[{"month":"12","department":[{"_id":"GaTk"}],"publisher":"Neural Information Processing Systems Foundation","oa":1,"corr_author":"1","day":"01","volume":29,"intvolume":"        29","quality_controlled":"1","year":"2016","publication_status":"published","main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods","open_access":"1"}],"article_processing_charge":"No","alternative_title":["Advances in Neural Information Processing Systems"],"date_published":"2016-12-01T00:00:00Z","conference":{"end_date":"2016-12-10","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems","location":"Barcelona; Spain"},"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.","ec_funded":1,"scopus_import":"1","publist_id":"6265","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"type":"conference","oa_version":"None","status":"public","date_created":"2018-12-11T11:50:10Z","author":[{"full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"}],"_id":"1105","title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-03T11:36:49Z","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"citation":{"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.","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.","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.","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.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 3610–3618.","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."},"page":"3610-3618"},{"fulldoi":"https://doi.org/10.1083/jcb.201603053","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1083/jcb.201603053"}],"date_published":"2016-10-03T00:00:00Z","keyword":["Cell Biology"],"article_processing_charge":"No","year":"2016","pmid":1,"quality_controlled":"1","publication_status":"published","intvolume":"       215","volume":215,"doi":"10.1083/jcb.201603053","external_id":{"pmid":["27697922"]},"month":"10","publisher":"Rockefeller University Press","day":"03","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-14T11:20:38Z","page":"27-36","citation":{"ista":"Hatch EM, Hetzer M. 2016. Nuclear envelope rupture is induced by actin-based nucleus confinement. Journal of Cell Biology. 215(1), 27–36.","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.","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>.","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>","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>","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>."},"article_type":"original","type":"journal_article","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"extern":"1","_id":"11069","title":"Nuclear envelope rupture is induced by actin-based nucleus confinement","status":"public","author":[{"full_name":"Hatch, Emily M.","last_name":"Hatch","first_name":"Emily M."},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W"}],"date_created":"2022-04-07T07:47:42Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9525","1540-8140"]},"publication":"Journal of Cell Biology","issue":"1","scopus_import":"1"},{"oa":1,"day":"02","publisher":"Cold Spring Harbor Laboratory","month":"11","external_id":{"pmid":["27807035"]},"doi":"10.1101/gad.287417.116","volume":30,"intvolume":"        30","publication_status":"published","quality_controlled":"1","year":"2016","pmid":1,"article_processing_charge":"No","keyword":["Developmental Biology","Genetics"],"date_published":"2016-11-02T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.287417.116"}],"fulldoi":"https://doi.org/10.1101/gad.287417.116","scopus_import":"1","issue":"20","publication":"Genes & Development","publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"language":[{"iso":"eng"}],"date_created":"2022-04-07T07:48:08Z","author":[{"last_name":"Ibarra","first_name":"Arkaitz","full_name":"Ibarra, Arkaitz"},{"full_name":"Benner, Chris","last_name":"Benner","first_name":"Chris"},{"first_name":"Swati","last_name":"Tyagi","full_name":"Tyagi, Swati"},{"full_name":"Cool, Jonah","last_name":"Cool","first_name":"Jonah"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"status":"public","title":"Nucleoporin-mediated regulation of cell identity genes","_id":"11070","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."}],"extern":"1","oa_version":"Published Version","type":"journal_article","article_type":"original","page":"2253-2258","citation":{"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>","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>.","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.","short":"A. Ibarra, C. Benner, S. Tyagi, J. Cool, M. Hetzer, Genes &#38; Development 30 (2016) 2253–2258.","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.","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>"},"date_updated":"2024-10-14T11:21:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"issue":"10","scopus_import":"1","publication":"Genes & Development","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-14T11:21:48Z","citation":{"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>","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>.","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.","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.","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.","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>.","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>"},"page":"1155-1171","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"}],"extern":"1","article_type":"original","oa_version":"Published Version","type":"journal_article","author":[{"full_name":"Franks, Tobias M.","first_name":"Tobias M.","last_name":"Franks"},{"full_name":"Benner, Chris","last_name":"Benner","first_name":"Chris"},{"first_name":"Iñigo","last_name":"Narvaiza","full_name":"Narvaiza, Iñigo"},{"full_name":"Marchetto, Maria C.N.","last_name":"Marchetto","first_name":"Maria C.N."},{"first_name":"Janet M.","last_name":"Young","full_name":"Young, Janet M."},{"full_name":"Malik, Harmit S.","last_name":"Malik","first_name":"Harmit S."},{"last_name":"Gage","first_name":"Fred H.","full_name":"Gage, Fred H."},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER"}],"date_created":"2022-04-07T07:48:20Z","status":"public","_id":"11071","title":"Evolution of a transcriptional regulator from a transmembrane nucleoporin","doi":"10.1101/gad.280941.116","volume":30,"month":"05","publisher":"Cold Spring Harbor Laboratory","external_id":{"pmid":["27198230"]},"oa":1,"day":"19","main_file_link":[{"url":"https://doi.org/10.1101/gad.280941.116","open_access":"1"}],"fulldoi":"https://doi.org/10.1101/gad.280941.116","keyword":["Developmental Biology","Genetics"],"article_processing_charge":"No","date_published":"2016-05-19T00:00:00Z","intvolume":"        30","quality_controlled":"1","pmid":1,"year":"2016","publication_status":"published"},{"language":[{"iso":"eng"}],"publication":"Nature Communications","scopus_import":"1","publication_identifier":{"issn":["2041-1723"]},"related_material":{"link":[{"url":"https://doi.org/10.1038/ncomms16030","relation":"erratum"}]},"citation":{"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>.","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>","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>","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>.","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.","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.","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)."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","date_updated":"2022-07-18T08:34:32Z","_id":"11072","title":"p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis","date_created":"2022-04-07T07:48:34Z","status":"public","author":[{"first_name":"Robert A.H.","last_name":"van de Ven","full_name":"van de Ven, Robert A.H."},{"first_name":"Jolien S.","last_name":"de Groot","full_name":"de Groot, Jolien S."},{"full_name":"Park, Danielle","last_name":"Park","first_name":"Danielle"},{"first_name":"Robert","last_name":"van Domselaar","full_name":"van Domselaar, Robert"},{"full_name":"de Jong, Danielle","last_name":"de Jong","first_name":"Danielle"},{"first_name":"Karoly","last_name":"Szuhai","full_name":"Szuhai, Karoly"},{"last_name":"van der Wall","first_name":"Elsken","full_name":"van der Wall, Elsken"},{"first_name":"Oscar M.","last_name":"Rueda","full_name":"Rueda, Oscar M."},{"last_name":"Ali","first_name":"H. Raza","full_name":"Ali, H. Raza"},{"full_name":"Caldas, Carlos","last_name":"Caldas","first_name":"Carlos"},{"last_name":"van Diest","first_name":"Paul J.","full_name":"van Diest, Paul J."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"first_name":"Erik","last_name":"Sahai","full_name":"Sahai, Erik"},{"first_name":"Patrick W.B.","last_name":"Derksen","full_name":"Derksen, Patrick W.B."}],"article_type":"original","oa_version":"Published Version","type":"journal_article","extern":"1","abstract":[{"lang":"eng","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"}],"article_number":"13874","volume":7,"doi":"10.1038/ncomms13874","day":"22","oa":1,"external_id":{"pmid":["28004812"]},"month":"12","publisher":"Springer Nature","date_published":"2016-12-22T00:00:00Z","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"article_processing_charge":"No","fulldoi":"https://doi.org/10.1038/ncomms13874","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms13874"}],"year":"2016","pmid":1,"quality_controlled":"1","publication_status":"published","intvolume":"         7"},{"article_processing_charge":"No","conference":{"end_date":"2016-06-10","start_date":"2016-06-05","name":"CLEO: Conference on Lasers and Electro Optics","location":"San Jose, CA, USA"},"date_published":"2016-12-16T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1601.07261","open_access":"1"}],"arxiv":1,"fulldoi":"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3","publication_status":"published","year":"2016","quality_controlled":"1","article_number":"7788479","doi":"10.1364/CLEO_SI.2016.SF2G.3","oa":1,"day":"16","publisher":"IEEE","month":"12","department":[{"_id":"JoFi"}],"external_id":{"arxiv":["1601.07261"]},"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>","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>.","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.","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.","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.","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>."},"related_material":{"link":[{"relation":"other","url":"http://ieeexplore.ieee.org/document/7788479/"}]},"date_updated":"2025-04-22T13:41:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"last_name":"Rueda","first_name":"Alfredo","full_name":"Rueda, Alfredo"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"last_name":"Collodo","first_name":"Michele","full_name":"Collodo, Michele"},{"last_name":"Vogl","first_name":"Ulrich","full_name":"Vogl, Ulrich"},{"last_name":"Stiller","first_name":"Birgit","full_name":"Stiller, Birgit"},{"full_name":"Schunk, Georg","first_name":"Georg","last_name":"Schunk"},{"last_name":"Strekalov","first_name":"Dimitry","full_name":"Strekalov, Dimitry"},{"full_name":"Marquardt, Christoph","first_name":"Christoph","last_name":"Marquardt"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"},{"full_name":"Leuchs, Gerd","first_name":"Gerd","last_name":"Leuchs"},{"last_name":"Schwefel","first_name":"Harald","full_name":"Schwefel, Harald"}],"date_created":"2018-12-11T11:50:14Z","title":"Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator","_id":"1115","abstract":[{"lang":"eng","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."}],"type":"conference","oa_version":"Preprint","language":[{"iso":"eng"}],"publist_id":"6251","scopus_import":"1"},{"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2021-11-17T13:46:55Z","date_published":"2016-07-07T00:00:00Z","alternative_title":["ISTA Thesis"],"main_file_link":[{"open_access":"1","url":"http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf"}],"degree_awarded":"PhD","fulldoi":"https://doi.org/10.15479/at:ista:1130","ddc":["000"],"publication_status":"published","year":"2016","doi":"10.15479/at:ista:1130","file":[{"file_size":1523935,"date_updated":"2021-02-22T11:39:32Z","content_type":"application/pdf","file_name":"2016_Tarrach_Thesis.pdf","file_id":"9179","relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2021-02-22T11:39:32Z","checksum":"319a506831650327e85376db41fc1094","success":1},{"file_name":"2016_Tarrach_Thesispdfa.pdf","date_updated":"2021-11-17T13:46:55Z","content_type":"application/pdf","file_size":1306068,"file_id":"10296","access_level":"closed","creator":"cchlebak","relation":"main_file","date_created":"2021-11-16T14:14:38Z","checksum":"39efcd789f0ad859ff15652cb7afc412"}],"oa":1,"corr_author":"1","day":"07","publisher":"Institute of Science and Technology Austria","month":"07","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"citation":{"ieee":"T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent programs,” Institute of Science and Technology Austria, 2016.","short":"T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent Programs, Institute of Science and Technology Austria, 2016.","ista":"Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent programs. Institute of Science and Technology Austria.","ama":"Tarrach T. Automatic synthesis of synchronisation primitives for concurrent programs. 2016. doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>","mla":"Tarrach, Thorsten. <i>Automatic Synthesis of Synchronisation Primitives for Concurrent Programs</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>.","apa":"Tarrach, T. (2016). <i>Automatic synthesis of synchronisation primitives for concurrent programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>","chicago":"Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for Concurrent Programs.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>."},"page":"151","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"2218","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"2445"},{"status":"public","relation":"part_of_dissertation","id":"1729"}]},"date_updated":"2026-04-09T10:54:01Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2018-12-11T11:50:19Z","author":[{"orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten","last_name":"Tarrach","first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87"}],"status":"public","title":"Automatic synthesis of synchronisation primitives for concurrent programs","_id":"1130","abstract":[{"text":"In this thesis we present a computer-aided programming approach to concurrency. Our approach helps the programmer by automatically fixing concurrency-related bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are program behaviours that are incorrect w.r.t. a specification. We consider both user-provided explicit specifications in the form of assertion\r\nstatements in the code as well as an implicit specification. The implicit specification is inferred from the non-preemptive behaviour. Let us consider sequences of calls that the program makes to an external interface. The implicit specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We consider several semantics-preserving fixes that go beyond atomic sections typically explored in the synchronisation synthesis literature. Our synthesis is able to place locks, barriers and wait-signal statements and last, but not least reorder independent statements. The latter may be useful if a thread is released to early, e.g., before some initialisation is completed. We guarantee that our synthesis does not introduce deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective function. We dub our solution trace-based synchronisation synthesis and it is loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis works by discovering a trace that is incorrect w.r.t. the specification and identifying ordering constraints crucial to trigger the specification violation. Synchronisation may be placed immediately (greedy approach) or delayed until all incorrect traces are found (non-greedy approach). For the non-greedy approach we construct a set of global constraints over synchronisation placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronisation placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronisation solution. We evaluate our approach on a number of realistic (albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions of the drivers with known concurrency-related bugs. For the experiments with an explicit specification we added assertions that would detect the bugs in the experiments. Device drivers lend themselves to implicit specification, where the device and the operating system are the external interfaces. Our experiments demonstrate that our synthesis method is precise and efficient. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronisation placements are produced for our experiments, favouring e.g. a minimal number of synchronisation operations or maximum concurrency.","lang":"eng"}],"supervisor":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"type":"dissertation","oa_version":"Published Version","OA_place":"publisher","language":[{"iso":"eng"}],"publist_id":"6230","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]}},{"citation":{"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>.","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>","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.","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.","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.","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>.","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>"},"conference":{"name":"CCA: Control Applications ","end_date":"2016-09-22","start_date":"2016-09-19","location":"Buenos Aires, Argentina "},"date_published":"2016-10-10T00:00:00Z","date_updated":"2021-01-12T06:48:32Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1109/CCA.2016.7587948","author":[{"full_name":"Duggirala, Parasara","first_name":"Parasara","last_name":"Duggirala"},{"last_name":"Fan","first_name":"Chuchu","full_name":"Fan, Chuchu"},{"last_name":"Potok","first_name":"Matthew","full_name":"Potok, Matthew"},{"full_name":"Qi, Bolun","last_name":"Qi","first_name":"Bolun"},{"full_name":"Mitra, Sayan","last_name":"Mitra","first_name":"Sayan"},{"full_name":"Viswanathan, Mahesh","last_name":"Viswanathan","first_name":"Mahesh"},{"full_name":"Bak, Stanley","last_name":"Bak","first_name":"Stanley"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365"},{"last_name":"Johnson","first_name":"Taylor","full_name":"Johnson, Taylor"},{"full_name":"Nguyen, Luan","first_name":"Luan","last_name":"Nguyen"},{"last_name":"Schilling","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"},{"full_name":"Sogokon, Andrew","first_name":"Andrew","last_name":"Sogokon"},{"full_name":"Tran, Hoang","first_name":"Hoang","last_name":"Tran"},{"last_name":"Xiang","first_name":"Weiming","full_name":"Xiang, Weiming"}],"date_created":"2018-12-11T11:50:20Z","status":"public","title":"Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP","_id":"1134","abstract":[{"lang":"eng","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."}],"type":"conference","publication_status":"published","oa_version":"None","quality_controlled":"1","year":"2016","article_number":"7587948","doi":"10.1109/CCA.2016.7587948","language":[{"iso":"eng"}],"publist_id":"6224","scopus_import":1,"publication":"2016 IEEE Conference on Control Applications","day":"10","publisher":"IEEE","department":[{"_id":"ToHe"}],"month":"10"},{"publication_status":"published","year":"2016","quality_controlled":"1","ddc":["000"],"fulldoi":"https://doi.org/10.1145/2968478.2968499","has_accepted_license":"1","conference":{"end_date":"2016-10-07","start_date":"2016-10-01","name":"EMSOFT: Embedded Software ","location":"Pittsburgh, PA, USA"},"date_published":"2016-10-01T00:00:00Z","file_date_updated":"2018-12-12T10:09:31Z","article_processing_charge":"No","external_id":{"isi":["000414220100026"]},"publisher":"ACM","month":"10","department":[{"_id":"ToHe"}],"day":"01","oa":1,"pubrep_id":"644","doi":"10.1145/2968478.2968499","file":[{"date_created":"2018-12-12T10:09:31Z","access_level":"open_access","creator":"system","relation":"main_file","file_id":"4755","date_updated":"2018-12-12T10:09:31Z","content_type":"application/pdf","file_name":"IST-2016-644-v1+1_emsoft-no-format.pdf","file_size":279240}],"isi":1,"article_number":"26","oa_version":"Submitted Version","type":"conference","abstract":[{"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.","lang":"eng"}],"title":"Synthesizing time triggered schedules for switched networks with faulty links","_id":"1135","date_created":"2018-12-11T11:50:20Z","status":"public","author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","last_name":"Avni"},{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"first_name":"Guillermo","last_name":"Rodríguez Navas","full_name":"Rodríguez Navas, Guillermo"}],"date_updated":"2025-09-22T14:14:05Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>.","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>","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.","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.","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>"},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"ec_funded":1,"publication":"Proceedings of the 13th International Conference on Embedded Software ","scopus_import":"1","publist_id":"6223","language":[{"iso":"eng"}]},{"article_number":"2994261","doi":"10.1145/2994258.2994261","oa":1,"day":"10","department":[{"_id":"ChWo"}],"month":"10","publisher":"ACM","article_processing_charge":"No","date_published":"2016-10-10T00:00:00Z","has_accepted_license":"1","conference":{"name":"MIG: Motion in Games","end_date":"2016-10-12","start_date":"2016-10-10","location":"San Francisco, CA, USA"},"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01367181"}],"fulldoi":"https://doi.org/10.1145/2994258.2994261","ddc":["004"],"year":"2016","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"publist_id":"6222","scopus_import":"1","publication":"Proceedings of the 9th International Conference on Motion in Games ","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).","ec_funded":1,"project":[{"grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"citation":{"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>.","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>","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>","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>.","short":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of the 9th International Conference on Motion in Games , ACM, 2016.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-22T09:58:18Z","date_created":"2018-12-11T11:50:20Z","status":"public","author":[{"full_name":"Manteaux, Pierre","first_name":"Pierre","last_name":"Manteaux"},{"full_name":"Vimont, Ulysse","last_name":"Vimont","first_name":"Ulysse"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"last_name":"Rohmer","first_name":"Damien","full_name":"Rohmer, Damien"},{"full_name":"Cani, Marie","last_name":"Cani","first_name":"Marie"}],"_id":"1136","title":"Space-time sculpting of liquid animation","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)."}],"type":"conference","oa_version":"Submitted Version"},{"publication":"Nature Immunology","scopus_import":"1","issue":"12","language":[{"iso":"eng"}],"publist_id":"6221","title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","_id":"1137","author":[{"last_name":"Salzer","first_name":"Elisabeth","full_name":"Salzer, Elisabeth"},{"full_name":"Çaǧdaş, Deniz","first_name":"Deniz","last_name":"Çaǧdaş"},{"orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav","first_name":"Miroslav","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emily","last_name":"Mace","full_name":"Mace, Emily"},{"first_name":"Wojciech","last_name":"Garncarz","full_name":"Garncarz, Wojciech"},{"full_name":"Petronczki, Oezlem","last_name":"Petronczki","first_name":"Oezlem"},{"first_name":"René","last_name":"Platzer","full_name":"Platzer, René"},{"first_name":"Laurène","last_name":"Pfajfer","full_name":"Pfajfer, Laurène"},{"first_name":"Ivan","last_name":"Bilic","full_name":"Bilic, Ivan"},{"full_name":"Ban, Sol","first_name":"Sol","last_name":"Ban"},{"last_name":"Willmann","first_name":"Katharina","full_name":"Willmann, Katharina"},{"last_name":"Mukherjee","first_name":"Malini","full_name":"Mukherjee, Malini"},{"first_name":"Verena","last_name":"Supper","full_name":"Supper, Verena"},{"full_name":"Hsu, Hsiangting","first_name":"Hsiangting","last_name":"Hsu"},{"full_name":"Banerjee, Pinaki","last_name":"Banerjee","first_name":"Pinaki"},{"last_name":"Sinha","first_name":"Papiya","full_name":"Sinha, Papiya"},{"last_name":"Mcclanahan","first_name":"Fabienne","full_name":"Mcclanahan, Fabienne"},{"full_name":"Zlabinger, Gerhard","first_name":"Gerhard","last_name":"Zlabinger"},{"last_name":"Pickl","first_name":"Winfried","full_name":"Pickl, Winfried"},{"last_name":"Gribben","first_name":"John","full_name":"Gribben, John"},{"full_name":"Stockinger, Hannes","last_name":"Stockinger","first_name":"Hannes"},{"full_name":"Bennett, Keiryn","last_name":"Bennett","first_name":"Keiryn"},{"last_name":"Huppa","first_name":"Johannes","full_name":"Huppa, Johannes"},{"full_name":"Dupré, Loï̈C","first_name":"Loï̈C","last_name":"Dupré"},{"first_name":"Özden","last_name":"Sanal","full_name":"Sanal, Özden"},{"full_name":"Jäger, Ulrich","first_name":"Ulrich","last_name":"Jäger"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Ilhan","last_name":"Tezcan","full_name":"Tezcan, Ilhan"},{"first_name":"Jordan","last_name":"Orange","full_name":"Orange, Jordan"},{"first_name":"Kaan","last_name":"Boztug","full_name":"Boztug, Kaan"}],"status":"public","date_created":"2018-12-11T11:50:21Z","type":"journal_article","oa_version":"Submitted Version","article_type":"original","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."}],"citation":{"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>.","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>","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>.","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>","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.","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.","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."},"page":"1352 - 1360","date_updated":"2025-09-22T14:13:22Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","oa":1,"external_id":{"pmid":["27776107"],"isi":["000388056400005"]},"publisher":"Nature Publishing Group","month":"12","department":[{"_id":"MiSi"}],"isi":1,"volume":17,"doi":"10.1038/ni.3575","publication_status":"published","pmid":1,"quality_controlled":"1","year":"2016","intvolume":"        17","date_published":"2016-12-01T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1038/ni.3575","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263"}]},{"status":"public","date_created":"2018-12-11T11:50:21Z","author":[{"full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","last_name":"Düllberg","first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas","last_name":"Cade","full_name":"Cade, Nicholas"},{"full_name":"Surrey, Thomas","last_name":"Surrey","first_name":"Thomas"}],"_id":"1139","title":"Microtubule aging probed by microfluidics assisted tubulin washout","abstract":[{"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.","lang":"eng"}],"extern":"1","intvolume":"        27","year":"2016","oa_version":"None","publication_status":"published","type":"journal_article","page":"3563 - 3573","citation":{"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>","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>.","ista":"Düllberg CF, Cade N, Surrey T. 2016. Microtubule aging probed by microfluidics assisted tubulin washout. Molecular Biology and Evolution. 27(22), 3563–3573.","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.","short":"C.F. Düllberg, N. Cade, T. Surrey, Molecular Biology and Evolution 27 (2016) 3563–3573.","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>","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>."},"article_processing_charge":"No","date_published":"2016-11-07T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1091/mbc.E16-07-0548","date_updated":"2021-01-12T06:48:34Z","issue":"22","publication":"Molecular Biology and Evolution","day":"07","month":"11","publisher":"Oxford University Press","doi":"10.1091/mbc.E16-07-0548","publist_id":"6218","language":[{"iso":"eng"}],"volume":27},{"doi":"10.1145/2933575.2935304","isi":1,"publisher":"IEEE","month":"07","department":[{"_id":"KrCh"}],"external_id":{"isi":["000387609200020"],"arxiv":["1602.02670"]},"oa":1,"day":"05","main_file_link":[{"url":"https://arxiv.org/abs/1602.02670","open_access":"1"}],"arxiv":1,"fulldoi":"https://doi.org/10.1145/2933575.2935304","article_processing_charge":"No","conference":{"name":"LICS: Logic in Computer Science","start_date":"2016-07-05","end_date":"2016-07-08","location":"New York, NY, USA"},"alternative_title":["Proceedings Symposium on Logic in Computer Science"],"date_published":"2016-07-05T00:00:00Z","publication_status":"published","quality_controlled":"1","year":"2016","language":[{"iso":"eng"}],"publist_id":"6219","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.","scopus_import":"1","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","date_updated":"2025-09-22T14:12:05Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>.","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>","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.","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.","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.","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>.","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>"},"page":"197 - 206","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","type":"conference","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dvoák","first_name":"Wolfgang","full_name":"Dvoák, Wolfgang"},{"last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Loitzenbauer, Veronika","first_name":"Veronika","last_name":"Loitzenbauer"}],"date_created":"2018-12-11T11:50:22Z","status":"public","title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","_id":"1140"},{"fulldoi":"https://doi.org/10.1016/j.jocs.2016.03.004","date_published":"2016-11-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","year":"2016","quality_controlled":"1","intvolume":"        17","volume":17,"doi":"10.1016/j.jocs.2016.03.004","isi":1,"external_id":{"isi":["000390625600021"]},"publisher":"Elsevier","department":[{"_id":"ChWo"}],"month":"11","day":"01","date_updated":"2025-09-22T14:11:23Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"249 - 260","citation":{"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>","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>.","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.","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.","short":"R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational Science 17 (2016) 249–260.","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>.","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>"},"oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","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."}],"title":"Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization","_id":"1141","status":"public","author":[{"first_name":"Radosław","last_name":"Łazarz","full_name":"Łazarz, Radosław"},{"last_name":"Idzik","first_name":"Michał","full_name":"Idzik, Michał"},{"first_name":"Konrad","last_name":"Gądek","full_name":"Gądek, Konrad"},{"full_name":"Gajda-Zagorska, Ewa P","id":"47794CF0-F248-11E8-B48F-1D18A9856A87","first_name":"Ewa P","last_name":"Gajda-Zagorska"}],"date_created":"2018-12-11T11:50:22Z","language":[{"iso":"eng"}],"publist_id":"6217","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.","publication":"Journal of Computational Science","scopus_import":"1","issue":"1"},{"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).","issue":"12","scopus_import":"1","publication":"Nature Immunology","publist_id":"6216","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","date_created":"2018-12-11T11:50:22Z","author":[{"full_name":"Martins, Rui","last_name":"Martins","first_name":"Rui"},{"last_name":"Maier","first_name":"Julia","full_name":"Maier, Julia"},{"full_name":"Gorki, Anna","last_name":"Gorki","first_name":"Anna"},{"full_name":"Huber, Kilian","first_name":"Kilian","last_name":"Huber"},{"full_name":"Sharif, Omar","first_name":"Omar","last_name":"Sharif"},{"full_name":"Starkl, Philipp","last_name":"Starkl","first_name":"Philipp"},{"last_name":"Saluzzo","first_name":"Simona","full_name":"Saluzzo, Simona"},{"first_name":"Federica","last_name":"Quattrone","full_name":"Quattrone, Federica"},{"last_name":"Gawish","first_name":"Riem","full_name":"Gawish, Riem"},{"first_name":"Karin","last_name":"Lakovits","full_name":"Lakovits, Karin"},{"last_name":"Aichinger","first_name":"Michael","full_name":"Aichinger, Michael"},{"full_name":"Radic Sarikas, Branka","last_name":"Radic Sarikas","first_name":"Branka"},{"full_name":"Lardeau, Charles","first_name":"Charles","last_name":"Lardeau"},{"full_name":"Hladik, Anastasiya","last_name":"Hladik","first_name":"Anastasiya"},{"full_name":"Korosec, Ana","first_name":"Ana","last_name":"Korosec"},{"full_name":"Brown, Markus","last_name":"Brown","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari"},{"full_name":"Duggan, Michelle","id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle","last_name":"Duggan"},{"last_name":"Kerjaschki","first_name":"Dontscho","full_name":"Kerjaschki, Dontscho"},{"first_name":"Harald","last_name":"Esterbauer","full_name":"Esterbauer, Harald"},{"first_name":"Jacques","last_name":"Colinge","full_name":"Colinge, Jacques"},{"last_name":"Eisenbarth","first_name":"Stephanie","full_name":"Eisenbarth, Stephanie"},{"last_name":"Decker","first_name":"Thomas","full_name":"Decker, Thomas"},{"full_name":"Bennett, Keiryn","last_name":"Bennett","first_name":"Keiryn"},{"full_name":"Kubicek, Stefan","first_name":"Stefan","last_name":"Kubicek"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"},{"last_name":"Superti Furga","first_name":"Giulio","full_name":"Superti Furga, Giulio"},{"last_name":"Knapp","first_name":"Sylvia","full_name":"Knapp, Sylvia"}],"status":"public","_id":"1142","title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:10:50Z","citation":{"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>.","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>","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.","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.","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>.","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>"},"page":"1361 - 1372","department":[{"_id":"MiSi"},{"_id":"PeJo"}],"month":"12","publisher":"Nature Publishing Group","external_id":{"isi":["000388056400006"]},"oa":1,"day":"01","doi":"10.1038/ni.3590","volume":17,"isi":1,"intvolume":"        17","year":"2016","quality_controlled":"1","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d"}],"fulldoi":"https://doi.org/10.1038/ni.3590","article_processing_charge":"No","date_published":"2016-12-01T00:00:00Z"},{"language":[{"iso":"eng"}],"publist_id":"6215","publication":"Analysis and PDE","issue":"2","scopus_import":"1","ec_funded":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"page":"459 - 485","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.","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.","short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","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>","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>.","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>","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>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:10:16Z","_id":"1143","title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","status":"public","author":[{"full_name":"Nam, Phan","first_name":"Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rougerie, Nicolas","first_name":"Nicolas","last_name":"Rougerie"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"date_created":"2018-12-11T11:50:23Z","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"isi":1,"volume":9,"doi":"10.2140/apde.2016.9.459","day":"24","oa":1,"external_id":{"arxiv":["1503.07061"],"isi":["000378287000006"]},"month":"03","department":[{"_id":"RoSe"}],"publisher":"Mathematical Sciences Publishers","date_published":"2016-03-24T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.2140/apde.2016.9.459","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1503.07061"}],"quality_controlled":"1","year":"2016","publication_status":"published","intvolume":"         9"},{"status":"public","author":[{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"}],"date_created":"2018-12-11T11:50:23Z","_id":"1145","title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","abstract":[{"lang":"eng","text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors"}],"oa_version":"Published Version","type":"journal_article","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"page":"1504 - 1519","citation":{"apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., &#38; Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>","chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>.","ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519.","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” <i>Molecular Plant</i>, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. 2016;9(11):1504-1519. doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>","mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:08:07Z","issue":"11","scopus_import":"1","publication":"Molecular Plant","ec_funded":1,"acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","language":[{"iso":"eng"}],"publist_id":"6213","ddc":["581"],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"intvolume":"         9","year":"2016","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","date_published":"2016-11-07T00:00:00Z","file_date_updated":"2018-12-12T10:13:22Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.1016/j.molp.2016.08.010","pubrep_id":"746","oa":1,"day":"07","month":"11","department":[{"_id":"JiFr"}],"publisher":"Cell Press","external_id":{"isi":["000389594100008"]},"isi":1,"file":[{"date_created":"2018-12-12T10:13:22Z","creator":"system","relation":"main_file","access_level":"open_access","file_id":"5004","file_size":5005876,"file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","content_type":"application/pdf","date_updated":"2018-12-12T10:13:22Z"}],"doi":"10.1016/j.molp.2016.08.010","volume":9},{"scopus_import":"1","publication":"Scientific Reports","acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).","language":[{"iso":"eng"}],"publist_id":"6211","date_created":"2018-12-11T11:50:24Z","author":[{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"full_name":"Medved'Ová, Zuzana","first_name":"Zuzana","last_name":"Medved'Ová"},{"first_name":"Petr","last_name":"Kalousek","full_name":"Kalousek, Petr"},{"full_name":"Matiješčuková, Natálie","first_name":"Natálie","last_name":"Matiješčuková"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Reinöhl, Vilém","last_name":"Reinöhl","first_name":"Vilém"},{"last_name":"Procházka","first_name":"Stanislav","full_name":"Procházka, Stanislav"}],"status":"public","_id":"1147","title":"Auxin flow mediated competition between axillary buds to restore apical dominance","abstract":[{"text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016.","lang":"eng"}],"oa_version":"Published Version","type":"journal_article","citation":{"chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>.","apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., &#38; Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>","mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>, vol. 6, 35955, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955.","ieee":"J. Balla <i>et al.</i>, “Auxin flow mediated competition between axillary buds to restore apical dominance,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T09:59:19Z","pubrep_id":"745","oa":1,"day":"08","month":"11","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","external_id":{"isi":["000387284700001"]},"article_number":"35955","isi":1,"file":[{"file_name":"IST-2017-745-v1+1_srep35955.pdf","date_updated":"2018-12-12T10:09:28Z","content_type":"application/pdf","file_size":1587544,"file_id":"4752","access_level":"open_access","relation":"main_file","creator":"system","date_created":"2018-12-12T10:09:28Z"}],"doi":"10.1038/srep35955","volume":6,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["581"],"intvolume":"         6","year":"2016","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","file_date_updated":"2018-12-12T10:09:28Z","date_published":"2016-11-08T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.1038/srep35955"},{"intvolume":"       149","quality_controlled":"1","year":"2016","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.biosystems.2016.07.005","article_processing_charge":"No","date_published":"2016-11-01T00:00:00Z","month":"11","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publisher":"Elsevier","external_id":{"isi":["000390743600003"]},"day":"01","doi":"10.1016/j.biosystems.2016.07.005","volume":149,"isi":1,"abstract":[{"lang":"eng","text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd"}],"oa_version":"None","type":"journal_article","status":"public","date_created":"2018-12-11T11:50:24Z","author":[{"last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian"},{"first_name":"Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Podelski, Andreas","last_name":"Podelski","first_name":"Andreas"},{"first_name":"Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"}],"_id":"1148","title":"Adaptive moment closure for parameter inference of biochemical reaction networks","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T07:44:57Z","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"page":"15 - 25","citation":{"apa":"Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., &#38; Ruess, J. (2016). Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>","chicago":"Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>.","ista":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.","ieee":"C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” <i>Biosystems</i>, vol. 149. Elsevier, pp. 15–25, 2016.","short":"C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.","ama":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. 2016;149:15-25. doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>","mla":"Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>, vol. 149, Elsevier, 2016, pp. 15–25, doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>."},"related_material":{"record":[{"status":"public","id":"1658","relation":"earlier_version"}]},"acknowledgement":"This work is based on the CMSB 2015 paper “Adaptive moment closure for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015). The work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","ec_funded":1,"scopus_import":"1","publication":"Biosystems","language":[{"iso":"eng"}],"publist_id":"6210"},{"date_published":"2016-09-01T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1016/j.apnum.2016.04.005","quality_controlled":"1","year":"2016","publication_status":"published","intvolume":"       107","isi":1,"volume":107,"doi":"10.1016/j.apnum.2016.04.005","day":"01","external_id":{"isi":["000378447000003"]},"department":[{"_id":"HeEd"}],"month":"09","publisher":"Elsevier","project":[{"call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033"}],"page":"34 - 47","citation":{"apa":"Miyaji, T., Pilarczyk, P., Gameiro, M., Kokubu, H., &#38; Mischaikow, K. (2016). A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>","chicago":"Miyaji, Tomoyuki, Pawel Pilarczyk, Marcio Gameiro, Hiroshi Kokubu, and Konstantin Mischaikow. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>.","ista":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. 2016. A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. 107, 34–47.","ieee":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, and K. Mischaikow, “A study of rigorous ODE integrators for multi scale set oriented computations,” <i>Applied Numerical Mathematics</i>, vol. 107. Elsevier, pp. 34–47, 2016.","short":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical Mathematics 107 (2016) 34–47.","ama":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. 2016;107:34-47. doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>","mla":"Miyaji, Tomoyuki, et al. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>, vol. 107, Elsevier, 2016, pp. 34–47, doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T09:58:16Z","_id":"1149","title":"A study of rigorous ODE integrators for multi scale set oriented computations","author":[{"last_name":"Miyaji","first_name":"Tomoyuki","full_name":"Miyaji, Tomoyuki"},{"first_name":"Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel"},{"first_name":"Marcio","last_name":"Gameiro","full_name":"Gameiro, Marcio"},{"full_name":"Kokubu, Hiroshi","first_name":"Hiroshi","last_name":"Kokubu"},{"full_name":"Mischaikow, Konstantin","first_name":"Konstantin","last_name":"Mischaikow"}],"status":"public","date_created":"2018-12-11T11:50:25Z","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"We study the usefulness of two most prominent publicly available rigorous ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable of handling entire sets of initial conditions and provide tight rigorous outer enclosures of the images under a time-T map. We conduct extensive benchmark computations using the well-known Lorenz system, and compare the computation time against the final accuracy achieved. We also discuss the effect of a few technical parameters, such as the order of the numerical integration method, the value of T, and the phase space resolution. We conclude that COSY may provide more precise results due to its ability of avoiding the variable dependency problem. However, the overall cost of computations conducted using CAPD is typically lower, especially when intervals of parameters are involved. Moreover, access to COSY is limited (registration required) and the rigorous ODE integrators are not publicly available, while CAPD is an open source free software project. Therefore, we recommend the latter integrator for this kind of computations. Nevertheless, proper choice of the various integration parameters turns out to be of even greater importance than the choice of the integrator itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved."}],"publist_id":"6209","language":[{"iso":"eng"}],"publication":"Applied Numerical Mathematics","scopus_import":"1","acknowledgement":"MG was partially supported by FAPESP grants 2013/07460-7 and 2010/00875-9, and by CNPq grants 305860/2013-5 and 306453/2009-6, Brazil. The work of HK was partially supported by Grant-in-Aid for Scientific Research (Nos.24654022, 25287029), Ministry of Education, Science, Technology, Culture and Sports, Japan. KM was supported by NSF grants NSF-DMS-0835621, 0915019, 1125174, 1248071, and contracts from AFOSR and DARPA. TM was supported by Grant-in-Aid for JSPS Fellows No. 245312. A part of the research of TM and HK was also supported by JST, CREST.\r\n\r\nResearch conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE – Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (Ref. FCT PTDC/MAT/098871/2008); from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 622033; and from the same sources as HK.\r\n\r\nThe authors express their gratitude to the Department of Mathematics of Kyoto University for making their server available for conducting the computations described in the paper, and to the reviewers for helpful comments that contributed towards increasing the quality of the paper.","ec_funded":1}]