://doi.org/10.1364/CLEO_SI.2016.SF2G.3</a>","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. CLEO: Conference on Lasers and Electro Optics, 7788479.","ieee":"A. Rueda <i>et al.</i>, “Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator,” presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA, 2016.","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">10.1364/CLEO_SI.2016.SF2G.3</a>","mla":"Rueda, Alfredo, et al. <i>Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator</i>. 7788479, IEEE, 2016, doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">10.1364/CLEO_SI.2016.SF2G.3</a>.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, IEEE, 2016.","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Georg Schunk, Dimitry Strekalov, et al. “Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator.” IEEE, 2016. <a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">https://doi.org/10.1364/CLEO_SI.2016.SF2G.3</a>."},"status":"public","arxiv":1,"day":"16","article_number":"7788479","date_published":"2016-12-16T00:00:00Z","publist_id":"6251","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.07261"}],"conference":{"name":"CLEO: Conference on Lasers and Electro Optics","location":"San Jose, CA, USA","end_date":"2016-06-10","start_date":"2016-06-05"},"_id":"1115","related_material":{"link":[{"relation":"other","url":"http://ieeexplore.ieee.org/document/7788479/"}]},"article_processing_charge":"No","publication_status":"published","scopus_import":"1","external_id":{"arxiv":["1601.07261"]},"language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"JoFi"}],"abstract":[{"text":"We present a coherent microwave to telecom signal converter based on the electro-optical effect using a crystalline WGM-resonator coupled to a 3D microwave cavity, achieving high photon conversion efficiency of 0.1% with MHz bandwidth.","lang":"eng"}],"title":"Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator","author":[{"first_name":"Alfredo","full_name":"Rueda, Alfredo","last_name":"Rueda"},{"last_name":"Sedlmeir","first_name":"Florian","full_name":"Sedlmeir, Florian"},{"last_name":"Collodo","full_name":"Collodo, Michele","first_name":"Michele"},{"full_name":"Vogl, Ulrich","first_name":"Ulrich","last_name":"Vogl"},{"full_name":"Stiller, Birgit","first_name":"Birgit","last_name":"Stiller"},{"full_name":"Schunk, Georg","first_name":"Georg","last_name":"Schunk"},{"full_name":"Strekalov, Dimitry","first_name":"Dimitry","last_name":"Strekalov"},{"last_name":"Marquardt","first_name":"Christoph","full_name":"Marquardt, Christoph"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M"},{"first_name":"Oskar","full_name":"Painter, Oskar","last_name":"Painter"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"full_name":"Schwefel, Harald","first_name":"Harald","last_name":"Schwefel"}],"oa_version":"Preprint","doi":"10.1364/CLEO_SI.2016.SF2G.3","oa":1,"publisher":"IEEE","year":"2016","month":"12","date_created":"2018-12-11T11:50:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-22T13:41:54Z"},{"quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":1,"abstract":[{"text":"Hybrid systems have both continuous and discrete dynamics and are useful for modeling a variety of control systems, from air traffic control protocols to robotic maneuvers and beyond. Recently, numerous powerful and scalable tools for analyzing hybrid systems have emerged. Several of these tools implement automated formal methods for mathematically proving a system meets a specification. This tutorial session will present three recent hybrid systems tools: C2E2, HyST, and TuLiP. C2E2 is a simulated-based verification tool for hybrid systems, and uses validated numerical solvers and bloating of simulation traces to verify systems meet specifications. HyST is a hybrid systems model transformation and translation tool, and uses a canonical intermediate representation to support most of the recent verification tools, as well as automated sound abstractions that simplify verification of a given hybrid system. TuLiP is a controller synthesis tool for hybrid systems, where given a temporal logic specification to be satisfied for a system (plant) model, TuLiP will find a controller that meets a given specification. © 2016 IEEE.","lang":"eng"}],"date_updated":"2021-01-12T06:48:32Z","department":[{"_id":"ToHe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:20Z","year":"2016","_id":"1134","conference":{"location":"Buenos Aires, Argentina ","name":"CCA: Control Applications ","start_date":"2016-09-19","end_date":"2016-09-22"},"publication":"2016 IEEE Conference on Control Applications","publication_status":"published","month":"10","type":"conference","publisher":"IEEE","citation":{"ama":"Duggirala P, Fan C, Potok M, et al. Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. In: <i>2016 IEEE Conference on Control Applications</i>. IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/CCA.2016.7587948\">10.1109/CCA.2016.7587948</a>","ieee":"P. Duggirala <i>et al.</i>, “Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP,” in <i>2016 IEEE Conference on Control Applications</i>, Buenos Aires, Argentina , 2016.","chicago":"Duggirala, Parasara, Chuchu Fan, Matthew Potok, Bolun Qi, Sayan Mitra, Mahesh Viswanathan, Stanley Bak, et al. “Tutorial: Software Tools for Hybrid Systems Verification Transformation and Synthesis C2E2 HyST and TuLiP.” In <i>2016 IEEE Conference on Control Applications</i>. IEEE, 2016. <a href=\"https://doi.org/10.1109/CCA.2016.7587948\">https://doi.org/10.1109/CCA.2016.7587948</a>.","short":"P. Duggirala, C. Fan, M. Potok, B. Qi, S. Mitra, M. Viswanathan, S. Bak, S. Bogomolov, T. Johnson, L. Nguyen, C. Schilling, A. Sogokon, H. Tran, W. Xiang, in:, 2016 IEEE Conference on Control Applications, IEEE, 2016.","mla":"Duggirala, Parasara, et al. “Tutorial: Software Tools for Hybrid Systems Verification Transformation and Synthesis C2E2 HyST and TuLiP.” <i>2016 IEEE Conference on Control Applications</i>, 7587948, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/CCA.2016.7587948\">10.1109/CCA.2016.7587948</a>.","apa":"Duggirala, P., Fan, C., Potok, M., Qi, B., Mitra, S., Viswanathan, M., … Xiang, W. (2016). Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. In <i>2016 IEEE Conference on Control Applications</i>. Buenos Aires, Argentina : IEEE. <a href=\"https://doi.org/10.1109/CCA.2016.7587948\">https://doi.org/10.1109/CCA.2016.7587948</a>","ista":"Duggirala P, Fan C, Potok M, Qi B, Mitra S, Viswanathan M, Bak S, Bogomolov S, Johnson T, Nguyen L, Schilling C, Sogokon A, Tran H, Xiang W. 2016. Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. 2016 IEEE Conference on Control Applications. CCA: Control Applications , 7587948."},"oa_version":"None","author":[{"full_name":"Duggirala, Parasara","first_name":"Parasara","last_name":"Duggirala"},{"last_name":"Fan","full_name":"Fan, Chuchu","first_name":"Chuchu"},{"last_name":"Potok","full_name":"Potok, Matthew","first_name":"Matthew"},{"full_name":"Qi, Bolun","first_name":"Bolun","last_name":"Qi"},{"first_name":"Sayan","full_name":"Mitra, Sayan","last_name":"Mitra"},{"first_name":"Mahesh","full_name":"Viswanathan, Mahesh","last_name":"Viswanathan"},{"full_name":"Bak, Stanley","first_name":"Stanley","last_name":"Bak"},{"last_name":"Bogomolov","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"first_name":"Taylor","full_name":"Johnson, Taylor","last_name":"Johnson"},{"last_name":"Nguyen","full_name":"Nguyen, Luan","first_name":"Luan"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","last_name":"Schilling","full_name":"Schilling, Christian","first_name":"Christian"},{"first_name":"Andrew","full_name":"Sogokon, Andrew","last_name":"Sogokon"},{"last_name":"Tran","full_name":"Tran, Hoang","first_name":"Hoang"},{"last_name":"Xiang","full_name":"Xiang, Weiming","first_name":"Weiming"}],"title":"Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP","date_published":"2016-10-10T00:00:00Z","publist_id":"6224","article_number":"7587948","day":"10","doi":"10.1109/CCA.2016.7587948","status":"public"},{"pubrep_id":"644","oa":1,"publisher":"ACM","doi":"10.1145/2968478.2968499","author":[{"last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","full_name":"Avni, Guy"},{"full_name":"Guha, Shibashis","first_name":"Shibashis","last_name":"Guha"},{"full_name":"Rodríguez Navas, Guillermo","first_name":"Guillermo","last_name":"Rodríguez Navas"}],"title":"Synthesizing time triggered schedules for switched networks with faulty links","oa_version":"Submitted Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:20Z","date_updated":"2025-09-22T14:14:05Z","month":"10","file":[{"file_name":"IST-2016-644-v1+1_emsoft-no-format.pdf","date_updated":"2018-12-12T10:09:31Z","relation":"main_file","file_id":"4755","date_created":"2018-12-12T10:09:31Z","access_level":"open_access","file_size":279240,"content_type":"application/pdf","creator":"system"}],"has_accepted_license":"1","year":"2016","type":"conference","ec_funded":1,"status":"public","publist_id":"6223","date_published":"2016-10-01T00:00:00Z","article_number":"26","day":"01","citation":{"ieee":"G. Avni, S. Guha, and G. Rodríguez Navas, “Synthesizing time triggered schedules for switched networks with faulty links,” in <i>Proceedings of the 13th International Conference on Embedded Software </i>, Pittsburgh, PA, USA, 2016.","ama":"Avni G, Guha S, Rodríguez Navas G. Synthesizing time triggered schedules for switched networks with faulty links. In: <i>Proceedings of the 13th International Conference on Embedded Software </i>. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2968478.2968499\">10.1145/2968478.2968499</a>","mla":"Avni, Guy, et al. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” <i>Proceedings of the 13th International Conference on Embedded Software </i>, 26, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2968478.2968499\">10.1145/2968478.2968499</a>.","short":"G. Avni, S. Guha, G. Rodríguez Navas, in:, Proceedings of the 13th International Conference on Embedded Software , ACM, 2016.","chicago":"Avni, Guy, Shibashis Guha, and Guillermo Rodríguez Navas. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” In <i>Proceedings of the 13th International Conference on Embedded Software </i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2968478.2968499\">https://doi.org/10.1145/2968478.2968499</a>.","apa":"Avni, G., Guha, S., &#38; Rodríguez Navas, G. (2016). Synthesizing time triggered schedules for switched networks with faulty links. In <i>Proceedings of the 13th International Conference on Embedded Software </i>. Pittsburgh, PA, USA: ACM. <a href=\"https://doi.org/10.1145/2968478.2968499\">https://doi.org/10.1145/2968478.2968499</a>","ista":"Avni G, Guha S, Rodríguez Navas G. 2016. Synthesizing time triggered schedules for switched networks with faulty links. Proceedings of the 13th International Conference on Embedded Software . EMSOFT: Embedded Software , 26."},"department":[{"_id":"ToHe"}],"ddc":["000"],"file_date_updated":"2018-12-12T10:09:31Z","abstract":[{"lang":"eng","text":"Time-triggered (TT) switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. These networks rely on the notion of globally discretized time (i.e. time slots) and a static TT schedule that prescribes which message is sent through which link at every time slot, such that all messages reach their destination before a global timeout. These schedules are generated offline, assuming a static network with fault-free links, and entrusting all error-handling functions to the end user. Assuming the network is static is an over-optimistic view, and indeed links tend to fail in practice. We study synthesis of TT schedules on a network in which links fail over time and we assume the switches run a very simple error-recovery protocol once they detect a crashed link. We address the problem of finding a pk; qresistant schedule; namely, one that, assuming the switches run a fixed error-recovery protocol, guarantees that the number of messages that arrive at their destination by the timeout is at least no matter what sequence of at most k links fail. Thus, we maintain the simplicity of the switches while giving a guarantee on the number of messages that meet the timeout. We show how a pk; q-resistant schedule can be obtained using a CEGAR-like approach: find a schedule, decide whether it is pk; q-resistant, and if it is not, use the witnessing fault sequence to generate a constraint that is added to the program. The newly added constraint disallows the schedule to be regenerated in a future iteration while also eliminating several other schedules that are not pk; q-resistant. We illustrate the applicability of our approach using an SMT-based implementation. © 2016 ACM."}],"scopus_import":"1","external_id":{"isi":["000414220100026"]},"quality_controlled":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_status":"published","publication":"Proceedings of the 13th International Conference on Embedded Software ","conference":{"name":"EMSOFT: Embedded Software ","location":"Pittsburgh, PA, USA","start_date":"2016-10-01","end_date":"2016-10-07"},"isi":1,"project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"_id":"1135"},{"oa_version":"Submitted Version","author":[{"last_name":"Manteaux","first_name":"Pierre","full_name":"Manteaux, Pierre"},{"last_name":"Vimont","first_name":"Ulysse","full_name":"Vimont, Ulysse"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"},{"last_name":"Rohmer","first_name":"Damien","full_name":"Rohmer, Damien"},{"full_name":"Cani, Marie","first_name":"Marie","last_name":"Cani"}],"title":"Space-time sculpting of liquid animation","doi":"10.1145/2994258.2994261","oa":1,"publisher":"ACM","year":"2016","has_accepted_license":"1","month":"10","date_updated":"2024-10-22T09:58:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:20Z","citation":{"apa":"Manteaux, P., Vimont, U., Wojtan, C., Rohmer, D., &#38; Cani, M. (2016). Space-time sculpting of liquid animation. In <i>Proceedings of the 9th International Conference on Motion in Games </i>. San Francisco, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>","ista":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. 2016. Space-time sculpting of liquid animation. Proceedings of the 9th International Conference on Motion in Games . MIG: Motion in Games, 2994261.","ama":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. Space-time sculpting of liquid animation. In: <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>","ieee":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, and M. Cani, “Space-time sculpting of liquid animation,” in <i>Proceedings of the 9th International Conference on Motion in Games </i>, San Francisco, CA, USA, 2016.","chicago":"Manteaux, Pierre, Ulysse Vimont, Chris Wojtan, Damien Rohmer, and Marie Cani. “Space-Time Sculpting of Liquid Animation.” In <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>.","short":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of the 9th International Conference on Motion in Games , ACM, 2016.","mla":"Manteaux, Pierre, et al. “Space-Time Sculpting of Liquid Animation.” <i>Proceedings of the 9th International Conference on Motion in Games </i>, 2994261, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>."},"acknowledgement":"This work was partly supported by the starting grant BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2014-StG 638176 , and ERC-2011-ADG 20110209).","publist_id":"6222","date_published":"2016-10-10T00:00:00Z","day":"10","article_number":"2994261","status":"public","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01367181"}],"type":"conference","_id":"1136","conference":{"end_date":"2016-10-12","start_date":"2016-10-10","name":"MIG: Motion in Games","location":"San Francisco, CA, USA"},"project":[{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"publication":"Proceedings of the 9th International Conference on Motion in Games ","publication_status":"published","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"We propose an interactive sculpting system for seamlessly editing pre-computed animations of liquid, without the need for any resimulation. The input is a sequence of meshes without correspondences representing the liquid surface over time. Our method enables the efficient selection of consistent space-time parts of this animation, such as moving waves or droplets, which we call space-time features. Once selected, a feature can be copied, edited, or duplicated and then pasted back anywhere in space and time in the same or in another liquid animation sequence. Our method circumvents tedious user interactions by automatically computing the spatial and temporal ranges of the selected feature. We also provide space-time shape editing tools for non-uniform scaling, rotation, trajectory changes, and temporal editing to locally speed up or slow down motion. Using our tools, the user can edit and progressively refine any input simulation result, possibly using a library of precomputed space-time features extracted from other animations. In contrast to the trial-and-error loop usually required to edit animation results through the tuning of indirect simulation parameters, our method gives the user full control over the edited space-time behaviors. © 2016 Copyright held by the owner/author(s)."}],"ddc":["004"],"department":[{"_id":"ChWo"}]},{"oa":1,"publisher":"Nature Publishing Group","title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","author":[{"full_name":"Salzer, Elisabeth","first_name":"Elisabeth","last_name":"Salzer"},{"last_name":"Çaǧdaş","first_name":"Deniz","full_name":"Çaǧdaş, Deniz"},{"orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","full_name":"Hons, Miroslav","first_name":"Miroslav"},{"first_name":"Emily","full_name":"Mace, Emily","last_name":"Mace"},{"last_name":"Garncarz","full_name":"Garncarz, Wojciech","first_name":"Wojciech"},{"full_name":"Petronczki, Oezlem","first_name":"Oezlem","last_name":"Petronczki"},{"last_name":"Platzer","full_name":"Platzer, René","first_name":"René"},{"full_name":"Pfajfer, Laurène","first_name":"Laurène","last_name":"Pfajfer"},{"last_name":"Bilic","full_name":"Bilic, Ivan","first_name":"Ivan"},{"last_name":"Ban","first_name":"Sol","full_name":"Ban, Sol"},{"full_name":"Willmann, Katharina","first_name":"Katharina","last_name":"Willmann"},{"last_name":"Mukherjee","full_name":"Mukherjee, Malini","first_name":"Malini"},{"full_name":"Supper, Verena","first_name":"Verena","last_name":"Supper"},{"first_name":"Hsiangting","full_name":"Hsu, Hsiangting","last_name":"Hsu"},{"last_name":"Banerjee","full_name":"Banerjee, Pinaki","first_name":"Pinaki"},{"last_name":"Sinha","full_name":"Sinha, Papiya","first_name":"Papiya"},{"full_name":"Mcclanahan, Fabienne","first_name":"Fabienne","last_name":"Mcclanahan"},{"last_name":"Zlabinger","first_name":"Gerhard","full_name":"Zlabinger, Gerhard"},{"full_name":"Pickl, Winfried","first_name":"Winfried","last_name":"Pickl"},{"last_name":"Gribben","full_name":"Gribben, John","first_name":"John"},{"first_name":"Hannes","full_name":"Stockinger, Hannes","last_name":"Stockinger"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"last_name":"Huppa","full_name":"Huppa, Johannes","first_name":"Johannes"},{"last_name":"Dupré","full_name":"Dupré, Loï̈C","first_name":"Loï̈C"},{"first_name":"Özden","full_name":"Sanal, Özden","last_name":"Sanal"},{"full_name":"Jäger, Ulrich","first_name":"Ulrich","last_name":"Jäger"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"},{"first_name":"Ilhan","full_name":"Tezcan, Ilhan","last_name":"Tezcan"},{"first_name":"Jordan","full_name":"Orange, Jordan","last_name":"Orange"},{"last_name":"Boztug","full_name":"Boztug, Kaan","first_name":"Kaan"}],"oa_version":"Submitted Version","doi":"10.1038/ni.3575","page":"1352 - 1360","date_created":"2018-12-11T11:50:21Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:13:22Z","article_type":"original","year":"2016","month":"12","type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263","open_access":"1"}],"intvolume":"        17","citation":{"apa":"Salzer, E., Çaǧdaş, D., Hons, M., Mace, E., Garncarz, W., Petronczki, O., … Boztug, K. (2016). RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>","ista":"Salzer E, Çaǧdaş D, Hons M, Mace E, Garncarz W, Petronczki O, Platzer R, Pfajfer L, Bilic I, Ban S, Willmann K, Mukherjee M, Supper V, Hsu H, Banerjee P, Sinha P, Mcclanahan F, Zlabinger G, Pickl W, Gribben J, Stockinger H, Bennett K, Huppa J, Dupré L, Sanal Ö, Jäger U, Sixt MK, Tezcan I, Orange J, Boztug K. 2016. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. 17(12), 1352–1360.","ama":"Salzer E, Çaǧdaş D, Hons M, et al. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. 2016;17(12):1352-1360. doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>","ieee":"E. Salzer <i>et al.</i>, “RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1352–1360, 2016.","chicago":"Salzer, Elisabeth, Deniz Çaǧdaş, Miroslav Hons, Emily Mace, Wojciech Garncarz, Oezlem Petronczki, René Platzer, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>.","mla":"Salzer, Elisabeth, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1352–60, doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>.","short":"E. Salzer, D. Çaǧdaş, M. Hons, E. Mace, W. Garncarz, O. Petronczki, R. Platzer, L. Pfajfer, I. Bilic, S. Ban, K. Willmann, M. Mukherjee, V. Supper, H. Hsu, P. Banerjee, P. Sinha, F. Mcclanahan, G. Zlabinger, W. Pickl, J. Gribben, H. Stockinger, K. Bennett, J. Huppa, L. Dupré, Ö. Sanal, U. Jäger, M.K. Sixt, I. Tezcan, J. Orange, K. Boztug, Nature Immunology 17 (2016) 1352–1360."},"status":"public","day":"01","publist_id":"6221","date_published":"2016-12-01T00:00:00Z","external_id":{"isi":["000388056400005"],"pmid":["27776107"]},"scopus_import":"1","language":[{"iso":"eng"}],"quality_controlled":"1","pmid":1,"department":[{"_id":"MiSi"}],"abstract":[{"lang":"eng","text":"RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency also resulted in defective proliferation, activation and motility of T cells and B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity with defective granule convergence and actin accumulation. Interaction proteomics identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed the migration and activation defects of RASGRP1-deficient lymphocytes."}],"volume":17,"isi":1,"_id":"1137","article_processing_charge":"No","issue":"12","publication":"Nature Immunology","publication_status":"published"},{"doi":"10.1145/2933575.2933588","page":"76 - 85","title":"Quantitative automata under probabilistic semantics","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","publisher":"IEEE","oa":1,"month":"07","year":"2016","date_created":"2018-12-11T11:50:21Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:12:47Z","status":"public","arxiv":1,"day":"05","publist_id":"6220","date_published":"2016-07-05T00:00:00Z","citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 76–85.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Quantitative automata under probabilistic semantics. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i> (pp. 76–85). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Automata under Probabilistic Semantics.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, 76–85. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, IEEE, 2016, pp. 76–85, doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic semantics. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>. IEEE; 2016:76-85. doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under probabilistic semantics,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, New York, NY, USA, 2016, pp. 76–85."},"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S114","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1604.06764","open_access":"1"}],"ec_funded":1,"article_processing_charge":"No","publication_status":"published","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"conference":{"start_date":"2016-07-05","end_date":"2016-07-08","name":"LICS: Logic in Computer Science","location":"New York, NY, USA"},"isi":1,"_id":"1138","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider. © 2016 ACM."}],"external_id":{"isi":["000387609200008"],"arxiv":["1604.06764"]},"scopus_import":"1","language":[{"iso":"eng"}],"quality_controlled":"1"},{"extern":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:34Z","abstract":[{"lang":"eng","text":"Microtubules switch stochastically between phases of growth and shrinkage. The molecular mechanism responsible for the end of a growth phase, an event called catastrophe, is still not understood. The probability for a catastrophe to occur increases with microtubule age, putting constraints on the possible molecular mechanism of catastrophe induction. Here we used microfluidics-Assisted fast tubulin washout experiments to induce microtubule depolymerization in a controlled manner at different times after the start of growth. We found that aging can also be observed in this assay, providing valuable new constraints against which theoretical models of catastrophe induction can be tested. We found that the data can be quantitatively well explained by a simple kinetic threshold model that assumes an age-dependent broadening of the protective cap at the microtubule end as a result of an evolving tapered end structure; this leads to a decrease of the cap density and its stability. This analysis suggests an intuitive picture of the role of morphological changes of the protective cap for the age dependence of microtubule stability."}],"volume":27,"_id":"1139","year":"2016","article_processing_charge":"No","month":"11","issue":"22","publication":"Molecular Biology and Evolution","publication_status":"published","publisher":"Oxford University Press","type":"journal_article","intvolume":"        27","title":"Microtubule aging probed by microfluidics assisted tubulin washout","author":[{"id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748","last_name":"Düllberg","full_name":"Düllberg, Christian F","first_name":"Christian F"},{"full_name":"Cade, Nicholas","first_name":"Nicholas","last_name":"Cade"},{"full_name":"Surrey, Thomas","first_name":"Thomas","last_name":"Surrey"}],"oa_version":"None","citation":{"short":"C.F. Düllberg, N. Cade, T. Surrey, Molecular Biology and Evolution 27 (2016) 3563–3573.","mla":"Düllberg, Christian F., et al. “Microtubule Aging Probed by Microfluidics Assisted Tubulin Washout.” <i>Molecular Biology and Evolution</i>, vol. 27, no. 22, Oxford University Press, 2016, pp. 3563–73, doi:<a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">10.1091/mbc.E16-07-0548</a>.","chicago":"Düllberg, Christian F, Nicholas Cade, and Thomas Surrey. “Microtubule Aging Probed by Microfluidics Assisted Tubulin Washout.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">https://doi.org/10.1091/mbc.E16-07-0548</a>.","ieee":"C. F. Düllberg, N. Cade, and T. Surrey, “Microtubule aging probed by microfluidics assisted tubulin washout,” <i>Molecular Biology and Evolution</i>, vol. 27, no. 22. Oxford University Press, pp. 3563–3573, 2016.","ama":"Düllberg CF, Cade N, Surrey T. Microtubule aging probed by microfluidics assisted tubulin washout. <i>Molecular Biology and Evolution</i>. 2016;27(22):3563-3573. doi:<a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">10.1091/mbc.E16-07-0548</a>","ista":"Düllberg CF, Cade N, Surrey T. 2016. Microtubule aging probed by microfluidics assisted tubulin washout. Molecular Biology and Evolution. 27(22), 3563–3573.","apa":"Düllberg, C. F., Cade, N., &#38; Surrey, T. (2016). Microtubule aging probed by microfluidics assisted tubulin washout. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">https://doi.org/10.1091/mbc.E16-07-0548</a>"},"status":"public","doi":"10.1091/mbc.E16-07-0548","day":"07","publist_id":"6218","date_published":"2016-11-07T00:00:00Z","page":"3563 - 3573"},{"scopus_import":"1","external_id":{"arxiv":["1602.02670"],"isi":["000387609200020"]},"quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental -regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical -regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. © 2016 ACM."}],"isi":1,"conference":{"name":"LICS: Logic in Computer Science","location":"New York, NY, USA","end_date":"2016-07-08","start_date":"2016-07-05"},"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"_id":"1140","article_processing_charge":"No","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","publication_status":"published","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02670"}],"acknowledgement":"K.  C.,  M.  H.,  and  W.  D.  are  partially  supported  by  the  Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK. C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H., and V. L. the research\r\nleading to these results has received funding from the European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme (FP/2007-2013) / ERC Grant Agreement no. 340506.","citation":{"apa":"Chatterjee, K., Dvoák, W., Henzinger, M., &#38; Loitzenbauer, V. (2016). Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 197–206). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>","ista":"Chatterjee K, Dvoák W, Henzinger M, Loitzenbauer V. 2016. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, , 197–206.","ieee":"K. Chatterjee, W. Dvoák, M. Henzinger, and V. Loitzenbauer, “Model and objective separation with conditional lower bounds: disjunction is harder than conjunction,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, New York, NY, USA, 2016, pp. 197–206.","ama":"Chatterjee K, Dvoák W, Henzinger M, Loitzenbauer V. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>. IEEE; 2016:197-206. doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>","short":"K. Chatterjee, W. Dvoák, M. Henzinger, V. Loitzenbauer, in:, Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206.","mla":"Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, IEEE, 2016, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvoák, Monika Henzinger, and Veronika Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 197–206. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>."},"arxiv":1,"status":"public","publist_id":"6219","date_published":"2016-07-05T00:00:00Z","day":"05","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:22Z","date_updated":"2025-09-22T14:12:05Z","year":"2016","month":"07","publisher":"IEEE","oa":1,"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Dvoák","full_name":"Dvoák, Wolfgang","first_name":"Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"last_name":"Loitzenbauer","first_name":"Veronika","full_name":"Loitzenbauer, Veronika"}],"title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","oa_version":"Preprint","alternative_title":["Proceedings Symposium on Logic in Computer Science"],"doi":"10.1145/2933575.2935304","page":"197 - 206"},{"month":"11","year":"2016","date_updated":"2025-09-22T14:11:23Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:22Z","page":"249 - 260","doi":"10.1016/j.jocs.2016.03.004","oa_version":"None","author":[{"last_name":"Łazarz","first_name":"Radosław","full_name":"Łazarz, Radosław"},{"last_name":"Idzik","full_name":"Idzik, Michał","first_name":"Michał"},{"last_name":"Gądek","full_name":"Gądek, Konrad","first_name":"Konrad"},{"id":"47794CF0-F248-11E8-B48F-1D18A9856A87","last_name":"Gajda-Zagorska","full_name":"Gajda-Zagorska, Ewa P","first_name":"Ewa P"}],"title":"Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization","publisher":"Elsevier","publication":"Journal of Computational Science","publication_status":"published","issue":"1","article_processing_charge":"No","_id":"1141","isi":1,"volume":17,"abstract":[{"text":"In this paper we introduce the Multiobjective Optimization Hierarchic Genetic Strategy with maturing (MO-mHGS), a meta-algorithm that performs evolutionary optimization in a hierarchy of populations. The maturing mechanism improves growth and reduces redundancy. The performance of MO-mHGS with selected state-of-the-art multiobjective evolutionary algorithms as internal algorithms is analysed on benchmark problems and their modifications for which single fitness evaluation time depends on the solution accuracy. We compare the proposed algorithm with the Island Model Genetic Algorithm as well as with single-deme methods, and discuss the impact of internal algorithms on the MO-mHGS meta-algorithm. © 2016 Elsevier B.V.","lang":"eng"}],"department":[{"_id":"ChWo"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000390625600021"]},"scopus_import":"1","publist_id":"6217","date_published":"2016-11-01T00:00:00Z","day":"01","status":"public","acknowledgement":"The work presented in this paper was partially supported by Polish National Science Centre grant nos. DEC-2012/05/N/ST6/03433 and DEC-2011/03/B/ST6/01393. Radosław Łazarz was supported by Polish National Science Centre grant no. DEC-2013/10/M/ST6/00531.","citation":{"ista":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. 2016. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. 17(1), 249–260.","apa":"Łazarz, R., Idzik, M., Gądek, K., &#38; Gajda-Zagorska, E. P. (2016). Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>","short":"R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational Science 17 (2016) 249–260.","mla":"Łazarz, Radosław, et al. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>, vol. 17, no. 1, Elsevier, 2016, pp. 249–60, doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>.","chicago":"Łazarz, Radosław, Michał Idzik, Konrad Gądek, and Ewa P Gajda-Zagorska. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>.","ieee":"R. Łazarz, M. Idzik, K. Gądek, and E. P. Gajda-Zagorska, “Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization,” <i>Journal of Computational Science</i>, vol. 17, no. 1. Elsevier, pp. 249–260, 2016.","ama":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. 2016;17(1):249-260. doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>"},"intvolume":"        17","type":"journal_article"},{"date_updated":"2025-09-22T14:10:50Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:22Z","year":"2016","month":"12","oa":1,"publisher":"Nature Publishing Group","oa_version":"Submitted Version","author":[{"last_name":"Martins","first_name":"Rui","full_name":"Martins, Rui"},{"last_name":"Maier","full_name":"Maier, Julia","first_name":"Julia"},{"last_name":"Gorki","first_name":"Anna","full_name":"Gorki, Anna"},{"last_name":"Huber","full_name":"Huber, Kilian","first_name":"Kilian"},{"last_name":"Sharif","full_name":"Sharif, Omar","first_name":"Omar"},{"last_name":"Starkl","first_name":"Philipp","full_name":"Starkl, Philipp"},{"full_name":"Saluzzo, Simona","first_name":"Simona","last_name":"Saluzzo"},{"first_name":"Federica","full_name":"Quattrone, Federica","last_name":"Quattrone"},{"first_name":"Riem","full_name":"Gawish, Riem","last_name":"Gawish"},{"first_name":"Karin","full_name":"Lakovits, Karin","last_name":"Lakovits"},{"full_name":"Aichinger, Michael","first_name":"Michael","last_name":"Aichinger"},{"last_name":"Radic Sarikas","first_name":"Branka","full_name":"Radic Sarikas, Branka"},{"first_name":"Charles","full_name":"Lardeau, Charles","last_name":"Lardeau"},{"full_name":"Hladik, Anastasiya","first_name":"Anastasiya","last_name":"Hladik"},{"last_name":"Korosec","full_name":"Korosec, Ana","first_name":"Ana"},{"first_name":"Markus","full_name":"Brown, Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kari","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Duggan","id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle","full_name":"Duggan, Michelle"},{"last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho","first_name":"Dontscho"},{"first_name":"Harald","full_name":"Esterbauer, Harald","last_name":"Esterbauer"},{"last_name":"Colinge","first_name":"Jacques","full_name":"Colinge, Jacques"},{"last_name":"Eisenbarth","first_name":"Stephanie","full_name":"Eisenbarth, Stephanie"},{"full_name":"Decker, Thomas","first_name":"Thomas","last_name":"Decker"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"last_name":"Kubicek","full_name":"Kubicek, Stefan","first_name":"Stefan"},{"first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Giulio","full_name":"Superti Furga, Giulio","last_name":"Superti Furga"},{"first_name":"Sylvia","full_name":"Knapp, Sylvia","last_name":"Knapp"}],"title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","page":"1361 - 1372","doi":"10.1038/ni.3590","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","external_id":{"isi":["000388056400006"]},"volume":17,"abstract":[{"lang":"eng","text":"Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders."}],"department":[{"_id":"MiSi"},{"_id":"PeJo"}],"_id":"1142","isi":1,"publication":"Nature Immunology","publication_status":"published","issue":"12","article_processing_charge":"No","main_file_link":[{"url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d","open_access":"1"}],"type":"journal_article","intvolume":"        17","citation":{"ama":"Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. 2016;17(12):1361-1372. doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>","ieee":"R. Martins <i>et al.</i>, “Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.","chicago":"Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>.","mla":"Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1361–72, doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>.","short":"R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo, F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau, A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer, J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.","apa":"Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp, S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>","ista":"Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 17(12), 1361–1372."},"acknowledgement":"Y. Fukui (Medical Institute of Bioregulation, Kyushu University) and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children's Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct. pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding retrovirus was kindly provided by A. Leithner (Institute of Science and Technology Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research, National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent technical support (Core imaging facility, Medical University of Vienna). We thank D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was supported by the Austrian Academy of Sciences, the Science Fund of the Austrian National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA framework (to S.Knapp).","publist_id":"6216","date_published":"2016-12-01T00:00:00Z","day":"01","status":"public"},{"abstract":[{"lang":"eng","text":"We study the ground state of a dilute Bose gas in a scaling limit where the Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger functional whose quartic term is proportional to the scattering length of the interparticle interaction potential. We propose a new derivation of this limit problem, with a method that bypasses some of the technical difficulties that previous derivations had to face. The new method is based on a combination of Dyson\\'s lemma, the quantum de Finetti theorem and a second moment estimate for ground states of the effective Dyson Hamiltonian. It applies equally well to the case where magnetic fields or rotation are present."}],"volume":9,"department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"quality_controlled":"1","external_id":{"isi":["000378287000006"],"arxiv":["1503.07061"]},"scopus_import":"1","publication":"Analysis and PDE","publication_status":"published","article_processing_charge":"No","issue":"2","_id":"1143","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"isi":1,"intvolume":"         9","main_file_link":[{"url":"https://arxiv.org/abs/1503.07061","open_access":"1"}],"ec_funded":1,"type":"journal_article","day":"24","publist_id":"6215","date_published":"2016-03-24T00:00:00Z","status":"public","arxiv":1,"citation":{"ista":"Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485.","apa":"Nam, P., Rougerie, N., &#38; Seiringer, R. (2016). Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>","short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","mla":"Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>, vol. 9, no. 2, Mathematical Sciences Publishers, 2016, pp. 459–85, doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>.","chicago":"Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>. Mathematical Sciences Publishers, 2016. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>.","ieee":"P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems: The gross Pitaevskii limit revisited,” <i>Analysis and PDE</i>, vol. 9, no. 2. Mathematical Sciences Publishers, pp. 459–485, 2016.","ama":"Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. 2016;9(2):459-485. doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>"},"date_updated":"2025-09-22T14:10:16Z","date_created":"2018-12-11T11:50:23Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"03","year":"2016","publisher":"Mathematical Sciences Publishers","oa":1,"page":"459 - 485","doi":"10.2140/apde.2016.9.459","oa_version":"Preprint","title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","author":[{"first_name":"Phan","full_name":"Nam, Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rougerie","full_name":"Rougerie, Nicolas","first_name":"Nicolas"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert"}]},{"type":"journal_article","intvolume":"         6","acknowledgement":"We acknowledge support from Microsoft Research, the National Science Foundation through Grant No. DMR-1341822 (J. A.); the Alfred P. Sloan Foundation (J. A.); the Caltech Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation through Grant No. GBMF1250; the Walter Burke Institute for Theoretical Physics at Caltech; the NSERC PGSD program (D. A.); the Crafoord Foundation (M. L. and M. H.) and the Swedish Research Council (M. L.); The Danish National Research Foundation, and the Villum Foundation (C. M.); The Danish Council for Independent Research/Natural Sciences, and Danmarks Nationalbank (J. F.). Part of this work was performed at the Aspen Center for Physics, which is supported by National Science Foundation Grant No. PHY-1066293 (R. V. M.).","citation":{"short":"D. Aasen, M. Hell, R. Mishmash, A.P. Higginbotham, J. Danon, M. Leijnse, T. Jespersen, J. Folk, C. Marcs, K. Flensberg, J. Alicea, Physical Review X 6 (2016).","mla":"Aasen, David, et al. “Milestones toward Majorana-Based Quantum Computing.” <i>Physical Review X</i>, vol. 6, no. 3, 031016, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">10.1103/PhysRevX.6.031016</a>.","chicago":"Aasen, David, Michael Hell, Ryan Mishmash, Andrew P Higginbotham, Jeroen Danon, Martin Leijnse, Thomas Jespersen, et al. “Milestones toward Majorana-Based Quantum Computing.” <i>Physical Review X</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">https://doi.org/10.1103/PhysRevX.6.031016</a>.","ieee":"D. Aasen <i>et al.</i>, “Milestones toward Majorana-based quantum computing,” <i>Physical Review X</i>, vol. 6, no. 3. American Physical Society, 2016.","ama":"Aasen D, Hell M, Mishmash R, et al. Milestones toward Majorana-based quantum computing. <i>Physical Review X</i>. 2016;6(3). doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">10.1103/PhysRevX.6.031016</a>","ista":"Aasen D, Hell M, Mishmash R, Higginbotham AP, Danon J, Leijnse M, Jespersen T, Folk J, Marcs C, Flensberg K, Alicea J. 2016. Milestones toward Majorana-based quantum computing. Physical Review X. 6(3), 031016.","apa":"Aasen, D., Hell, M., Mishmash, R., Higginbotham, A. P., Danon, J., Leijnse, M., … Alicea, J. (2016). Milestones toward Majorana-based quantum computing. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">https://doi.org/10.1103/PhysRevX.6.031016</a>"},"status":"public","date_published":"2016-08-03T00:00:00Z","publist_id":"7954","day":"03","article_number":"031016","extern":"1","quality_controlled":"1","language":[{"iso":"eng"}],"ddc":["530"],"file_date_updated":"2019-05-15T14:12:31Z","volume":6,"abstract":[{"lang":"eng","text":"We introduce a scheme for preparation, manipulation, and read out of Majorana zero modes in semiconducting wires with mesoscopic superconducting islands. Our approach synthesizes recent advances in materials growth with tools commonly used in quantum-dot experiments, including gate control of tunnel barriers and Coulomb effects, charge sensing, and charge pumping. We outline a sequence of milestones interpolating between zero-mode detection and quantum computing that includes (1) detection of fusion rules for non-Abelian anyons using either proximal charge sensors or pumped current, (2) validation of a prototype topological qubit, and (3) demonstration of non-Abelian statistics by braiding in a branched geometry. The first two milestones require only a single wire with two islands, and additionally enable sensitive measurements of the system\\'s excitation gap, quasiparticle poisoning rates, residual Majorana zero-mode splittings, and topological-qubit coherence times. These pre-braiding experiments can be adapted to other manipulation and read out schemes as well."}],"_id":"100","issue":"3","publication":"Physical Review X","publication_status":"published","publisher":"American Physical Society","oa":1,"author":[{"first_name":"David","full_name":"Aasen, David","last_name":"Aasen"},{"full_name":"Hell, Michael","first_name":"Michael","last_name":"Hell"},{"last_name":"Mishmash","full_name":"Mishmash, Ryan","first_name":"Ryan"},{"orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","first_name":"Andrew P"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"},{"first_name":"Martin","full_name":"Leijnse, Martin","last_name":"Leijnse"},{"last_name":"Jespersen","full_name":"Jespersen, Thomas","first_name":"Thomas"},{"last_name":"Folk","first_name":"Joshua","full_name":"Folk, Joshua"},{"last_name":"Marcs","full_name":"Marcs, Charles","first_name":"Charles"},{"last_name":"Flensberg","first_name":"Karsten","full_name":"Flensberg, Karsten"},{"last_name":"Alicea","first_name":"Jason","full_name":"Alicea, Jason"}],"title":"Milestones toward Majorana-based quantum computing","oa_version":"Published Version","doi":"10.1103/PhysRevX.6.031016","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:37Z","date_updated":"2021-01-12T06:47:33Z","file":[{"file_name":"2016_PhysRevX_Aasen.pdf","date_created":"2019-05-15T14:12:31Z","relation":"main_file","file_id":"6458","date_updated":"2019-05-15T14:12:31Z","content_type":"application/pdf","file_size":2142676,"success":1,"access_level":"open_access","creator":"kschuh"}],"has_accepted_license":"1","year":"2016","month":"08"},{"publication_status":"published","publication":"ACS Synthetic Biology","issue":"10","article_processing_charge":"No","_id":"1008","isi":1,"volume":5,"abstract":[{"lang":"eng","text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways."}],"department":[{"_id":"CaGu"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000386196100008"]},"date_published":"2016-05-05T00:00:00Z","publist_id":"6390","day":"05","status":"public","citation":{"ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.","apa":"Gnügge, R., Dharmarajan, L., Lang, M., &#38; Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>.","chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>.","ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” <i>ACS Synthetic Biology</i>, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016.","ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. 2016;5(10):1098-1107. doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>"},"acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","intvolume":"         5","type":"journal_article","month":"05","year":"2016","date_updated":"2025-09-22T14:20:45Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:49:40Z","page":"1098 - 1107","doi":"10.1021/acssynbio.6b00013","oa_version":"None","author":[{"last_name":"Gnügge","full_name":"Gnügge, Robert","first_name":"Robert"},{"last_name":"Dharmarajan","first_name":"Lekshmi","full_name":"Dharmarajan, Lekshmi"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","full_name":"Lang, Moritz","first_name":"Moritz"},{"first_name":"Jörg","full_name":"Stelling, Jörg","last_name":"Stelling"}],"title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","publisher":"American Chemical Society"}]