[{"scopus_import":1,"day":"01","month":"09","publication":"Journal of Comparative Neurology","citation":{"chicago":"Javdani, Fariba, Krisztina Holló, Krisztina Hegedűs, Gréta Kis, Zoltán Hegyi, Klaudia Dócs, Yu Kasugai, Yugo Fukazawa, Ryuichi Shigemoto, and Miklós Antal. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology. Wiley-Blackwell, 2015. https://doi.org/10.1002/cne.23774.","short":"F. Javdani, K. Holló, K. Hegedűs, G. Kis, Z. Hegyi, K. Dócs, Y. Kasugai, Y. Fukazawa, R. Shigemoto, M. Antal, Journal of Comparative Neurology 523 (2015) 1967–1983.","mla":"Javdani, Fariba, et al. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology, vol. 523, no. 13, Wiley-Blackwell, 2015, pp. 1967–83, doi:10.1002/cne.23774.","ieee":"F. Javdani et al., “Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats,” Journal of Comparative Neurology, vol. 523, no. 13. Wiley-Blackwell, pp. 1967–1983, 2015.","apa":"Javdani, F., Holló, K., Hegedűs, K., Kis, G., Hegyi, Z., Dócs, K., … Antal, M. (2015). Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23774","ista":"Javdani F, Holló K, Hegedűs K, Kis G, Hegyi Z, Dócs K, Kasugai Y, Fukazawa Y, Shigemoto R, Antal M. 2015. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 523(13), 1967–1983.","ama":"Javdani F, Holló K, Hegedűs K, et al. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 2015;523(13):1967-1983. doi:10.1002/cne.23774"},"quality_controlled":"1","page":"1967 - 1983","date_published":"2015-09-01T00:00:00Z","doi":"10.1002/cne.23774","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"γ-Aminobutyric acid (GABA)- and glycine-mediated hyperpolarizing inhibition is associated with a chloride influx that depends on the inwardly directed chloride electrochemical gradient. In neurons, the extrusion of chloride from the cytosol primarily depends on the expression of an isoform of potassium-chloride cotransporters (KCC2s). KCC2 is crucial in the regulation of the inhibitory tone of neural circuits, including pain processing neural assemblies. Thus we investigated the cellular distribution of KCC2 in neurons underlying pain processing in the superficial spinal dorsal horn of rats by using high-resolution immunocytochemical methods. We demonstrated that perikarya and dendrites widely expressed KCC2, but axon terminals proved to be negative for KCC2. In single ultrathin sections, silver deposits labeling KCC2 molecules showed different densities on the surface of dendritic profiles, some of which were negative for KCC2. In freeze fracture replicas and tissue sections double stained for the β3-subunit of GABAA receptors and KCC2, GABAA receptors were revealed on dendritic segments with high and also with low KCC2 densities. By measuring the distances between spots immunoreactive for gephyrin (a scaffolding protein of GABAA and glycine receptors) and KCC2 on the surface of neurokinin 1 (NK1) receptor-immunoreactive dendrites, we found that gephyrin-immunoreactive spots were located at various distances from KCC2 cotransporters; 5.7 % of them were recovered in the middle of 4-10-μm-long dendritic segments that were free of KCC2 immunostaining. The variable local densities of KCC2 may result in variable postsynaptic potentials evoked by the activation of GABAA and glycine receptors along the dendrites of spinal neurons.","lang":"eng"}],"publist_id":"5614","issue":"13","_id":"1557","year":"2015","acknowledgement":"Funded by:\r\nHungarian Academy of Sciences. Grant Number: MTA-TKI 242\r\nHungarian Brain Research Program. Grant Number: KTIA_NAP_13-1-2013-0001\r\nSolution Oriented Research for Science and Technology from the Japan Science and Technology Agency Japanese Ministry of Education, Culture, Sports, Science and Technology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats","publication_status":"published","status":"public","publisher":"Wiley-Blackwell","department":[{"_id":"RySh"}],"intvolume":" 523","author":[{"full_name":"Javdani, Fariba","last_name":"Javdani","first_name":"Fariba"},{"last_name":"Holló","first_name":"Krisztina","full_name":"Holló, Krisztina"},{"first_name":"Krisztina","last_name":"Hegedűs","full_name":"Hegedűs, Krisztina"},{"full_name":"Kis, Gréta","last_name":"Kis","first_name":"Gréta"},{"first_name":"Zoltán","last_name":"Hegyi","full_name":"Hegyi, Zoltán"},{"full_name":"Dócs, Klaudia","last_name":"Dócs","first_name":"Klaudia"},{"full_name":"Kasugai, Yu","last_name":"Kasugai","first_name":"Yu"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"last_name":"Antal","first_name":"Miklós","full_name":"Antal, Miklós"}],"date_created":"2018-12-11T11:52:42Z","date_updated":"2021-01-12T06:51:35Z","oa_version":"None","volume":523},{"date_published":"2015-12-22T00:00:00Z","page":"15636 - 15641","citation":{"chicago":"Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511366112.","short":"R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641.","mla":"Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS, vol. 112, no. 51, National Academy of Sciences, 2015, pp. 15636–41, doi:10.1073/pnas.1511366112.","apa":"Ibsen-Jensen, R., Chatterjee, K., & Nowak, M. (2015). Computational complexity of ecological and evolutionary spatial dynamics. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511366112","ieee":"R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of ecological and evolutionary spatial dynamics,” PNAS, vol. 112, no. 51. National Academy of Sciences, pp. 15636–15641, 2015.","ista":"Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641.","ama":"Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 2015;112(51):15636-15641. doi:10.1073/pnas.1511366112"},"publication":"PNAS","day":"22","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 112","status":"public","title":"Computational complexity of ecological and evolutionary spatial dynamics","_id":"1559","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"51","abstract":[{"lang":"eng","text":"There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP)."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1511366112","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/","open_access":"1"}],"oa":1,"external_id":{"pmid":["26644569"]},"month":"12","volume":112,"date_updated":"2021-01-12T06:51:36Z","date_created":"2018-12-11T11:52:43Z","author":[{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2015","publist_id":"5612"},{"oa_version":"None","volume":45,"date_created":"2018-12-11T11:52:44Z","date_updated":"2021-01-12T06:51:36Z","author":[{"last_name":"Heger","first_name":"Klaus","full_name":"Heger, Klaus"},{"full_name":"Kober, Maike","last_name":"Kober","first_name":"Maike"},{"full_name":"Rieß, David","first_name":"David","last_name":"Rieß"},{"full_name":"Drees, Christoph","first_name":"Christoph","last_name":"Drees"},{"last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid"},{"last_name":"Bertossi","first_name":"Arianna","full_name":"Bertossi, Arianna"},{"full_name":"Roers, Axel","last_name":"Roers","first_name":"Axel"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Marc","last_name":"Schmidt Supprian","full_name":"Schmidt Supprian, Marc"}],"publisher":"Wiley","intvolume":" 45","department":[{"_id":"MiSi"}],"title":"A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors","publication_status":"published","status":"public","year":"2015","_id":"1561","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","publist_id":"5610","abstract":[{"lang":"eng","text":"Replication-deficient recombinant adenoviruses are potent vectors for the efficient transient expression of exogenous genes in resting immune cells. However, most leukocytes are refractory to efficient adenoviral transduction as they lack expression of the coxsackie/adenovirus receptor (CAR). To circumvent this obstacle, we generated the R26/CAG-CARΔ1StopF (where R26 is ROSA26 and CAG is CMV early enhancer/chicken β actin promoter) knock-in mouse line. This strain allows monitoring of in situ Cre recombinase activity through expression of CARΔ1. Simultaneously, CARΔ1 expression permits selective and highly efficient adenoviral transduction of immune cell populations, such as mast cells or T cells, directly ex vivo in bulk cultures without prior cell purification or activation. Furthermore, we show that CARΔ1 expression dramatically improves adenoviral infection of in vitro differentiated conventional and plasmacytoid dendritic cells (DCs), basophils, mast cells, as well as Hoxb8-immortalized hematopoietic progenitor cells. This novel dual function mouse strain will hence be a valuable tool to rapidly dissect the function of specific genes in leukocyte physiology."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1002/eji.201545457","date_published":"2015-06-01T00:00:00Z","page":"1614 - 1620","quality_controlled":"1","citation":{"ista":"Heger K, Kober M, Rieß D, Drees C, de Vries I, Bertossi A, Roers A, Sixt MK, Schmidt Supprian M. 2015. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 45(6), 1614–1620.","ieee":"K. Heger et al., “A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors,” European Journal of Immunology, vol. 45, no. 6. Wiley, pp. 1614–1620, 2015.","apa":"Heger, K., Kober, M., Rieß, D., Drees, C., de Vries, I., Bertossi, A., … Schmidt Supprian, M. (2015). A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. Wiley. https://doi.org/10.1002/eji.201545457","ama":"Heger K, Kober M, Rieß D, et al. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 2015;45(6):1614-1620. doi:10.1002/eji.201545457","chicago":"Heger, Klaus, Maike Kober, David Rieß, Christoph Drees, Ingrid de Vries, Arianna Bertossi, Axel Roers, Michael K Sixt, and Marc Schmidt Supprian. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology. Wiley, 2015. https://doi.org/10.1002/eji.201545457.","mla":"Heger, Klaus, et al. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology, vol. 45, no. 6, Wiley, 2015, pp. 1614–20, doi:10.1002/eji.201545457.","short":"K. Heger, M. Kober, D. Rieß, C. Drees, I. de Vries, A. Bertossi, A. Roers, M.K. Sixt, M. Schmidt Supprian, European Journal of Immunology 45 (2015) 1614–1620."},"publication":"European Journal of Immunology","day":"01","month":"06","scopus_import":1},{"doi":"10.1038/nmeth.3279","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/"}],"external_id":{"pmid":["25643149"]},"oa":1,"quality_controlled":"1","month":"02","author":[{"full_name":"Liao, Cheyang","last_name":"Liao","first_name":"Cheyang"},{"last_name":"Smet","first_name":"Wouter","full_name":"Smet, Wouter"},{"full_name":"Brunoud, Géraldine","last_name":"Brunoud","first_name":"Géraldine"},{"full_name":"Yoshida, Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"volume":12,"date_created":"2018-12-11T11:52:41Z","date_updated":"2021-01-12T06:51:34Z","pmid":1,"year":"2015","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","publist_id":"5617","date_published":"2015-02-26T00:00:00Z","citation":{"ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279","chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279.","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279."},"publication":"Nature Methods","page":"207 - 210","day":"26","scopus_import":1,"oa_version":"Submitted Version","_id":"1554","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 12","title":"Reporters for sensitive and quantitative measurement of auxin response","status":"public","issue":"3","abstract":[{"lang":"eng","text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species."}],"type":"journal_article"},{"type":"journal_article","publist_id":"5611","issue":"4","abstract":[{"text":"Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP is a crucial component of this selector function.","lang":"eng"}],"publisher":"Nature Publishing Group","department":[{"_id":"MiSi"}],"intvolume":" 16","status":"public","publication_status":"published","title":"The lymph node filter revealed","_id":"1560","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":16,"date_created":"2018-12-11T11:52:43Z","date_updated":"2021-01-12T06:51:36Z","author":[{"full_name":"Hons, Miroslav","first_name":"Miroslav","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"scopus_import":1,"month":"03","day":"19","page":"338 - 340","quality_controlled":"1","citation":{"ista":"Hons M, Sixt MK. 2015. The lymph node filter revealed. Nature Immunology. 16(4), 338–340.","apa":"Hons, M., & Sixt, M. K. (2015). The lymph node filter revealed. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3126","ieee":"M. Hons and M. K. Sixt, “The lymph node filter revealed,” Nature Immunology, vol. 16, no. 4. Nature Publishing Group, pp. 338–340, 2015.","ama":"Hons M, Sixt MK. The lymph node filter revealed. Nature Immunology. 2015;16(4):338-340. doi:10.1038/ni.3126","chicago":"Hons, Miroslav, and Michael K Sixt. “The Lymph Node Filter Revealed.” Nature Immunology. Nature Publishing Group, 2015. https://doi.org/10.1038/ni.3126.","mla":"Hons, Miroslav, and Michael K. Sixt. “The Lymph Node Filter Revealed.” Nature Immunology, vol. 16, no. 4, Nature Publishing Group, 2015, pp. 338–40, doi:10.1038/ni.3126.","short":"M. Hons, M.K. Sixt, Nature Immunology 16 (2015) 338–340."},"publication":"Nature Immunology","language":[{"iso":"eng"}],"date_published":"2015-03-19T00:00:00Z","doi":"10.1038/ni.3126"},{"external_id":{"pmid":["26282459"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/"}],"quality_controlled":"1","doi":"10.1113/JP271078","language":[{"iso":"eng"}],"month":"11","pmid":1,"acknowledgement":"This work was supported by the Compagnia di San Paolo Foundation ‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank Dr Claudio Franchino for cell preparation and for providing excellent technical support.","year":"2015","publisher":"Wiley-Blackwell","department":[{"_id":"PeJo"}],"publication_status":"published","author":[{"last_name":"Gavello","first_name":"Daniela","full_name":"Gavello, Daniela"},{"last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"full_name":"Gosso, Sara","last_name":"Gosso","first_name":"Sara"},{"full_name":"Carbone, Emilio","first_name":"Emilio","last_name":"Carbone"},{"full_name":"Carabelli, Valentina","first_name":"Valentina","last_name":"Carabelli"}],"volume":593,"date_updated":"2021-01-12T06:51:38Z","date_created":"2018-12-11T11:52:45Z","publist_id":"5606","citation":{"mla":"Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell, 2015, pp. 4835–53, doi:10.1113/JP271078.","short":"D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853.","chicago":"Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078.","ama":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 2015;593(22):4835-4853. doi:10.1113/JP271078","ista":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 593(22), 4835–4853.","apa":"Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015). Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078","ieee":"D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015."},"publication":"Journal of Physiology","page":"4835 - 4853","date_published":"2015-11-15T00:00:00Z","scopus_import":1,"day":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1565","intvolume":" 593","title":"Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"22","abstract":[{"text":"Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release.","lang":"eng"}]},{"_id":"1562","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles","intvolume":" 66","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor."}],"issue":"16","publication":"Journal of Experimental Botany","citation":{"chicago":"Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv177.","short":"P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E. Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065.","mla":"Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:10.1093/jxb/erv177.","apa":"Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T., … Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv177","ieee":"P. Grones et al., “Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.","ista":"Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065.","ama":"Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 2015;66(16):5055-5065. doi:10.1093/jxb/erv177"},"article_type":"original","page":"5055 - 5065","date_published":"2015-08-01T00:00:00Z","scopus_import":1,"day":"01","year":"2015","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG- 20101109-PSDP to JF); the European Social Fund and the state budget of the Czech Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR) [project 13-40637S to JF].","publication_status":"published","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publisher":"Oxford University Press","author":[{"first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"first_name":"Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu"},{"last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:52:44Z","date_updated":"2023-02-23T10:04:26Z","volume":66,"publist_id":"5609","ec_funded":1,"quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"doi":"10.1093/jxb/erv177","language":[{"iso":"eng"}],"month":"08"},{"publication":"Frontiers in Computational Neuroscience","citation":{"ista":"Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.","ieee":"M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.","apa":"Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145","ama":"Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 2015;9(11). doi:10.3389/fncom.2015.00145","chicago":"Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.","mla":"Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.","short":"M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015)."},"date_published":"2015-11-30T00:00:00Z","scopus_import":1,"day":"30","has_accepted_license":"1","status":"public","ddc":["570"],"title":"Editorial: Emergent neural computation from the interaction of different forms of plasticity","intvolume":" 9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1564","file":[{"access_level":"open_access","file_name":"IST-2016-479-v1+1_fncom-09-00145.pdf","creator":"system","file_size":187038,"content_type":"application/pdf","file_id":"4927","relation":"main_file","checksum":"cea73b6d3ef1579f32da10b82f4de4fd","date_created":"2018-12-12T10:12:09Z","date_updated":"2020-07-14T12:45:02Z"}],"oa_version":"Published Version","pubrep_id":"479","type":"journal_article","issue":"11","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.3389/fncom.2015.00145","month":"11","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Frontiers Research Foundation","year":"2015","date_created":"2018-12-11T11:52:45Z","date_updated":"2021-01-12T06:51:37Z","volume":9,"author":[{"full_name":"Gilson, Matthieu","first_name":"Matthieu","last_name":"Gilson"},{"last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina"},{"first_name":"Friedemann","last_name":"Zenke","full_name":"Zenke, Friedemann"}],"article_number":"145","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:45:02Z","publist_id":"5607","ec_funded":1},{"conference":{"name":"SYNASC: Symbolic and Numeric Algorithms for Scientific Computing","end_date":"2014-09-25","start_date":"2014-09-22","location":"Timisoara, Romania"},"doi":"10.1109/SYNASC.2014.81","date_published":"2015-02-05T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing","citation":{"chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, and Daria Malkova. “The Classification of Endoscopy Images with Persistent Homology.” In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, 7034731. IEEE, 2015. https://doi.org/10.1109/SYNASC.2014.81.","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731, doi:10.1109/SYNASC.2014.81.","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, in:, Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731.","ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. 2015. The classification of endoscopy images with persistent homology. Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC: Symbolic and Numeric Algorithms for Scientific Computing, 7034731.","apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., & Malkova, D. (2015). The classification of endoscopy images with persistent homology. In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (p. 7034731). Timisoara, Romania: IEEE. https://doi.org/10.1109/SYNASC.2014.81","ieee":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, and D. Malkova, “The classification of endoscopy images with persistent homology,” in Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, Timisoara, Romania, 2015, p. 7034731.","ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. The classification of endoscopy images with persistent homology. In: Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. 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Demidov Yaroslavl State University within State Assignment for Research.","title":"The classification of endoscopy images with persistent homology","status":"public","publication_status":"published","publisher":"IEEE","department":[{"_id":"HeEd"}],"abstract":[{"text":"Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI) magnifying endoscopy (ME) images of the stomach, we combine methods from image processing, computational topology, and machine learning to classify patterns into normal, tubular, vessel. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.","lang":"eng"}],"publist_id":"5603","type":"conference"},{"alternative_title":["LNCS"],"type":"conference","publist_id":"5604","abstract":[{"lang":"eng","text":"My personal journey to the fascinating world of geometric forms started more than 30 years ago with the invention of alpha shapes in the plane. It took about 10 years before we generalized the concept to higher dimensions, we produced working software with a graphics interface for the three-dimensional case. At the same time, we added homology to the computations. Needless to say that this foreshadowed the inception of persistent homology, because it suggested the study of filtrations to capture the scale of a shape or data set. Importantly, this method has fast algorithms. The arguably most useful result on persistent homology is the stability of its diagrams under perturbations."}],"publisher":"Springer Nature","department":[{"_id":"HeEd"}],"intvolume":" 9411","status":"public","publication_status":"published","title":"Shape, homology, persistence, and stability","_id":"1567","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2015","oa_version":"None","volume":9411,"date_updated":"2022-01-28T08:25:00Z","date_created":"2018-12-11T11:52:46Z","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"scopus_import":"1","article_processing_charge":"No","day":"01","month":"01","quality_controlled":"1","citation":{"chicago":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” In 23rd International Symposium, Vol. 9411. Springer Nature, 2015.","mla":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” 23rd International Symposium, vol. 9411, Springer Nature, 2015.","short":"H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015.","ista":"Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411.","ieee":"H. Edelsbrunner, “Shape, homology, persistence, and stability,” in 23rd International Symposium, Los Angeles, CA, United States, 2015, vol. 9411.","apa":"Edelsbrunner, H. (2015). Shape, homology, persistence, and stability. In 23rd International Symposium (Vol. 9411). Los Angeles, CA, United States: Springer Nature.","ama":"Edelsbrunner H. Shape, homology, persistence, and stability. In: 23rd International Symposium. Vol 9411. Springer Nature; 2015."},"publication":"23rd International Symposium","language":[{"iso":"eng"}],"date_published":"2015-01-01T00:00:00Z","conference":{"location":"Los Angeles, CA, United States","start_date":"2015-09-24","end_date":"2015-09-26","name":"GD: Graph Drawing and Network Visualization"}},{"language":[{"iso":"eng"}],"date_published":"2015-03-01T00:00:00Z","doi":"10.12775/TMNA.2015.014","page":"273 - 286","quality_controlled":"1","citation":{"short":"G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015) 273–286.","mla":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis, vol. 45, no. 1, Juliusz Schauder Center for Nonlinear Studies, 2015, pp. 273–86, doi:10.12775/TMNA.2015.014.","chicago":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies, 2015. https://doi.org/10.12775/TMNA.2015.014.","ama":"Graff G, Pilarczyk P. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 2015;45(1):273-286. doi:10.12775/TMNA.2015.014","apa":"Graff, G., & Pilarczyk, P. (2015). An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies. https://doi.org/10.12775/TMNA.2015.014","ieee":"G. Graff and P. Pilarczyk, “An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds,” Topological Methods in Nonlinear Analysis, vol. 45, no. 1. Juliusz Schauder Center for Nonlinear Studies, pp. 273–286, 2015.","ista":"Graff G, Pilarczyk P. 2015. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 45(1), 273–286."},"publication":"Topological Methods in Nonlinear Analysis","month":"03","day":"01","scopus_import":1,"volume":45,"oa_version":"None","date_created":"2018-12-11T11:52:44Z","date_updated":"2021-01-12T06:51:37Z","author":[{"last_name":"Graff","first_name":"Grzegorz","full_name":"Graff, Grzegorz"},{"full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"HeEd"}],"publisher":"Juliusz Schauder Center for Nonlinear Studies","intvolume":" 45","publication_status":"published","status":"public","title":"An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1563","year":"2015","publist_id":"5608","issue":"1","abstract":[{"text":"For a given self-map $f$ of $M$, a closed smooth connected and simply-connected manifold of dimension $m\\geq 4$, we provide an algorithm for estimating the values of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic points in the smooth homotopy class of $f$. Our results are based on the combinatorial scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm programmed in C++ is publicly available at {\\tt http://www.pawelpilarczyk.com/combtop/}.","lang":"eng"}],"type":"journal_article"},{"month":"11","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/ncomms9821","article_number":"8821","file_date_updated":"2020-07-14T12:45:02Z","publist_id":"5597","publication_status":"published","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Nature Publishing Group","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","year":"2015","date_created":"2018-12-11T11:52:48Z","date_updated":"2021-01-12T06:51:42Z","volume":6,"author":[{"full_name":"Chen, Qian","last_name":"Chen","first_name":"Qian"},{"full_name":"Liu, Yang","last_name":"Liu","first_name":"Yang"},{"full_name":"Maere, Steven","last_name":"Maere","first_name":"Steven"},{"first_name":"Eunkyoung","last_name":"Lee","full_name":"Lee, Eunkyoung"},{"last_name":"Van Isterdael","first_name":"Gert","full_name":"Van Isterdael, Gert"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"last_name":"Lucas","first_name":"Jessica","full_name":"Lucas, Jessica"},{"first_name":"Valya","last_name":"Vassileva","full_name":"Vassileva, Valya"},{"full_name":"Kitakura, Saeko","first_name":"Saeko","last_name":"Kitakura"},{"full_name":"Marhavy, Peter","first_name":"Peter","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741"},{"full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","first_name":"Krzysztof T"},{"full_name":"Geldner, Niko","last_name":"Geldner","first_name":"Niko"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"last_name":"Le","first_name":"Jie","full_name":"Le, Jie"},{"full_name":"Fukaki, Hidehiro","last_name":"Fukaki","first_name":"Hidehiro"},{"full_name":"Grotewold, Erich","last_name":"Grotewold","first_name":"Erich"},{"first_name":"Chuanyou","last_name":"Li","full_name":"Li, Chuanyou"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"last_name":"Sack","first_name":"Fred","full_name":"Sack, Fred"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"scopus_import":1,"day":"18","has_accepted_license":"1","publication":"Nature Communications","citation":{"mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.","short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.","ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821","ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821.","ieee":"Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821"},"date_published":"2015-11-18T00:00:00Z","type":"journal_article","abstract":[{"text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.","lang":"eng"}],"ddc":["580"],"title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","status":"public","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1574","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5085","checksum":"8ff5c108899b548806e1cb7a302fe76d","date_created":"2018-12-12T10:14:32Z","date_updated":"2020-07-14T12:45:02Z","access_level":"open_access","file_name":"IST-2016-477-v1+1_ncomms9821.pdf","content_type":"application/pdf","file_size":1701815,"creator":"system"}],"pubrep_id":"477"},{"department":[{"_id":"MiSi"}],"publisher":"Nature Publishing Group","publication_status":"published","acknowledgement":"M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie).","year":"2015","volume":6,"date_updated":"2021-01-12T06:51:42Z","date_created":"2018-12-11T11:52:48Z","author":[{"first_name":"Mélanie","last_name":"Chabaud","full_name":"Chabaud, Mélanie"},{"full_name":"Heuzé, Mélina","last_name":"Heuzé","first_name":"Mélina"},{"full_name":"Bretou, Marine","first_name":"Marine","last_name":"Bretou"},{"last_name":"Vargas","first_name":"Pablo","full_name":"Vargas, Pablo"},{"first_name":"Paolo","last_name":"Maiuri","full_name":"Maiuri, Paolo"},{"first_name":"Paola","last_name":"Solanes","full_name":"Solanes, Paola"},{"full_name":"Maurin, Mathieu","last_name":"Maurin","first_name":"Mathieu"},{"full_name":"Terriac, Emmanuel","first_name":"Emmanuel","last_name":"Terriac"},{"full_name":"Le Berre, Maël","first_name":"Maël","last_name":"Le Berre"},{"first_name":"Danielle","last_name":"Lankar","full_name":"Lankar, Danielle"},{"full_name":"Piolot, Tristan","first_name":"Tristan","last_name":"Piolot"},{"full_name":"Adelstein, Robert","last_name":"Adelstein","first_name":"Robert"},{"first_name":"Yingfan","last_name":"Zhang","full_name":"Zhang, Yingfan"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Jacobelli, Jordan","last_name":"Jacobelli","first_name":"Jordan"},{"full_name":"Bénichou, Olivier","first_name":"Olivier","last_name":"Bénichou"},{"full_name":"Voituriez, Raphaël","first_name":"Raphaël","last_name":"Voituriez"},{"first_name":"Matthieu","last_name":"Piel","full_name":"Piel, Matthieu"},{"full_name":"Lennon Duménil, Ana","first_name":"Ana","last_name":"Lennon Duménil"}],"article_number":"7526","publist_id":"5596","file_date_updated":"2020-07-14T12:45:02Z","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms8526","month":"06","intvolume":" 6","status":"public","ddc":["570"],"title":"Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1575","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":4530215,"creator":"system","access_level":"open_access","file_name":"IST-2016-476-v1+1_ncomms8526.pdf","checksum":"bae12e86be2adb28253f890b8bba8315","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:11:58Z","relation":"main_file","file_id":"4915"}],"pubrep_id":"476","type":"journal_article","abstract":[{"lang":"eng","text":"The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space."}],"citation":{"ista":"Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526.","ieee":"M. Chabaud et al., “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms8526","ama":"Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 2015;6. doi:10.1038/ncomms8526","chicago":"Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526.","mla":"Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications, vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526.","short":"M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015)."},"publication":"Nature Communications","date_published":"2015-06-25T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"25"},{"doi":"10.1073/pnas.1424856112","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/","open_access":"1"}],"oa":1,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","month":"02","author":[{"full_name":"Doyle, Siamsa","first_name":"Siamsa","last_name":"Doyle"},{"full_name":"Haegera, Ash","last_name":"Haegera","first_name":"Ash"},{"full_name":"Vain, Thomas","first_name":"Thomas","last_name":"Vain"},{"full_name":"Rigala, Adeline","last_name":"Rigala","first_name":"Adeline"},{"last_name":"Viotti","first_name":"Corrado","full_name":"Viotti, Corrado"},{"full_name":"Łangowskaa, Małgorzata","first_name":"Małgorzata","last_name":"Łangowskaa"},{"last_name":"Maa","first_name":"Qian","full_name":"Maa, Qian"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"full_name":"Raikhel, Natasha","last_name":"Raikhel","first_name":"Natasha"},{"first_name":"Glenn","last_name":"Hickse","full_name":"Hickse, Glenn"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"}],"volume":112,"date_updated":"2021-01-12T06:51:39Z","date_created":"2018-12-11T11:52:46Z","year":"2015","acknowledgement":"This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","ec_funded":1,"publist_id":"5602","date_published":"2015-02-17T00:00:00Z","citation":{"short":"S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.","mla":"Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112.","chicago":"Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112.","ama":"Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112","ieee":"S. Doyle et al., “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.","apa":"Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112","ista":"Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815."},"publication":"PNAS","page":"E806 - E815","day":"17","scopus_import":1,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1569","intvolume":" 112","title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","status":"public","issue":"7","abstract":[{"text":"Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.","lang":"eng"}],"type":"journal_article"},{"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/"}],"external_id":{"pmid":["26504200"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1508400112","month":"11","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2015","volume":112,"date_updated":"2021-01-12T06:51:40Z","date_created":"2018-12-11T11:52:47Z","author":[{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"},{"first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"}],"publist_id":"5601","ec_funded":1,"page":"E6224 - E6232","citation":{"mla":"Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112.","short":"R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.","chicago":"Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1508400112.","ama":"Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112","ista":"Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.","ieee":"R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015.","apa":"Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1508400112"},"publication":"PNAS","date_published":"2015-11-10T00:00:00Z","scopus_import":1,"day":"10","intvolume":" 112","title":"Novel plasticity rule can explain the development of sensorimotor intelligence","status":"public","_id":"1570","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"45","abstract":[{"text":"Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.","lang":"eng"}]},{"doi":"10.1073/pnas.1510282112","date_published":"2015-12-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"mla":"de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11, doi:10.1073/pnas.1510282112.","short":"M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.","chicago":"Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510282112.","ama":"de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 2015;112(48):14906-14911. doi:10.1073/pnas.1510282112","ista":"de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 112(48), 14906–14911.","apa":"de Vos, M., Dawid, A., Šunderlíková, V., & Tans, S. (2015). Breaking evolutionary constraint with a tradeoff ratchet. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510282112","ieee":"M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary constraint with a tradeoff ratchet,” PNAS, vol. 112, no. 48. National Academy of Sciences, pp. 14906–14911, 2015."},"publication":"PNAS","page":"14906 - 14911","quality_controlled":"1","month":"12","day":"01","scopus_import":1,"author":[{"full_name":"De Vos, Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","first_name":"Marjon"},{"first_name":"Alexandre","last_name":"Dawid","full_name":"Dawid, Alexandre"},{"first_name":"Vanda","last_name":"Šunderlíková","full_name":"Šunderlíková, Vanda"},{"first_name":"Sander","last_name":"Tans","full_name":"Tans, Sander"}],"oa_version":"None","volume":112,"date_updated":"2021-01-12T06:51:40Z","date_created":"2018-12-11T11:52:47Z","_id":"1571","year":"2015","acknowledgement":"This work is part of the research program of the Foundation for Fundamental Research on Matter, which is part of the Netherlands Organization for Scientific Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences (ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão, J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for discussions and suggestions on the Markov computation. Furthermore, we thank F. J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial version of the manuscript.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","department":[{"_id":"ToBo"}],"intvolume":" 112","title":"Breaking evolutionary constraint with a tradeoff ratchet","status":"public","publication_status":"published","publist_id":"5600","issue":"48","abstract":[{"lang":"eng","text":"Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance."}],"type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.\r\n"}],"publist_id":"5599","issue":"1","status":"public","title":"Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet","publication_status":"published","intvolume":" 339","publisher":"Springer","department":[{"_id":"RoSe"}],"year":"2015","_id":"1572","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:47Z","date_updated":"2021-01-12T06:51:41Z","oa_version":"Preprint","volume":339,"author":[{"last_name":"Correggi","first_name":"Michele","full_name":"Correggi, Michele"},{"first_name":"Alessandro","last_name":"Giuliani","full_name":"Giuliani, Alessandro"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"scopus_import":1,"day":"23","month":"06","quality_controlled":"1","page":"279 - 307","publication":"Communications in Mathematical Physics","main_file_link":[{"url":"http://arxiv.org/abs/1312.7873","open_access":"1"}],"citation":{"ama":"Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015.","apa":"Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0","ista":"Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 339(1), 279–307.","short":"M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics 339 (2015) 279–307.","mla":"Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0.","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00220-015-2402-0","date_published":"2015-06-23T00:00:00Z"},{"title":"Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti","status":"public","intvolume":" 68","_id":"1573","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau."}],"issue":"10","page":"1845 - 1884","publication":"Communications on Pure and Applied Mathematics","citation":{"chicago":"Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015. https://doi.org/10.1002/cpa.21552.","mla":"Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics, vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552.","short":"T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884.","ista":"Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 68(10), 1845–1884.","apa":"Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552","ieee":"T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015.","ama":"Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552"},"date_published":"2015-10-01T00:00:00Z","scopus_import":1,"day":"01","publication_status":"published","publisher":"Wiley","department":[{"_id":"RoSe"}],"year":"2015","date_created":"2018-12-11T11:52:48Z","date_updated":"2021-01-12T06:51:41Z","volume":68,"author":[{"full_name":"Chen, Thomas","first_name":"Thomas","last_name":"Chen"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"first_name":"Nataša","last_name":"Pavlović","full_name":"Pavlović, Nataša"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5598","quality_controlled":"1","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3168"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/cpa.21552","month":"10"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:45:02Z","publist_id":"5591","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Elsevier","year":"2015","date_updated":"2021-01-12T06:51:44Z","date_created":"2018-12-11T11:52:50Z","volume":311,"author":[{"full_name":"Brenes, Oscar","last_name":"Brenes","first_name":"Oscar"},{"full_name":"Vandael, David H","last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emilio","last_name":"Carbone","full_name":"Carbone, Emilio"},{"full_name":"Montarolo, Pier","first_name":"Pier","last_name":"Montarolo"},{"full_name":"Ghirardi, Mirella","last_name":"Ghirardi","first_name":"Mirella"}],"month":"12","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.neuroscience.2015.10.046","type":"journal_article","abstract":[{"text":"Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs.","lang":"eng"}],"status":"public","ddc":["570"],"title":"Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons","intvolume":" 311","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1580","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"7849","date_created":"2020-05-15T06:50:20Z","date_updated":"2020-07-14T12:45:02Z","checksum":"af2c4c994718c7be417eba0dc746aac9","file_name":"2015_Neuroscience_Brenes.pdf","access_level":"open_access","content_type":"application/pdf","file_size":5563015,"creator":"dernst"}],"scopus_import":1,"day":"17","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"430 - 443","publication":"Neuroscience","citation":{"chicago":"Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience. Elsevier, 2015. https://doi.org/10.1016/j.neuroscience.2015.10.046.","mla":"Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience, vol. 311, Elsevier, 2015, pp. 430–43, doi:10.1016/j.neuroscience.2015.10.046.","short":"O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience 311 (2015) 430–443.","ista":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 311, 430–443.","apa":"Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., & Ghirardi, M. (2015). Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2015.10.046","ieee":"O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons,” Neuroscience, vol. 311. Elsevier, pp. 430–443, 2015.","ama":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 2015;311:430-443. doi:10.1016/j.neuroscience.2015.10.046"},"date_published":"2015-12-17T00:00:00Z"},{"publist_id":"5594","volume":112,"date_created":"2018-12-11T11:52:49Z","date_updated":"2021-01-12T06:51:43Z","author":[{"full_name":"Carvalho, Antonio","last_name":"Carvalho","first_name":"Antonio"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"},{"full_name":"Russo, Claudia","first_name":"Claudia","last_name":"Russo"},{"full_name":"Swenor, Bonnielin","last_name":"Swenor","first_name":"Bonnielin"},{"last_name":"Clark","first_name":"Andrew","full_name":"Clark, Andrew"}],"publisher":"National Academy of Sciences","department":[{"_id":"BeVi"}],"publication_status":"published","pmid":1,"year":"2015","acknowledgement":"This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript.","month":"10","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1516543112","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/","open_access":"1"}],"external_id":{"pmid":["26385968"]},"issue":"40","abstract":[{"lang":"eng","text":"Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 112","status":"public","title":"Birth of a new gene on the Y chromosome of Drosophila melanogaster","_id":"1577","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"06","scopus_import":1,"date_published":"2015-10-06T00:00:00Z","page":"12450 - 12455","article_type":"original","citation":{"chicago":"Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112.","short":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.","mla":"Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:10.1073/pnas.1516543112.","apa":"Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1516543112","ieee":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015.","ista":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.","ama":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455. doi:10.1073/pnas.1516543112"},"publication":"PNAS"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1579","intvolume":" 367","status":"public","title":"Galois groups of Schubert problems of lines are at least alternating","oa_version":"Preprint","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality."}],"citation":{"ista":"Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 367(6), 4183–4206.","apa":"Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8","ieee":"C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of Schubert problems of lines are at least alternating,” Transactions of the American Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp. 4183–4206, 2015.","ama":"Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8","chicago":"Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/S0002-9947-2014-06192-8.","mla":"Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society, vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8.","short":"C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American Mathematical Society 367 (2015) 4183–4206."},"publication":"Transactions of the American Mathematical Society","page":"4183 - 4206","date_published":"2015-06-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"01","year":"2015","acknowledgement":"This research was supported in part by NSF grant DMS-915211 and the Institut Mittag-Leffler.\r\n","department":[{"_id":"CaUh"}],"publisher":"American Mathematical Society","publication_status":"published","author":[{"full_name":"Brooks, Christopher","first_name":"Christopher","last_name":"Brooks"},{"full_name":"Martin Del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","first_name":"Abraham","last_name":"Martin Del Campo Sanchez"},{"full_name":"Sottile, Frank","first_name":"Frank","last_name":"Sottile"}],"volume":367,"date_updated":"2021-01-12T06:51:43Z","date_created":"2018-12-11T11:52:50Z","publist_id":"5592","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.4280"}],"oa":1,"quality_controlled":"1","doi":"10.1090/S0002-9947-2014-06192-8","language":[{"iso":"eng"}],"month":"06"},{"quality_controlled":"1","page":"507 - 519","publication":"Computational Geometry","citation":{"ama":"Cao T, Edelsbrunner H, Tan T. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 2015;48(7):507-519. doi:10.1016/j.comgeo.2015.04.001","ista":"Cao T, Edelsbrunner H, Tan T. 2015. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 48(7), 507–519.","ieee":"T. Cao, H. Edelsbrunner, and T. Tan, “Triangulations from topologically correct digital Voronoi diagrams,” Computational Geometry, vol. 48, no. 7. Elsevier, pp. 507–519, 2015.","apa":"Cao, T., Edelsbrunner, H., & Tan, T. (2015). Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. Elsevier. https://doi.org/10.1016/j.comgeo.2015.04.001","mla":"Cao, Thanhtung, et al. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry, vol. 48, no. 7, Elsevier, 2015, pp. 507–19, doi:10.1016/j.comgeo.2015.04.001.","short":"T. Cao, H. Edelsbrunner, T. Tan, Computational Geometry 48 (2015) 507–519.","chicago":"Cao, Thanhtung, Herbert Edelsbrunner, and Tiowseng Tan. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.04.001."},"language":[{"iso":"eng"}],"doi":"10.1016/j.comgeo.2015.04.001","date_published":"2015-08-01T00:00:00Z","scopus_import":1,"month":"08","day":"01","status":"public","publication_status":"published","title":"Triangulations from topologically correct digital Voronoi diagrams","department":[{"_id":"HeEd"}],"publisher":"Elsevier","intvolume":" 48","_id":"1578","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The research of the second author is partially supported by NSF under grant DBI-0820624 and by DARPA under grants HR011-05-1-0057 and HR0011-09-006\r\n","date_updated":"2021-01-12T06:51:43Z","date_created":"2018-12-11T11:52:49Z","oa_version":"None","volume":48,"author":[{"full_name":"Cao, Thanhtung","last_name":"Cao","first_name":"Thanhtung"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"first_name":"Tiowseng","last_name":"Tan","full_name":"Tan, Tiowseng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We prove that the dual of the digital Voronoi diagram constructed by flooding the plane from the data points gives a geometrically and topologically correct dual triangulation. This provides the proof of correctness for recently developed GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional Delaunay triangulations."}],"issue":"7","publist_id":"5593"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2015.04.009","date_published":"2015-04-23T00:00:00Z","quality_controlled":"1","page":"431 - 432","publication":"Cell","citation":{"ama":"Bollenbach MT, Heisenberg C-PJ. Gradients are shaping up. Cell. 2015;161(3):431-432. doi:10.1016/j.cell.2015.04.009","ieee":"M. T. Bollenbach and C.-P. J. Heisenberg, “Gradients are shaping up,” Cell, vol. 161, no. 3. Cell Press, pp. 431–432, 2015.","apa":"Bollenbach, M. T., & Heisenberg, C.-P. J. (2015). Gradients are shaping up. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.04.009","ista":"Bollenbach MT, Heisenberg C-PJ. 2015. Gradients are shaping up. Cell. 161(3), 431–432.","short":"M.T. Bollenbach, C.-P.J. Heisenberg, Cell 161 (2015) 431–432.","mla":"Bollenbach, Mark Tobias, and Carl-Philipp J. Heisenberg. “Gradients Are Shaping Up.” Cell, vol. 161, no. 3, Cell Press, 2015, pp. 431–32, doi:10.1016/j.cell.2015.04.009.","chicago":"Bollenbach, Mark Tobias, and Carl-Philipp J Heisenberg. “Gradients Are Shaping Up.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.04.009."},"month":"04","day":"23","article_processing_charge":"No","scopus_import":"1","date_updated":"2022-08-25T13:56:10Z","date_created":"2018-12-11T11:52:50Z","oa_version":"None","volume":161,"author":[{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"publication_status":"published","title":"Gradients are shaping up","status":"public","intvolume":" 161","department":[{"_id":"ToBo"},{"_id":"CaHe"}],"publisher":"Cell Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1581","year":"2015","abstract":[{"text":"In animal embryos, morphogen gradients determine tissue patterning and morphogenesis. Shyer et al. provide evidence that, during vertebrate gut formation, tissue folding generates graded activity of signals required for subsequent steps of gut growth and differentiation, thereby revealing an intriguing link between tissue morphogenesis and morphogen gradient formation.","lang":"eng"}],"issue":"3","publist_id":"5590","type":"journal_article"},{"pubrep_id":"472","oa_version":"Published Version","file":[{"creator":"system","file_size":2771236,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-472-v1+1_srep18589.pdf","checksum":"927e151674347661ce36eae2818dafdc","date_updated":"2020-07-14T12:45:03Z","date_created":"2018-12-12T10:13:49Z","file_id":"5036","relation":"main_file"}],"_id":"1589","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","ddc":["530","540"],"title":"Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system","status":"public","abstract":[{"text":"We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices.","lang":"eng"}],"type":"journal_article","date_published":"2015-12-21T00:00:00Z","citation":{"chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep18589.","mla":"Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports, vol. 5, 18589, Nature Publishing Group, 2015, doi:10.1038/srep18589.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","ista":"Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589.","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep18589","ama":"Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 2015;5. doi:10.1038/srep18589"},"publication":"Scientific Reports","article_type":"original","has_accepted_license":"1","day":"21","scopus_import":1,"author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","first_name":"Sebastian","last_name":"Altmeyer","full_name":"Altmeyer, Sebastian"},{"first_name":"Younghae","last_name":"Do","full_name":"Do, Younghae"},{"last_name":"Lai","first_name":"Ying","full_name":"Lai, Ying"}],"volume":5,"date_created":"2018-12-11T11:52:53Z","date_updated":"2021-01-12T06:51:48Z","year":"2015","publisher":"Nature Publishing Group","department":[{"_id":"BjHo"}],"publication_status":"published","publist_id":"5582","file_date_updated":"2020-07-14T12:45:03Z","article_number":"18589","doi":"10.1038/srep18589","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"12"},{"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"mla":"Biedl, Therese, et al. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 5, Elsevier, 2015, pp. 429–42, doi:10.1016/j.comgeo.2015.01.004.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 429–442.","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.01.004.","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(5):429-442. doi:10.1016/j.comgeo.2015.01.004","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(5), 429–442.","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Reprint of: Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 5. Elsevier, pp. 429–442, 2015.","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2015.01.004"},"publication":"Computational Geometry: Theory and Applications","page":"429 - 442","date_published":"2015-07-01T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights.","lang":"eng"}],"_id":"1584","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 48","title":"Reprint of: Weighted straight skeletons in the plane","status":"public","ddc":["000"],"pubrep_id":"475","file":[{"file_size":508379,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-475-v1+1_1-s2.0-S092577211500005X-main.pdf","checksum":"5b33719a86f7f4c8e5dc62c1b6893f49","date_updated":"2020-07-14T12:45:03Z","date_created":"2018-12-12T10:17:36Z","relation":"main_file","file_id":"5292"}],"oa_version":"Published Version","month":"07","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1016/j.comgeo.2015.01.004","language":[{"iso":"eng"}],"publist_id":"5587","file_date_updated":"2020-07-14T12:45:03Z","year":"2015","publisher":"Elsevier","department":[{"_id":"HeEd"}],"publication_status":"published","related_material":{"record":[{"relation":"other","status":"public","id":"1582"}]},"author":[{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"full_name":"Huber, Stefan","first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814"},{"full_name":"Kaaser, Dominik","last_name":"Kaaser","first_name":"Dominik"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"}],"volume":48,"date_updated":"2023-02-23T10:05:22Z","date_created":"2018-12-11T11:52:51Z"},{"month":"02","doi":"10.1016/j.comgeo.2014.08.006","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","publist_id":"5589","file_date_updated":"2020-07-14T12:45:02Z","related_material":{"record":[{"id":"1584","relation":"other","status":"public"}]},"author":[{"full_name":"Biedl, Therese","last_name":"Biedl","first_name":"Therese"},{"full_name":"Held, Martin","first_name":"Martin","last_name":"Held"},{"orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87","last_name":"Huber","first_name":"Stefan","full_name":"Huber, Stefan"},{"last_name":"Kaaser","first_name":"Dominik","full_name":"Kaaser, Dominik"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"}],"volume":48,"date_created":"2018-12-11T11:52:51Z","date_updated":"2023-02-23T10:05:27Z","year":"2015","department":[{"_id":"HeEd"}],"publisher":"Elsevier","publication_status":"published","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2015-02-01T00:00:00Z","citation":{"ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 2. Elsevier, pp. 120–133, 2015.","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.006","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(2), 120–133.","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(2):120-133. doi:10.1016/j.comgeo.2014.08.006","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.006.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 120–133.","mla":"Biedl, Therese, et al. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 2, Elsevier, 2015, pp. 120–33, doi:10.1016/j.comgeo.2014.08.006."},"publication":"Computational Geometry: Theory and Applications","page":"120 - 133","issue":"2","abstract":[{"lang":"eng","text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights."}],"type":"journal_article","pubrep_id":"474","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":505987,"access_level":"open_access","file_name":"IST-2016-474-v1+1_1-s2.0-S0925772114000807-main.pdf","checksum":"c1ef67f6ec925e12f73a96b8fe285ab4","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:16:28Z","file_id":"5215","relation":"main_file"}],"_id":"1582","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 48","ddc":["000"],"title":"Weighted straight skeletons in the plane","status":"public"},{"publication":"Information Processing Letters","citation":{"chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.021.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Information Processing Letters 115 (2015) 243–247.","mla":"Biedl, Therese, et al. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters, vol. 115, no. 2, Elsevier, 2015, pp. 243–47, doi:10.1016/j.ipl.2014.09.021.","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.021","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “A simple algorithm for computing positively weighted straight skeletons of monotone polygons,” Information Processing Letters, vol. 115, no. 2. Elsevier, pp. 243–247, 2015.","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 115(2), 243–247.","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 2015;115(2):243-247. doi:10.1016/j.ipl.2014.09.021"},"page":"243 - 247","date_published":"2015-02-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1583","title":"A simple algorithm for computing positively weighted straight skeletons of monotone polygons","status":"public","ddc":["000"],"intvolume":" 115","pubrep_id":"473","oa_version":"Published Version","file":[{"file_name":"IST-2016-473-v1+1_1-s2.0-S0020019014001987-main.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":270137,"file_id":"5367","relation":"main_file","date_created":"2018-12-12T10:18:45Z","date_updated":"2020-07-14T12:45:03Z","checksum":"2779a648610c9b5c86d0b51a62816d23"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We study the characteristics of straight skeletons of monotone polygonal chains and use them to devise an algorithm for computing positively weighted straight skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space, where n denotes the number of vertices of the polygon."}],"issue":"2","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1016/j.ipl.2014.09.021","language":[{"iso":"eng"}],"month":"02","year":"2015","publication_status":"published","publisher":"Elsevier","department":[{"_id":"HeEd"}],"author":[{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"first_name":"Martin","last_name":"Held","full_name":"Held, Martin"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","first_name":"Stefan","last_name":"Huber","full_name":"Huber, Stefan"},{"first_name":"Dominik","last_name":"Kaaser","full_name":"Kaaser, Dominik"},{"last_name":"Palfrader","first_name":"Peter","full_name":"Palfrader, Peter"}],"date_updated":"2021-01-12T06:51:45Z","date_created":"2018-12-11T11:52:51Z","volume":115,"file_date_updated":"2020-07-14T12:45:03Z","publist_id":"5588"},{"date_published":"2015-12-31T00:00:00Z","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","citation":{"ama":"Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 2015;92(6). doi:10.1103/PhysRevA.92.062506","apa":"Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R., & Santos, J. (2015). Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.92.062506","ieee":"P. Amaro et al., “Quantum interference shifts in laser spectroscopy with elliptical polarization,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6. American Physical Society, 2015.","ista":"Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J. 2015. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 92(6), 062506.","short":"P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 92 (2015).","mla":"Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:10.1103/PhysRevA.92.062506.","chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato, Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.062506."},"article_type":"original","day":"31","article_processing_charge":"No","scopus_import":1,"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1587","title":"Quantum interference shifts in laser spectroscopy with elliptical polarization","status":"public","intvolume":" 92","abstract":[{"text":"We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme.","lang":"eng"}],"issue":"6","type":"journal_article","doi":"10.1103/PhysRevA.92.062506","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1511.03585","open_access":"1"}],"external_id":{"arxiv":["1511.03585"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"month":"12","author":[{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"first_name":"Filippo","last_name":"Fratini","full_name":"Fratini, Filippo"},{"id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","first_name":"Laleh","full_name":"Safari, Laleh"},{"full_name":"Antognini, Aldo","last_name":"Antognini","first_name":"Aldo"},{"full_name":"Indelicato, Paul","last_name":"Indelicato","first_name":"Paul"},{"full_name":"Pohl, Randolf","first_name":"Randolf","last_name":"Pohl"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"}],"date_created":"2018-12-11T11:52:53Z","date_updated":"2021-01-12T06:51:47Z","volume":92,"year":"2015","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"ec_funded":1,"publist_id":"5584","article_number":"062506"},{"_id":"1588","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","intvolume":" 92","status":"public","publication_status":"published","title":"Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows","author":[{"full_name":"Altmeyer, Sebastian","last_name":"Altmeyer","first_name":"Sebastian","orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Do","first_name":"Younghae","full_name":"Do, Younghae"},{"full_name":"Lai, Ying","last_name":"Lai","first_name":"Ying"}],"volume":92,"oa_version":"None","date_updated":"2021-01-12T06:51:47Z","date_created":"2018-12-11T11:52:53Z","type":"journal_article","article_number":"053018","publist_id":"5583","issue":"5","abstract":[{"text":"We investigate the Taylor-Couette system where the radius ratio is close to unity. Systematically increasing the Reynolds number, we observe a number of previously known transitions, such as one from the classical Taylor vortex flow (TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence. Prior to the onset of turbulence, we observe intermittent bursting patterns of localized turbulent patches, confirming the experimentally observed pattern of very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds number larger than that for the onset of VSWBs, a new type of intermittently bursting behavior emerges: patterns of azimuthally closed rings of various orders. We call them ring-bursting patterns, which surround the cylinder completely but remain localized and separated in the axial direction through nonturbulent wavy structures. We employ a number of quantitative measures including the cross-flow energy to characterize the ring-bursting patterns and to distinguish them from the background flow. These patterns are interesting because they do not occur in the wide-gap Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly deserves further attention to gain deeper insights into complex flow dynamics in fluids.","lang":"eng"}],"citation":{"ama":"Altmeyer S, Do Y, Lai Y. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 2015;92(5). doi:10.1103/PhysRevE.92.053018","ista":"Altmeyer S, Do Y, Lai Y. 2015. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 92(5), 053018.","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.92.053018","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows,” Physical Review E, vol. 92, no. 5. American Physical Society, 2015.","mla":"Altmeyer, Sebastian, et al. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E, vol. 92, no. 5, 053018, American Physical Society, 2015, doi:10.1103/PhysRevE.92.053018.","short":"S. Altmeyer, Y. Do, Y. Lai, Physical Review E 92 (2015).","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.92.053018."},"publication":"Physical Review E","quality_controlled":"1","doi":"10.1103/PhysRevE.92.053018","date_published":"2015-11-24T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"month":"11","day":"24"},{"type":"journal_article","abstract":[{"text":"Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass.","lang":"eng"}],"issue":"6","publist_id":"5585","_id":"1586","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2015","publication_status":"published","title":"Metabolic engineering of cyanobacteria for the synthesis of commodity products","status":"public","department":[{"_id":"ToBo"}],"intvolume":" 33","publisher":"Elsevier","author":[{"full_name":"Angermayr, Andreas","first_name":"Andreas","last_name":"Angermayr","id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223"},{"first_name":"Aleix","last_name":"Gorchs","full_name":"Gorchs, Aleix"},{"first_name":"Klaas","last_name":"Hellingwerf","full_name":"Hellingwerf, Klaas"}],"date_created":"2018-12-11T11:52:52Z","date_updated":"2021-01-12T06:51:46Z","volume":33,"oa_version":"None","scopus_import":1,"month":"06","day":"01","publication":"Trends in Biotechnology","citation":{"ista":"Angermayr A, Gorchs A, Hellingwerf K. 2015. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 33(6), 352–361.","ieee":"A. Angermayr, A. Gorchs, and K. Hellingwerf, “Metabolic engineering of cyanobacteria for the synthesis of commodity products,” Trends in Biotechnology, vol. 33, no. 6. Elsevier, pp. 352–361, 2015.","apa":"Angermayr, A., Gorchs, A., & Hellingwerf, K. (2015). Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. Elsevier. https://doi.org/10.1016/j.tibtech.2015.03.009","ama":"Angermayr A, Gorchs A, Hellingwerf K. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 2015;33(6):352-361. doi:10.1016/j.tibtech.2015.03.009","chicago":"Angermayr, Andreas, Aleix Gorchs, and Klaas Hellingwerf. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology. Elsevier, 2015. https://doi.org/10.1016/j.tibtech.2015.03.009.","mla":"Angermayr, Andreas, et al. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology, vol. 33, no. 6, Elsevier, 2015, pp. 352–61, doi:10.1016/j.tibtech.2015.03.009.","short":"A. Angermayr, A. Gorchs, K. Hellingwerf, Trends in Biotechnology 33 (2015) 352–361."},"quality_controlled":"1","page":"352 - 361","doi":"10.1016/j.tibtech.2015.03.009","date_published":"2015-06-01T00:00:00Z","language":[{"iso":"eng"}]},{"author":[{"last_name":"Bao","first_name":"Zhigang","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang"},{"first_name":"Guangming","last_name":"Pan","full_name":"Pan, Guangming"},{"last_name":"Zhou","first_name":"Wang","full_name":"Zhou, Wang"}],"oa_version":"None","volume":61,"date_created":"2018-12-11T11:52:52Z","date_updated":"2021-01-12T06:51:46Z","acknowledgement":"G. Pan was supported by MOE Tier 2 under Grant 2014-T2-2-060 and in part by Tier 1 under Grant RG25/14 through the Nanyang Technological University, Singapore. W. Zhou was supported by the National University of Singapore, Singapore, under Grant R-155-000-131-112.\r\n","_id":"1585","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","intvolume":" 61","department":[{"_id":"LaEr"}],"publisher":"IEEE","publication_status":"published","title":"Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices","status":"public","issue":"6","publist_id":"5586","abstract":[{"text":"In this paper, we consider the fluctuation of mutual information statistics of a multiple input multiple output channel communication systems without assuming that the entries of the channel matrix have zero pseudovariance. To this end, we also establish a central limit theorem of the linear spectral statistics for sample covariance matrices under general moment conditions by removing the restrictions imposed on the second moment and fourth moment on the matrix entries in Bai and Silverstein (2004).","lang":"eng"}],"type":"journal_article","doi":"10.1109/TIT.2015.2421894","date_published":"2015-06-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Bao Z, Pan G, Zhou W. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 2015;61(6):3413-3426. doi:10.1109/TIT.2015.2421894","ieee":"Z. Bao, G. Pan, and W. Zhou, “Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices,” IEEE Transactions on Information Theory, vol. 61, no. 6. IEEE, pp. 3413–3426, 2015.","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2015.2421894","ista":"Bao Z, Pan G, Zhou W. 2015. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 61(6), 3413–3426.","short":"Z. Bao, G. Pan, W. Zhou, IEEE Transactions on Information Theory 61 (2015) 3413–3426.","mla":"Bao, Zhigang, et al. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory, vol. 61, no. 6, IEEE, 2015, pp. 3413–26, doi:10.1109/TIT.2015.2421894.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory. IEEE, 2015. https://doi.org/10.1109/TIT.2015.2421894."},"publication":"IEEE Transactions on Information Theory","page":"3413 - 3426","quality_controlled":"1","month":"06","day":"01","scopus_import":1},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fpls.2015.00218","month":"04","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Frontiers Research Foundation","year":"2015","date_created":"2018-12-11T11:52:55Z","date_updated":"2021-01-12T06:51:50Z","volume":6,"author":[{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"full_name":"Smet, Dajo","last_name":"Smet","first_name":"Dajo"},{"id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu","first_name":"Qiang","full_name":"Zhu, Qiang"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"file_date_updated":"2020-07-14T12:45:03Z","ec_funded":1,"publist_id":"5578","publication":"Frontiers in Plant Science","citation":{"chicago":"Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fpls.2015.00218.","short":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers in Plant Science 6 (2015).","mla":"Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science, vol. 6, no. 4, Frontiers Research Foundation, 2015, doi:10.3389/fpls.2015.00218.","apa":"Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., & Benková, E. (2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.00218","ieee":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies of seedlings to overcome their sessile nature: Auxin in mobility control,” Frontiers in Plant Science, vol. 6, no. 4. Frontiers Research Foundation, 2015.","ista":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 6(4).","ama":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 2015;6(4). doi:10.3389/fpls.2015.00218"},"date_published":"2015-04-14T00:00:00Z","scopus_import":1,"day":"14","has_accepted_license":"1","title":"Strategies of seedlings to overcome their sessile nature: Auxin in mobility control","status":"public","ddc":["570"],"intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1593","file":[{"access_level":"open_access","file_name":"IST-2016-471-v1+1_fpls-06-00218.pdf","creator":"system","file_size":965690,"content_type":"application/pdf","file_id":"5142","relation":"main_file","checksum":"c454d642e18dfa86820b97a86cd6d3cc","date_updated":"2020-07-14T12:45:03Z","date_created":"2018-12-12T10:15:23Z"}],"oa_version":"Published Version","pubrep_id":"471","type":"journal_article","abstract":[{"text":"Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.","lang":"eng"}],"issue":"4"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-27261-0_9","conference":{"name":"GD: Graph Drawing and Network Visualization","start_date":"2015-09-24","location":"Los Angeles, CA, USA","end_date":"2015-09-26"},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","oa":1,"month":"11","volume":9411,"date_created":"2018-12-11T11:52:55Z","date_updated":"2023-02-21T16:23:36Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"1113"},{"status":"public","relation":"later_version","id":"1164"}]},"author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav"},{"full_name":"Pelsmajer, Michael","first_name":"Michael","last_name":"Pelsmajer"},{"full_name":"Schaefer, Marcus","first_name":"Marcus","last_name":"Schaefer"}],"publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].","year":"2015","publist_id":"5576","ec_funded":1,"file_date_updated":"2020-07-14T12:45:03Z","date_published":"2015-11-27T00:00:00Z","page":"99 - 110","citation":{"ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA, 2015, vol. 9411, pp. 99–110.","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2015). Hanani-Tutte for radial planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA: Springer. https://doi.org/10.1007/978-3-319-27261-0_9","ista":"Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol 9411. Springer; 2015:99-110. doi:10.1007/978-3-319-27261-0_9","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity,” 9411:99–110. Springer, 2015. https://doi.org/10.1007/978-3-319-27261-0_9.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110.","mla":"Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity. Vol. 9411, Springer, 2015, pp. 99–110, doi:10.1007/978-3-319-27261-0_9."},"has_accepted_license":"1","day":"27","scopus_import":1,"file":[{"creator":"system","file_size":330135,"content_type":"application/pdf","file_name":"IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:03Z","date_created":"2018-12-12T10:08:36Z","checksum":"685f91bd077a951ba067d42cce75409e","file_id":"4697","relation":"main_file"}],"oa_version":"Submitted Version","pubrep_id":"594","intvolume":" 9411","ddc":["510"],"status":"public","title":"Hanani-Tutte for radial planarity","_id":"1595","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth."}],"alternative_title":["LNCS"],"type":"conference"},{"oa_version":"Preprint","intvolume":" 9411","status":"public","title":"Representing directed trees as straight skeletons","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1590","abstract":[{"text":"The straight skeleton of a polygon is the geometric graph obtained by tracing the vertices during a mitered offsetting process. It is known that the straight skeleton of a simple polygon is a tree, and one can naturally derive directions on the edges of the tree from the propagation of the shrinking process. In this paper, we ask the reverse question: Given a tree with directed edges, can it be the straight skeleton of a polygon? And if so, can we find a suitable simple polygon? We answer these questions for all directed trees where the order of edges around each node is fixed.","lang":"eng"}],"alternative_title":["LNCS"],"type":"book_chapter","date_published":"2015-11-27T00:00:00Z","page":"335 - 347","citation":{"ama":"Aichholzer O, Biedl T, Hackl T, et al. Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:335-347. doi:10.1007/978-3-319-27261-0_28","ieee":"O. Aichholzer et al., “Representing directed trees as straight skeletons,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–347.","apa":"Aichholzer, O., Biedl, T., Hackl, T., Held, M., Huber, S., Palfrader, P., & Vogtenhuber, B. (2015). Representing directed trees as straight skeletons. In Graph Drawing and Network Visualization (Vol. 9411, pp. 335–347). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_28","ista":"Aichholzer O, Biedl T, Hackl T, Held M, Huber S, Palfrader P, Vogtenhuber B. 2015.Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 335–347.","short":"O. Aichholzer, T. Biedl, T. Hackl, M. Held, S. Huber, P. Palfrader, B. Vogtenhuber, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 335–347.","mla":"Aichholzer, Oswin, et al. “Representing Directed Trees as Straight Skeletons.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–47, doi:10.1007/978-3-319-27261-0_28.","chicago":"Aichholzer, Oswin, Therese Biedl, Thomas Hackl, Martin Held, Stefan Huber, Peter Palfrader, and Birgit Vogtenhuber. “Representing Directed Trees as Straight Skeletons.” In Graph Drawing and Network Visualization, 9411:335–47. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_28."},"publication":"Graph Drawing and Network Visualization","article_processing_charge":"No","day":"27","scopus_import":"1","volume":9411,"date_updated":"2022-01-28T09:10:37Z","date_created":"2018-12-11T11:52:54Z","author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"last_name":"Hackl","first_name":"Thomas","full_name":"Hackl, Thomas"},{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan"},{"last_name":"Palfrader","first_name":"Peter","full_name":"Palfrader, Peter"},{"first_name":"Birgit","last_name":"Vogtenhuber","full_name":"Vogtenhuber, Birgit"}],"department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","year":"2015","publist_id":"5581","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-27261-0_28","conference":{"name":"GD: International Symposium on Graph Drawing","end_date":"2015-09-26","start_date":"2015-09-24","location":"Los Angeles, CA, United States"},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1508.01076","open_access":"1"}],"publication_identifier":{"eisbn":["978-3-319-27261-0"],"isbn":["978-3-319-27260-3"]},"month":"11"},{"month":"11","conference":{"name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning","location":"Suva, Fiji","start_date":"2015-11-24","end_date":"2015-11-28"},"doi":"10.1007/978-3-662-48899-7_12","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"publist_id":"5577","ec_funded":1,"author":[{"last_name":"Forejt","first_name":"Vojtěch","full_name":"Forejt, Vojtěch"},{"full_name":"Krčál, Jan","last_name":"Krčál","first_name":"Jan"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan"}],"date_updated":"2021-01-12T06:51:50Z","date_created":"2018-12-11T11:52:55Z","volume":9450,"acknowledgement":"This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the Czech Science Foundation under grant agreement P202/12/G061, by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the CDZ project 1023 (CAP), by the CAS/SAFEA International Partnership Program for Creative Research Teams, by the EPSRC grant EP/M023656/1, by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734, by the Austrian Science Fund (FWF) S11407-N23 (RiSE/SHiNE), and by the ERC Start Grant (279307: Graph Games).\r\n","year":"2015","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"day":"22","scopus_import":1,"date_published":"2015-11-22T00:00:00Z","citation":{"mla":"Forejt, Vojtěch, et al. Controller Synthesis for MDPs and Frequency LTL\\GU. Vol. 9450, Springer, 2015, pp. 162–77, doi:10.1007/978-3-662-48899-7_12.","short":"V. Forejt, J. Krčál, J. Kretinsky, in:, Springer, 2015, pp. 162–177.","chicago":"Forejt, Vojtěch, Jan Krčál, and Jan Kretinsky. “Controller Synthesis for MDPs and Frequency LTL\\GU,” 9450:162–77. Springer, 2015. https://doi.org/10.1007/978-3-662-48899-7_12.","ama":"Forejt V, Krčál J, Kretinsky J. Controller synthesis for MDPs and frequency LTL\\GU. In: Vol 9450. Springer; 2015:162-177. doi:10.1007/978-3-662-48899-7_12","ista":"Forejt V, Krčál J, Kretinsky J. 2015. Controller synthesis for MDPs and frequency LTL\\GU. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 9450, 162–177.","apa":"Forejt, V., Krčál, J., & Kretinsky, J. (2015). Controller synthesis for MDPs and frequency LTL\\GU (Vol. 9450, pp. 162–177). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji: Springer. https://doi.org/10.1007/978-3-662-48899-7_12","ieee":"V. Forejt, J. Krčál, and J. Kretinsky, “Controller synthesis for MDPs and frequency LTL\\GU,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji, 2015, vol. 9450, pp. 162–177."},"page":"162 - 177","abstract":[{"text":"Quantitative extensions of temporal logics have recently attracted significant attention. In this work, we study frequency LTL (fLTL), an extension of LTL which allows to speak about frequencies of events along an execution. Such an extension is particularly useful for probabilistic systems that often cannot fulfil strict qualitative guarantees on the behaviour. It has been recently shown that controller synthesis for Markov decision processes and fLTL is decidable when all the bounds on frequencies are 1. As a step towards a complete quantitative solution, we show that the problem is decidable for the fragment fLTL\\GU, where U does not occur in the scope of G (but still F can). Our solution is based on a novel translation of such quantitative formulae into equivalent deterministic automata.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1594","title":"Controller synthesis for MDPs and frequency LTL\\GU","status":"public","intvolume":" 9450"},{"oa":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","doi":"10.1007/978-3-319-27261-0_31","conference":{"location":"Los Angeles, CA, United States","start_date":"2015-09-24","end_date":"2015-09-26","name":"GD: Graph Drawing and Network Visualization"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-319-27260-3"]},"month":"11","year":"2015","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","author":[{"first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"first_name":"Radoš","last_name":"Radoičić","full_name":"Radoičić, Radoš"}],"volume":9411,"date_created":"2018-12-11T11:52:56Z","date_updated":"2022-01-28T09:20:50Z","ec_funded":1,"publist_id":"5575","file_date_updated":"2020-07-14T12:45:04Z","citation":{"short":"R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 373–379.","mla":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–79, doi:10.1007/978-3-319-27261-0_31.","chicago":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” In Graph Drawing and Network Visualization, 9411:373–79. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_31.","ama":"Fulek R, Radoičić R. Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:373-379. doi:10.1007/978-3-319-27261-0_31","ieee":"R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in three dimensions,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–379.","apa":"Fulek, R., & Radoičić, R. (2015). Vertical visibility among parallel polygons in three dimensions. In Graph Drawing and Network Visualization (Vol. 9411, pp. 373–379). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_31","ista":"Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 373–379."},"publication":"Graph Drawing and Network Visualization","page":"373 - 379","date_published":"2015-11-27T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1596","intvolume":" 9411","title":"Vertical visibility among parallel polygons in three dimensions","ddc":["510"],"status":"public","pubrep_id":"595","file":[{"checksum":"eec04f86c5921d04f025d5791db9b965","date_updated":"2020-07-14T12:45:04Z","date_created":"2018-12-12T10:17:06Z","relation":"main_file","file_id":"5258","file_size":312992,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf"}],"oa_version":"Submitted Version","type":"book_chapter","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon in the plane with the stacking order. The collection C forms a visibility clique if for everyi < j the intersection Ci and (Ci ∩ Cj)\\⋃i<l<jCl =∅.elements that are stacked between them, i.e., We show that if C forms a visibility clique its size is bounded from above by O(k4) thereby improving the upper bound of 22k from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the size of a visibility clique for homothetes of a convex (not necessarily regular) k-gon."}]},{"doi":"10.1007/978-3-319-21690-4_31","conference":{"name":"CAV: Computer Aided Verification","start_date":"2015-07-18","location":"San Francisco, CA, United States","end_date":"2015-07-24"},"language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","month":"07","author":[{"full_name":"Babiak, Tomáš","first_name":"Tomáš","last_name":"Babiak"},{"first_name":"František","last_name":"Blahoudek","full_name":"Blahoudek, František"},{"full_name":"Duret Lutz, Alexandre","last_name":"Duret Lutz","first_name":"Alexandre"},{"last_name":"Klein","first_name":"Joachim","full_name":"Klein, Joachim"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"full_name":"Mueller, Daniel","last_name":"Mueller","first_name":"Daniel"},{"full_name":"Parker, David","last_name":"Parker","first_name":"David"},{"first_name":"Jan","last_name":"Strejček","full_name":"Strejček, Jan"}],"volume":9206,"date_created":"2018-12-11T11:52:57Z","date_updated":"2021-01-12T06:51:54Z","year":"2015","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"publist_id":"5566","file_date_updated":"2020-07-14T12:45:04Z","date_published":"2015-07-16T00:00:00Z","citation":{"ista":"Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification, LNCS, vol. 9206, 479–486.","ieee":"T. Babiak et al., “The Hanoi omega-automata format,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 479–486.","apa":"Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller, D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_31","ama":"Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format. In: Vol 9206. Springer; 2015:479-486. doi:10.1007/978-3-319-21690-4_31","chicago":"Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein, Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata Format,” 9206:479–86. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_31.","mla":"Babiak, Tomáš, et al. The Hanoi Omega-Automata Format. Vol. 9206, Springer, 2015, pp. 479–86, doi:10.1007/978-3-319-21690-4_31.","short":"T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller, D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486."},"page":"479 - 486","has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":1,"oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2015_CAV_Babiak.pdf","file_size":1651779,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7850","checksum":"5885236fa88a439baba9ac6f3e801e93","date_updated":"2020-07-14T12:45:04Z","date_created":"2020-05-15T08:38:12Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1601","intvolume":" 9206","title":"The Hanoi omega-automata format","status":"public","ddc":["000"],"abstract":[{"lang":"eng","text":"We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata."}],"type":"conference","alternative_title":["LNCS"]},{"oa_version":"Submitted Version","file":[{"creator":"dernst","file_size":1053207,"content_type":"application/pdf","file_name":"2015_LNCS_Bogomolov.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:05Z","date_created":"2020-05-15T08:43:19Z","checksum":"3aab260f3f34641d622030ba22645b3e","file_id":"7851","relation":"main_file"}],"_id":"1605","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Abstraction-based parameter synthesis for multiaffine systems","status":"public","ddc":["000"],"intvolume":" 9434","abstract":[{"text":"Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2015-11-28T00:00:00Z","citation":{"chicago":"Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,” 9434:19–35. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_2.","short":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:, Springer, 2015, pp. 19–35.","mla":"Bogomolov, Sergiy, et al. Abstraction-Based Parameter Synthesis for Multiaffine Systems. Vol. 9434, Springer, 2015, pp. 19–35, doi:10.1007/978-3-319-26287-1_2.","ieee":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu, “Abstraction-based parameter synthesis for multiaffine systems,” presented at the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.","apa":"Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., & Grosu, R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol. 9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_2","ista":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference, LNCS, vol. 9434, 19–35.","ama":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35. doi:10.1007/978-3-319-26287-1_2"},"page":"19 - 35","day":"28","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"author":[{"last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy"},{"last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"full_name":"Batt, Grégory","first_name":"Grégory","last_name":"Batt"},{"full_name":"Kong, Hui","last_name":"Kong","first_name":"Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"date_updated":"2021-01-12T06:51:56Z","date_created":"2018-12-11T11:52:59Z","volume":9434,"acknowledgement":"This work was partly supported by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS, http://www.avacs.org/).","year":"2015","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","file_date_updated":"2020-07-14T12:45:05Z","publist_id":"5561","ec_funded":1,"conference":{"name":"HVC: Haifa Verification Conference","location":"Haifa, Israel","start_date":"2015-11-17","end_date":"2015-11-19"},"doi":"10.1007/978-3-319-26287-1_2","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"month":"11"},{"_id":"1606","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Runtime verification for hybrid analysis tools","status":"public","intvolume":" 9333","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"In this paper, we present the first steps toward a runtime verification framework for monitoring hybrid and cyber-physical systems (CPS) development tools based on randomized differential testing. The development tools include hybrid systems reachability analysis tools, model-based development environments like Simulink/Stateflow (SLSF), etc. First, hybrid automaton models are randomly generated. Next, these hybrid automaton models are translated to a number of different tools (currently, SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using the HyST source transformation and translation tool. Then, the hybrid automaton models are executed in the different tools and their outputs are parsed. The final step is the differential comparison: the outputs of the different tools are compared. If the results do not agree (in the sense that an analysis or verification result from one tool does not match that of another tool, ignoring timeouts, etc.), a candidate bug is flagged and the model is saved for future analysis by the user. The process then repeats and the monitoring continues until the user terminates the process. We present preliminary results that have been useful in identifying a few bugs in the analysis methods of different development tools, and in an earlier version of HyST.","lang":"eng"}],"publication":"6th International Conference","citation":{"ista":"Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Runtime verification for hybrid analysis tools. 6th International Conference. RV: Runtime Verification, LNCS, vol. 9333, 281–286.","apa":"Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Runtime verification for hybrid analysis tools. In 6th International Conference (Vol. 9333, pp. 281–286). Vienna, Austria: Springer Nature. https://doi.org/10.1007/978-3-319-23820-3_19","ieee":"L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, “Runtime verification for hybrid analysis tools,” in 6th International Conference, Vienna, Austria, 2015, vol. 9333, pp. 281–286.","ama":"Nguyen L, Schilling C, Bogomolov S, Johnson T. Runtime verification for hybrid analysis tools. In: 6th International Conference. Vol 9333. Springer Nature; 2015:281-286. doi:10.1007/978-3-319-23820-3_19","chicago":"Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson. “Runtime Verification for Hybrid Analysis Tools.” In 6th International Conference, 9333:281–86. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-23820-3_19.","mla":"Nguyen, Luan, et al. “Runtime Verification for Hybrid Analysis Tools.” 6th International Conference, vol. 9333, Springer Nature, 2015, pp. 281–86, doi:10.1007/978-3-319-23820-3_19.","short":"L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, in:, 6th International Conference, Springer Nature, 2015, pp. 281–286."},"page":"281 - 286","date_published":"2015-11-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","year":"2015","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"author":[{"full_name":"Nguyen, Luan","last_name":"Nguyen","first_name":"Luan"},{"first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"},{"orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"first_name":"Taylor","last_name":"Johnson","full_name":"Johnson, Taylor"}],"date_updated":"2022-02-01T14:52:59Z","date_created":"2018-12-11T11:52:59Z","volume":9333,"ec_funded":1,"publist_id":"5562","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"RV: Runtime Verification","end_date":"2015-09-25","start_date":"2015-09-22","location":"Vienna, Austria"},"doi":"10.1007/978-3-319-23820-3_19","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"isbn":["978-3-319-23819-7"]}},{"ec_funded":1,"publist_id":"5557","acknowledgement":"This research was supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.","year":"2015","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"first_name":"Moshe","last_name":"Vardi","full_name":"Vardi, Moshe"}],"volume":9135,"date_updated":"2022-02-01T15:04:44Z","date_created":"2018-12-11T11:53:00Z","publication_identifier":{"isbn":["978-3-662-47665-9"]},"month":"06","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.04844"}],"oa":1,"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/978-3-662-47666-6_9","conference":{"name":"ICALP: Automata, Languages and Programming","location":"Kyoto, Japan","start_date":"2015-07-06","end_date":"2015-07-10"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound."}],"_id":"1609","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 9135","title":"The complexity of synthesis from probabilistic components","status":"public","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"20","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity of Synthesis from Probabilistic Components.” In 42nd International Colloquium, 9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9.","short":"K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 108–120.","mla":"Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic Components.” 42nd International Colloquium, vol. 9135, Springer Nature, 2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9.","ieee":"K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol. 9135, pp. 108–120.","apa":"Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis from probabilistic components. In 42nd International Colloquium (Vol. 9135, pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9","ista":"Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic components. 42nd International Colloquium. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 108–120.","ama":"Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic components. In: 42nd International Colloquium. Vol 9135. Springer Nature; 2015:108-120. doi:10.1007/978-3-662-47666-6_9"},"publication":"42nd International Colloquium","page":"108 - 120","date_published":"2015-06-20T00:00:00Z"},{"type":"journal_article","issue":"3","abstract":[{"text":"Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches.","lang":"eng"}],"intvolume":" 13","ddc":["570"],"status":"public","title":"Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1615","file":[{"content_type":"application/pdf","file_size":2314406,"creator":"system","file_name":"IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf","access_level":"open_access","date_created":"2018-12-12T10:13:23Z","date_updated":"2020-07-14T12:45:07Z","checksum":"44d30fbb543774b076b4938bd36af9d7","relation":"main_file","file_id":"5005"}],"oa_version":"Published Version","pubrep_id":"470","scopus_import":1,"has_accepted_license":"1","day":"20","page":"516 - 523","citation":{"chicago":"Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011.","short":"M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523.","mla":"Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011.","apa":"Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2015.09.011","ieee":"M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13, no. 3. Cell Press, pp. 516–523, 2015.","ista":"Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523.","ama":"Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011"},"publication":"Cell Reports","date_published":"2015-10-20T00:00:00Z","publist_id":"5551","file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"PeJo"}],"publisher":"Cell Press","publication_status":"published","acknowledgement":"This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry.","year":"2015","volume":13,"date_updated":"2021-01-12T06:52:01Z","date_created":"2018-12-11T11:53:02Z","author":[{"last_name":"Hammer","first_name":"Matthieu","full_name":"Hammer, Matthieu"},{"full_name":"Krueger Burg, Dilja","last_name":"Krueger Burg","first_name":"Dilja"},{"last_name":"Tuffy","first_name":"Liam","full_name":"Tuffy, Liam"},{"full_name":"Cooper, Benjamin","first_name":"Benjamin","last_name":"Cooper"},{"last_name":"Taschenberger","first_name":"Holger","full_name":"Taschenberger, Holger"},{"id":"3A578F32-F248-11E8-B48F-1D18A9856A87","first_name":"Sarit","last_name":"Goswami","full_name":"Goswami, Sarit"},{"first_name":"Hannelore","last_name":"Ehrenreich","full_name":"Ehrenreich, Hannelore"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"},{"full_name":"Varoqueaux, Frederique","first_name":"Frederique","last_name":"Varoqueaux"},{"full_name":"Rhee, Jeong","last_name":"Rhee","first_name":"Jeong"},{"last_name":"Brose","first_name":"Nils","full_name":"Brose, Nils"}],"month":"10","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2015.09.011"},{"file_date_updated":"2020-07-14T12:45:07Z","ec_funded":1,"publist_id":"5552","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"National Academy of Sciences","year":"2015","pmid":1,"date_created":"2018-12-11T11:53:02Z","date_updated":"2021-01-12T06:52:01Z","volume":112,"author":[{"full_name":"Strüber, Michael","first_name":"Michael","last_name":"Strüber"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"},{"last_name":"Bartos","first_name":"Marlene","full_name":"Bartos, Marlene"}],"month":"01","quality_controlled":"1","project":[{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}],"oa":1,"external_id":{"pmid":["25583495"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1412996112","type":"journal_article","abstract":[{"lang":"eng","text":"GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. "}],"issue":"4","ddc":["570"],"status":"public","title":"Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells","intvolume":" 112","_id":"1614","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1280860,"access_level":"open_access","file_name":"2015_PNAS_Strueber.pdf","checksum":"6703309a1f58493cf5a704211fb6ebed","date_created":"2019-01-17T07:52:40Z","date_updated":"2020-07-14T12:45:07Z","file_id":"5838","relation":"main_file"}],"scopus_import":1,"day":"27","has_accepted_license":"1","page":"1220 - 1225","publication":"PNAS","citation":{"chicago":"Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112.","mla":"Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112, no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112.","short":"M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.","ista":"Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 112(4), 1220–1225.","apa":"Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112","ieee":"M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells,” PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.","ama":"Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 2015;112(4):1220-1225. doi:10.1073/pnas.1412996112"},"date_published":"2015-01-27T00:00:00Z"},{"_id":"1611","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","status":"public","title":"Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction","oa_version":"Submitted Version","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue."}],"citation":{"ama":"Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 2015;24(9):1412-1422. doi:10.1002/pro.2721","apa":"Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak, H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721","ieee":"J. Whitfield et al., “Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction,” Protein Science, vol. 24, no. 9. Wiley, pp. 1412–1422, 2015.","ista":"Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.","short":"J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak, C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.","mla":"Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no. 9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721.","chicago":"Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski, Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721."},"publication":"Protein Science","page":"1412 - 1422","date_published":"2015-09-01T00:00:00Z","scopus_import":1,"day":"01","pmid":1,"year":"2015","publisher":"Wiley","department":[{"_id":"HaJa"}],"publication_status":"published","author":[{"full_name":"Whitfield, Jason","first_name":"Jason","last_name":"Whitfield"},{"full_name":"Zhang, William","first_name":"William","last_name":"Zhang"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"first_name":"Ben","last_name":"Clifton","full_name":"Clifton, Ben"},{"last_name":"Radziejewski","first_name":"Johanna","full_name":"Radziejewski, Johanna"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"volume":24,"date_updated":"2021-01-12T06:52:00Z","date_created":"2018-12-11T11:53:01Z","publist_id":"5555","oa":1,"external_id":{"pmid":["26061224"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/","open_access":"1"}],"project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1002/pro.2721","language":[{"iso":"eng"}],"month":"09"},{"month":"11","quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/srep17147","article_number":"17147","file_date_updated":"2020-07-14T12:45:07Z","publist_id":"5536","ec_funded":1,"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"year":"2015","acknowledgement":"The research was supported by the Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton foundation is gratefully acknowledged.","date_created":"2018-12-11T11:53:06Z","date_updated":"2021-01-12T06:52:05Z","volume":5,"author":[{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Ben","last_name":"Adlam","full_name":"Adlam, Ben"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"scopus_import":1,"day":"25","has_accepted_license":"1","publication":"Scientific Reports","citation":{"chicago":"Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep17147.","short":"A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5 (2015).","mla":"Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports, vol. 5, 17147, Nature Publishing Group, 2015, doi:10.1038/srep17147.","ieee":"A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation with shift updating and repulsion,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","apa":"Pavlogiannis, A., Chatterjee, K., Adlam, B., & Nowak, M. (2015). Cellular cooperation with shift updating and repulsion. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep17147","ista":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation with shift updating and repulsion. Scientific Reports. 5, 17147.","ama":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift updating and repulsion. Scientific Reports. 2015;5. doi:10.1038/srep17147"},"date_published":"2015-11-25T00:00:00Z","type":"journal_article","abstract":[{"text":"Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an extremely strong amplifier of cooperation in a one dimensional spatial model. For the shift update rule, an individual is chosen for reproduction proportional to fecundity; the offspring is placed next to the parent; a random individual dies. Subsequently, the population is rearranged (shifted) until all individual cells are again evenly spaced out. For large population size and a one dimensional population structure, the shift update rule favors cooperation for any benefit-to-cost ratio greater than one. But every attempt to generalize shift updating to higher dimensions while maintaining its strong effect has failed. The reason is that in two dimensions the clusters are fragmented by the movements caused by rearranging the cells. Here we introduce the natural phenomenon of a repulsive force between cells of different types. After a birth and death event, the cells are being rearranged minimizing the overall energy expenditure. If the repulsive force is sufficiently high, shift becomes a strong promoter of cooperation in two dimensions.","lang":"eng"}],"title":"Cellular cooperation with shift updating and repulsion","status":"public","ddc":["000"],"intvolume":" 5","_id":"1624","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:12:29Z","date_updated":"2020-07-14T12:45:07Z","checksum":"38e06d8310d2087cae5f6d4d4bfe082b","relation":"main_file","file_id":"4947","file_size":1021931,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-466-v1+1_srep17147.pdf","access_level":"open_access"}],"pubrep_id":"466"},{"issue":"1","abstract":[{"text":"Background\r\nPhotosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.\r\n","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":2914089,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-467-v1+1_s13068-015-0380-2.pdf","access_level":"open_access","date_created":"2018-12-12T10:10:11Z","date_updated":"2020-07-14T12:45:07Z","checksum":"172b0b6f4eb2e5c22b7cec1d57dc0107","relation":"main_file","file_id":"4796"}],"pubrep_id":"467","intvolume":" 8","status":"public","ddc":["570"],"title":"Single-cell screening of photosynthetic growth and lactate production by cyanobacteria","_id":"1623","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"25","scopus_import":1,"date_published":"2015-11-25T00:00:00Z","citation":{"mla":"Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels, vol. 8, no. 1, 193, BioMed Central, 2015, doi:10.1186/s13068-015-0380-2.","short":"P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E. Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015).","chicago":"Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer, Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels. BioMed Central, 2015. https://doi.org/10.1186/s13068-015-0380-2.","ama":"Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 2015;8(1). doi:10.1186/s13068-015-0380-2","ista":"Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E, Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 8(1), 193.","apa":"Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K., Hudson, E., & Joensson, H. (2015). Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. BioMed Central. https://doi.org/10.1186/s13068-015-0380-2","ieee":"P. Hammar et al., “Single-cell screening of photosynthetic growth and lactate production by cyanobacteria,” Biotechnology for Biofuels, vol. 8, no. 1. BioMed Central, 2015."},"publication":"Biotechnology for Biofuels","publist_id":"5537","file_date_updated":"2020-07-14T12:45:07Z","article_number":"193","volume":8,"date_created":"2018-12-11T11:53:05Z","date_updated":"2021-01-12T06:52:04Z","author":[{"full_name":"Hammar, Petter","first_name":"Petter","last_name":"Hammar"},{"last_name":"Angermayr","first_name":"Andreas","orcid":"0000-0001-8619-2223","id":"4677C796-F248-11E8-B48F-1D18A9856A87","full_name":"Angermayr, Andreas"},{"last_name":"Sjostrom","first_name":"Staffan","full_name":"Sjostrom, Staffan"},{"first_name":"Josefin","last_name":"Van Der Meer","full_name":"Van Der Meer, Josefin"},{"full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf","first_name":"Klaas"},{"last_name":"Hudson","first_name":"Elton","full_name":"Hudson, Elton"},{"full_name":"Joensson, Hakaan","first_name":"Hakaan","last_name":"Joensson"}],"publisher":"BioMed Central","department":[{"_id":"ToBo"}],"publication_status":"published","year":"2015","month":"11","language":[{"iso":"eng"}],"doi":"10.1186/s13068-015-0380-2","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1625","year":"2015","department":[{"_id":"BeBi"}],"intvolume":" 34","publisher":"ACM","publication_status":"published","status":"public","title":"Detailed spatio-temporal reconstruction of eyelids","author":[{"last_name":"Bermano","first_name":"Amit","full_name":"Bermano, Amit"},{"full_name":"Beeler, Thabo","last_name":"Beeler","first_name":"Thabo"},{"first_name":"Yeara","last_name":"Kozlov","full_name":"Kozlov, Yeara"},{"full_name":"Bradley, Derek","last_name":"Bradley","first_name":"Derek"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"full_name":"Gross, Markus","last_name":"Gross","first_name":"Markus"}],"oa_version":"None","volume":34,"date_created":"2018-12-11T11:53:06Z","date_updated":"2021-01-12T06:52:05Z","type":"conference","article_number":"44","publist_id":"5535","issue":"4","abstract":[{"text":"In recent years we have seen numerous improvements on 3D scanning and tracking of human faces, greatly advancing the creation of digital doubles for film and video games. However, despite the high-resolution quality of the reconstruction approaches available, current methods are unable to capture one of the most important regions of the face - the eye region. In this work we present the first method for detailed spatio-temporal reconstruction of eyelids. Tracking and reconstructing eyelids is extremely challenging, as this region exhibits very complex and unique skin deformation where skin is folded under while opening the eye. Furthermore, eyelids are often only partially visible and obstructed due to selfocclusion and eyelashes. Our approach is to combine a geometric deformation model with image data, leveraging multi-view stereo, optical flow, contour tracking and wrinkle detection from local skin appearance. Our deformation model serves as a prior that enables reconstruction of eyelids even under strong self-occlusions caused by rolling and folding skin as the eye opens and closes. The output is a person-specific, time-varying eyelid reconstruction with anatomically plausible deformations. Our high-resolution detailed eyelids couple naturally with current facial performance capture approaches. As a result, our method can largely increase the fidelity of facial capture and the creation of digital doubles.","lang":"eng"}],"citation":{"chicago":"Bermano, Amit, Thabo Beeler, Yeara Kozlov, Derek Bradley, Bernd Bickel, and Markus Gross. “Detailed Spatio-Temporal Reconstruction of Eyelids,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766924.","short":"A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, M. Gross, in:, ACM, 2015.","mla":"Bermano, Amit, et al. Detailed Spatio-Temporal Reconstruction of Eyelids. Vol. 34, no. 4, 44, ACM, 2015, doi:10.1145/2766924.","apa":"Bermano, A., Beeler, T., Kozlov, Y., Bradley, D., Bickel, B., & Gross, M. (2015). Detailed spatio-temporal reconstruction of eyelids (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766924","ieee":"A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, and M. Gross, “Detailed spatio-temporal reconstruction of eyelids,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","ista":"Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. 2015. Detailed spatio-temporal reconstruction of eyelids. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 44.","ama":"Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. Detailed spatio-temporal reconstruction of eyelids. In: Vol 34. ACM; 2015. doi:10.1145/2766924"},"quality_controlled":"1","date_published":"2015-07-27T00:00:00Z","doi":"10.1145/2766924","conference":{"location":"Los Angeles, CA, United States","start_date":"2015-08-09","end_date":"2015-08-13","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"language":[{"iso":"eng"}],"scopus_import":1,"day":"27","month":"07"},{"quality_controlled":"1","citation":{"mla":"Martin, Tobias, et al. OmniAD: Data-Driven Omni-Directional Aerodynamics. Vol. 34, no. 4, 113, ACM, 2015, doi:10.1145/2766919.","short":"T. Martin, N. Umetani, B. Bickel, in:, ACM, 2015.","chicago":"Martin, Tobias, Nobuyuki Umetani, and Bernd Bickel. “OmniAD: Data-Driven Omni-Directional Aerodynamics,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766919.","ama":"Martin T, Umetani N, Bickel B. OmniAD: Data-driven omni-directional aerodynamics. In: Vol 34. ACM; 2015. doi:10.1145/2766919","ista":"Martin T, Umetani N, Bickel B. 2015. OmniAD: Data-driven omni-directional aerodynamics. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 113.","apa":"Martin, T., Umetani, N., & Bickel, B. (2015). OmniAD: Data-driven omni-directional aerodynamics (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766919","ieee":"T. Martin, N. Umetani, and B. Bickel, “OmniAD: Data-driven omni-directional aerodynamics,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4."},"language":[{"iso":"eng"}],"date_published":"2015-07-27T00:00:00Z","doi":"10.1145/2766919","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2015-08-13","location":"Los Angeles, CA, United States","start_date":"2015-08-09"},"scopus_import":1,"month":"07","day":"27","department":[{"_id":"BeBi"}],"intvolume":" 34","publisher":"ACM","status":"public","publication_status":"published","title":"OmniAD: Data-driven omni-directional aerodynamics","year":"2015","_id":"1626","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":34,"oa_version":"None","date_updated":"2021-01-12T06:52:05Z","date_created":"2018-12-11T11:53:06Z","author":[{"last_name":"Martin","first_name":"Tobias","full_name":"Martin, Tobias"},{"full_name":"Umetani, Nobuyuki","last_name":"Umetani","first_name":"Nobuyuki"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"}],"alternative_title":["ACM Transactions on Graphics"],"type":"conference","article_number":"113","publist_id":"5532","issue":"4","abstract":[{"text":"This paper introduces "OmniAD," a novel data-driven pipeline to model and acquire the aerodynamics of three-dimensional rigid objects. Traditionally, aerodynamics are examined through elaborate wind tunnel experiments or expensive fluid dynamics computations, and are only measured for a small number of discrete wind directions. OmniAD allows the evaluation of aerodynamic forces, such as drag and lift, for any incoming wind direction using a novel representation based on spherical harmonics. Our datadriven technique acquires the aerodynamic properties of an object simply by capturing its falling motion using a single camera. Once model parameters are estimated, OmniAD enables realistic realtime simulation of rigid bodies, such as the tumbling and gliding of leaves, without simulating the surrounding air. In addition, we propose an intuitive user interface based on OmniAD to interactively design three-dimensional kites that actually fly. Various nontraditional kites were designed to demonstrate the physical validity of our model.","lang":"eng"}]},{"month":"08","doi":"10.1145/2766926","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2015-08-13","start_date":"2015-08-09","location":"Los Angeles, CA, USA"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1145/2766926","open_access":"1"}],"oa":1,"quality_controlled":"1","publist_id":"5529","article_number":"136","author":[{"full_name":"Schumacher, Christian","last_name":"Schumacher","first_name":"Christian"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"full_name":"Rys, Jan","last_name":"Rys","first_name":"Jan"},{"first_name":"Steve","last_name":"Marschner","full_name":"Marschner, Steve"},{"full_name":"Daraio, Chiara","first_name":"Chiara","last_name":"Daraio"},{"last_name":"Gross","first_name":"Markus","full_name":"Gross, Markus"}],"volume":34,"date_updated":"2021-01-12T06:52:06Z","date_created":"2018-12-11T11:53:07Z","year":"2015","department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":1,"date_published":"2015-08-01T00:00:00Z","citation":{"ista":"Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. 2015. Microstructures to control elasticity in 3D printing. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 136.","ieee":"C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, and M. Gross, “Microstructures to control elasticity in 3D printing,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.","apa":"Schumacher, C., Bickel, B., Rys, J., Marschner, S., Daraio, C., & Gross, M. (2015). Microstructures to control elasticity in 3D printing (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766926","ama":"Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. Microstructures to control elasticity in 3D printing. In: Vol 34. ACM; 2015. doi:10.1145/2766926","chicago":"Schumacher, Christian, Bernd Bickel, Jan Rys, Steve Marschner, Chiara Daraio, and Markus Gross. “Microstructures to Control Elasticity in 3D Printing,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766926.","mla":"Schumacher, Christian, et al. Microstructures to Control Elasticity in 3D Printing. Vol. 34, no. 4, 136, ACM, 2015, doi:10.1145/2766926.","short":"C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, M. Gross, in:, ACM, 2015."},"issue":"4","abstract":[{"lang":"eng","text":"We propose a method for fabricating deformable objects with spatially varying elasticity using 3D printing. Using a single, relatively stiff printer material, our method designs an assembly of smallscale microstructures that have the effect of a softer material at the object scale, with properties depending on the microstructure used in each part of the object. We build on work in the area of metamaterials, using numerical optimization to design tiled microstructures with desired properties, but with the key difference that our method designs families of related structures that can be interpolated to smoothly vary the material properties over a wide range. To create an object with spatially varying elastic properties, we tile the object's interior with microstructures drawn from these families, generating a different microstructure for each cell using an efficient algorithm to select compatible structures for neighboring cells. We show results computed for both 2D and 3D objects, validating several 2D and 3D printed structures using standard material tests as well as demonstrating various example applications."}],"type":"conference","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1628","intvolume":" 34","status":"public","title":"Microstructures to control elasticity in 3D printing"},{"abstract":[{"lang":"eng","text":"We present a computational tool for fabrication-oriented design of flexible rod meshes. Given a deformable surface and a set of deformed poses as input, our method automatically computes a printable rod mesh that, once manufactured, closely matches the input poses under the same boundary conditions. The core of our method is formed by an optimization scheme that adjusts the cross-sectional profiles of the rods and their rest centerline in order to best approximate the target deformations. This approach allows us to locally control the bending and stretching resistance of the surface with a single material, yielding high design flexibility and low fabrication cost."}],"issue":"4","publist_id":"5530","article_number":"138","type":"conference","author":[{"full_name":"Pérez, Jesús","first_name":"Jesús","last_name":"Pérez"},{"last_name":"Thomaszewski","first_name":"Bernhard","full_name":"Thomaszewski, Bernhard"},{"first_name":"Stelian","last_name":"Coros","full_name":"Coros, Stelian"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"},{"full_name":"Canabal, José","first_name":"José","last_name":"Canabal"},{"last_name":"Sumner","first_name":"Robert","full_name":"Sumner, Robert"},{"full_name":"Otaduy, Miguel","first_name":"Miguel","last_name":"Otaduy"}],"date_created":"2018-12-11T11:53:07Z","date_updated":"2021-01-12T06:52:06Z","volume":34,"oa_version":"None","_id":"1627","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by grants from the Spanish Ministry of Economy (TIN2012-35840), and the European Research Council (ERC Starting Grant no. 280135 Animetrics).","title":"Design and fabrication of flexible rod meshes","status":"public","publication_status":"published","department":[{"_id":"BeBi"}],"intvolume":" 34","publisher":"ACM","month":"07","day":"27","scopus_import":1,"conference":{"end_date":"2015-08-13","start_date":"2015-08-09","location":"Los Angeles, CA, United States","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"doi":"10.1145/2766998","date_published":"2015-07-27T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Pérez, Jesús, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, José Canabal, Robert Sumner, and Miguel Otaduy. “Design and Fabrication of Flexible Rod Meshes,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766998.","mla":"Pérez, Jesús, et al. Design and Fabrication of Flexible Rod Meshes. Vol. 34, no. 4, 138, ACM, 2015, doi:10.1145/2766998.","short":"J. Pérez, B. Thomaszewski, S. Coros, B. Bickel, J. Canabal, R. Sumner, M. Otaduy, in:, ACM, 2015.","ista":"Pérez J, Thomaszewski B, Coros S, Bickel B, Canabal J, Sumner R, Otaduy M. 2015. Design and fabrication of flexible rod meshes. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 138.","ieee":"J. Pérez et al., “Design and fabrication of flexible rod meshes,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","apa":"Pérez, J., Thomaszewski, B., Coros, S., Bickel, B., Canabal, J., Sumner, R., & Otaduy, M. (2015). Design and fabrication of flexible rod meshes (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766998","ama":"Pérez J, Thomaszewski B, Coros S, et al. Design and fabrication of flexible rod meshes. In: Vol 34. ACM; 2015. doi:10.1145/2766998"},"quality_controlled":"1"},{"type":"conference","abstract":[{"text":"Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally required the use of a fully three-dimensional many-phase Navier-Stokes solver, even though their visual appearance is completely dominated by the thin liquid surface. We depart from earlier work on soap bubbles and foams by noting that their dynamics are naturally described by a Lagrangian vortex sheet model in which circulation is the primary variable. This leads us to derive a novel circulation-preserving surface-only discretization of foam dynamics driven by surface tension on a non-manifold triangle mesh. We represent the surface using a mesh-based multimaterial surface tracker which supports complex bubble topology changes, and evolve the surface according to the ambient air flow induced by a scalar circulation field stored on the mesh. Surface tension forces give rise to a simple update rule for circulation, even at non-manifold Plateau borders, based on a discrete measure of signed scalar mean curvature. We further incorporate vertex constraints to enable the interaction of soap films with wires. The result is a method that is at once simple, robust, and efficient, yet able to capture an array of soap films behaviors including foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being pulled apart.","lang":"eng"}],"issue":"4","status":"public","title":"Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams","ddc":["000"],"intvolume":" 34","_id":"1634","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2016-608-v1+1_doublebubbles.pdf","access_level":"open_access","content_type":"application/pdf","file_size":8973215,"creator":"system","relation":"main_file","file_id":"4867","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:11:14Z","checksum":"57b07d78d2d612a8052744b37d4a71fa"}],"oa_version":"Submitted Version","pubrep_id":"608","scopus_import":1,"day":"27","has_accepted_license":"1","citation":{"chicago":"Da, Fang, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2767003.","short":"F. Da, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2015.","mla":"Da, Fang, et al. Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams. Vol. 34, no. 4, 149, ACM, 2015, doi:10.1145/2767003.","apa":"Da, F., Batty, C., Wojtan, C., & Grinspun, E. (2015). Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2767003","ieee":"F. Da, C. Batty, C. Wojtan, and E. Grinspun, “Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","ista":"Da F, Batty C, Wojtan C, Grinspun E. 2015. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 149.","ama":"Da F, Batty C, Wojtan C, Grinspun E. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. In: Vol 34. ACM; 2015. doi:10.1145/2767003"},"date_published":"2015-07-27T00:00:00Z","article_number":"149","file_date_updated":"2020-07-14T12:45:07Z","ec_funded":1,"publist_id":"5521","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","year":"2015","date_updated":"2023-02-23T10:07:42Z","date_created":"2018-12-11T11:53:09Z","volume":34,"author":[{"full_name":"Da, Fang","last_name":"Da","first_name":"Fang"},{"first_name":"Christopher","last_name":"Batty","full_name":"Batty, Christopher"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"},{"full_name":"Grinspun, Eitan","first_name":"Eitan","last_name":"Grinspun"}],"month":"07","quality_controlled":"1","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2015-08-09","location":"Los Angeles, CA, United States","end_date":"2015-08-13","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"doi":"10.1145/2767003"},{"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem that appears in many areas of Computer Science. It can be equivalently stated as computing a homomorphism R→ΓΓ between two relational structures, e.g. between two directed graphs. Analyzing its complexity has been a prominent research direction, especially for the fixed template CSPs where the right side ΓΓ is fixed and the left side R is unconstrained.\r\n\r\nFar fewer results are known for the hybrid setting that restricts both sides simultaneously. It assumes that R belongs to a certain class of relational structures (called a structural restriction in this paper). We study which structural restrictions are effective, i.e. there exists a fixed template ΓΓ (from a certain class of languages) for which the problem is tractable when R is restricted, and NP-hard otherwise. We provide a characterization for structural restrictions that are closed under inverse homomorphisms. The criterion is based on the chromatic number of a relational structure defined in this paper; it generalizes the standard chromatic number of a graph.\r\n\r\nAs our main tool, we use the algebraic machinery developed for fixed template CSPs. To apply it to our case, we introduce a new construction called a “lifted language”. We also give a characterization for structural restrictions corresponding to minor-closed families of graphs, extend results to certain Valued CSPs (namely conservative valued languages), and state implications for (valued) CSPs with ordered variables and for the maximum weight independent set problem on some restricted families of graphs."}],"title":"Effectiveness of structural restrictions for hybrid CSPs","status":"public","intvolume":" 9472","_id":"1636","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","page":"566 - 577","publication":"26th International Symposium","citation":{"ieee":"V. Kolmogorov, M. Rolinek, and R. Takhanov, “Effectiveness of structural restrictions for hybrid CSPs,” in 26th International Symposium, Nagoya, Japan, 2015, vol. 9472, pp. 566–577.","apa":"Kolmogorov, V., Rolinek, M., & Takhanov, R. (2015). Effectiveness of structural restrictions for hybrid CSPs. In 26th International Symposium (Vol. 9472, pp. 566–577). Nagoya, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-48971-0_48","ista":"Kolmogorov V, Rolinek M, Takhanov R. 2015. Effectiveness of structural restrictions for hybrid CSPs. 26th International Symposium. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 9472, 566–577.","ama":"Kolmogorov V, Rolinek M, Takhanov R. Effectiveness of structural restrictions for hybrid CSPs. In: 26th International Symposium. Vol 9472. Springer Nature; 2015:566-577. doi:10.1007/978-3-662-48971-0_48","chicago":"Kolmogorov, Vladimir, Michal Rolinek, and Rustem Takhanov. “Effectiveness of Structural Restrictions for Hybrid CSPs.” In 26th International Symposium, 9472:566–77. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48971-0_48.","short":"V. Kolmogorov, M. Rolinek, R. Takhanov, in:, 26th International Symposium, Springer Nature, 2015, pp. 566–577.","mla":"Kolmogorov, Vladimir, et al. “Effectiveness of Structural Restrictions for Hybrid CSPs.” 26th International Symposium, vol. 9472, Springer Nature, 2015, pp. 566–77, doi:10.1007/978-3-662-48971-0_48."},"date_published":"2015-12-01T00:00:00Z","ec_funded":1,"publist_id":"5519","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"VlKo"}],"year":"2015","date_created":"2018-12-11T11:53:10Z","date_updated":"2022-02-01T15:12:35Z","volume":9472,"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","last_name":"Rolinek","first_name":"Michal","full_name":"Rolinek, Michal"},{"first_name":"Rustem","last_name":"Takhanov","full_name":"Takhanov, Rustem"}],"month":"12","publication_identifier":{"isbn":["978-3-662-48970-3"]},"quality_controlled":"1","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"oa":1,"external_id":{"arxiv":["1504.07067"]},"main_file_link":[{"url":"http://arxiv.org/abs/1504.07067","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2015-12-09","location":"Nagoya, Japan","end_date":"2015-12-11","name":"ISAAC: International Symposium on Algorithms and Computation"},"doi":"10.1007/978-3-662-48971-0_48"},{"month":"07","language":[{"iso":"eng"}],"doi":"10.1145/2766935","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2015-08-13","location":"Los Angeles, CA, USA","start_date":"2015-08-09"},"quality_controlled":"1","oa":1,"publist_id":"5523","file_date_updated":"2020-07-14T12:45:07Z","article_number":"53","volume":34,"date_created":"2018-12-11T11:53:09Z","date_updated":"2023-02-23T10:07:37Z","author":[{"full_name":"Ando, Ryoichi","last_name":"Ando","first_name":"Ryoichi"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"publisher":"ACM","department":[{"_id":"ChWo"}],"publication_status":"published","acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad. This work was also supported by the ERC projects ERC-2014-StG-637014 realFlow and ERC-2014- StG-638176 BigSplash.","year":"2015","has_accepted_license":"1","day":"27","scopus_import":1,"date_published":"2015-07-27T00:00:00Z","citation":{"short":"R. Ando, N. Thuerey, C. Wojtan, in:, ACM, 2015.","mla":"Ando, Ryoichi, et al. A Stream Function Solver for Liquid Simulations. Vol. 34, no. 4, 53, ACM, 2015, doi:10.1145/2766935.","chicago":"Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “A Stream Function Solver for Liquid Simulations,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766935.","ama":"Ando R, Thuerey N, Wojtan C. A stream function solver for liquid simulations. In: Vol 34. ACM; 2015. doi:10.1145/2766935","apa":"Ando, R., Thuerey, N., & Wojtan, C. (2015). A stream function solver for liquid simulations (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766935","ieee":"R. Ando, N. Thuerey, and C. Wojtan, “A stream function solver for liquid simulations,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.","ista":"Ando R, Thuerey N, Wojtan C. 2015. A stream function solver for liquid simulations. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 53."},"issue":"4","abstract":[{"lang":"eng","text":"This paper presents a liquid simulation technique that enforces the incompressibility condition using a stream function solve instead of a pressure projection. Previous methods have used stream function techniques for the simulation of detailed single-phase flows, but a formulation for liquid simulation has proved elusive in part due to the free surface boundary conditions. In this paper, we introduce a stream function approach to liquid simulations with novel boundary conditions for free surfaces, solid obstacles, and solid-fluid coupling.\r\n\r\nAlthough our approach increases the dimension of the linear system necessary to enforce incompressibility, it provides interesting and surprising benefits. First, the resulting flow is guaranteed to be divergence-free regardless of the accuracy of the solve. Second, our free-surface boundary conditions guarantee divergence-free motion even in the un-simulated air phase, which enables two-phase flow simulation by only computing a single phase. We implemented this method using a variant of FLIP simulation which only samples particles within a narrow band of the liquid surface, and we illustrate the effectiveness of our method for detailed two-phase flow simulations with complex boundaries, detailed bubble interactions, and two-way solid-fluid coupling."}],"alternative_title":["ACM Transactions on Graphics"],"type":"conference","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":21831121,"access_level":"open_access","file_name":"IST-2016-610-v1+1_vecpotential.pdf","checksum":"7a9afdfaba9209157ce19376e15bc90b","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:11:52Z","file_id":"4909","relation":"main_file"}],"pubrep_id":"610","intvolume":" 34","ddc":["000"],"title":"A stream function solver for liquid simulations","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1632"},{"has_accepted_license":"1","day":"27","scopus_import":1,"date_published":"2015-07-27T00:00:00Z","citation":{"ista":"Guerrero P, Jeschke S, Wimmer M, Wonka P. 2015. Learning shape placements by example. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 108.","apa":"Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2015). Learning shape placements by example (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766933","ieee":"P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Learning shape placements by example,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","ama":"Guerrero P, Jeschke S, Wimmer M, Wonka P. Learning shape placements by example. In: Vol 34. ACM; 2015. doi:10.1145/2766933","chicago":"Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Learning Shape Placements by Example,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766933.","mla":"Guerrero, Paul, et al. Learning Shape Placements by Example. Vol. 34, no. 4, 108, ACM, 2015, doi:10.1145/2766933.","short":"P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, in:, ACM, 2015."},"issue":"4","abstract":[{"lang":"eng","text":"We present a method to learn and propagate shape placements in 2D polygonal scenes from a few examples provided by a user. The placement of a shape is modeled as an oriented bounding box. Simple geometric relationships between this bounding box and nearby scene polygons define a feature set for the placement. The feature sets of all example placements are then used to learn a probabilistic model over all possible placements and scenes. With this model, we can generate a new set of placements with similar geometric relationships in any given scene. We introduce extensions that enable propagation and generation of shapes in 3D scenes, as well as the application of a learned modeling session to large scenes without additional user interaction. These concepts allow us to generate complex scenes with thousands of objects with relatively little user interaction."}],"type":"conference","pubrep_id":"576","file":[{"date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:07:49Z","checksum":"8b05a51e372c9b0b5af9a00098a9538b","file_id":"4647","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":11902290,"file_name":"IST-2016-576-v1+1_guerrero-2015-lsp-paper.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1630","intvolume":" 34","title":"Learning shape placements by example","status":"public","ddc":["000"],"month":"07","doi":"10.1145/2766933","conference":{"end_date":"2015-08-13","start_date":"2015-08-09","location":"Los Angeles, CA, United States","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Deep Pictures: Creating Visual and Haptic Vector Images","call_identifier":"FWF","grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publist_id":"5525","file_date_updated":"2020-07-14T12:45:07Z","article_number":"108","author":[{"full_name":"Guerrero, Paul","last_name":"Guerrero","first_name":"Paul"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wimmer, Michael","first_name":"Michael","last_name":"Wimmer"},{"first_name":"Peter","last_name":"Wonka","full_name":"Wonka, Peter"}],"volume":34,"date_created":"2018-12-11T11:53:08Z","date_updated":"2021-01-12T06:52:07Z","year":"2015","acknowledgement":"This publication is based upon work supported by the KAUST Office of Competitive Research Funds (OCRF) under Award No. 62140401, the KAUST Visual Computing Center and the Austrian Science Fund (FWF) projects DEEP PICTURES (no. P24352-N23) and Data-Driven Procedural Modeling of Interiors (no. P24600-N23).","publisher":"ACM","department":[{"_id":"ChWo"}],"publication_status":"published"},{"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"year":"2015","acknowledgement":"This work was supported by the European Research Council Starting Independent Research grant (ERC-2007-Stg-207362-HCPO to E.B., M.S., C.C.), by the Ghent University Multidisciplinary Research Partnership ‘Biotechnology for a Sustainable Economy’ no.01MRB510W, by the Research Foundation—Flanders (grant 3G033711 to J.-A.O.), by the Austrian Science Fund (FWF01_I1774S) to K.Ö.,E.B., and by the Interuniversity Attraction Poles Programme (IUAP P7/29 ‘MARS’) initiated by the Belgian Science Policy Office. I.D.C. and S.V. are post-doctoral fellows of the Research Foundation—Flanders (FWO). This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF).","date_updated":"2021-01-12T06:52:11Z","date_created":"2018-12-11T11:53:12Z","volume":6,"author":[{"full_name":"Šimášková, Mária","first_name":"Mária","last_name":"Šimášková"},{"full_name":"O'Brien, José","last_name":"O'Brien","first_name":"José"},{"id":"391B5BBC-F248-11E8-B48F-1D18A9856A87","last_name":"Khan-Djamei","first_name":"Mamoona","full_name":"Khan-Djamei, Mamoona"},{"full_name":"Van Noorden, Giel","last_name":"Van Noorden","first_name":"Giel"},{"full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","first_name":"Krisztina","last_name":"Ötvös"},{"first_name":"Anne","last_name":"Vieten","full_name":"Vieten, Anne"},{"full_name":"De Clercq, Inge","first_name":"Inge","last_name":"De Clercq"},{"first_name":"Johanna","last_name":"Van Haperen","full_name":"Van Haperen, Johanna"},{"last_name":"Cuesta","first_name":"Candela","orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela"},{"first_name":"Klára","last_name":"Hoyerová","full_name":"Hoyerová, Klára"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","first_name":"Peter","last_name":"Marhavy","full_name":"Marhavy, Peter"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T"},{"full_name":"Van Breusegem, Frank","last_name":"Van Breusegem","first_name":"Frank"},{"first_name":"Moritz","last_name":"Nowack","full_name":"Nowack, Moritz"},{"last_name":"Murphy","first_name":"Angus","full_name":"Murphy, Angus"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiřĺ","last_name":"Friml","full_name":"Friml, Jiřĺ"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"article_number":"8717","file_date_updated":"2020-07-14T12:45:08Z","ec_funded":1,"publist_id":"5513","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"},{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"}],"oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1038/ncomms9717","month":"01","status":"public","ddc":["580"],"title":"Cytokinin response factors regulate PIN-FORMED auxin transporters","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1640","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5358","date_created":"2018-12-12T10:18:36Z","date_updated":"2020-07-14T12:45:08Z","checksum":"c2c84bca37401435fedf76bad0ba0579","file_name":"IST-2018-1020-v1+1_Simaskova_et_al_NatCom_2015.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1471217,"creator":"system"}],"pubrep_id":"1020","type":"journal_article","abstract":[{"text":"Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.","lang":"eng"}],"publication":"Nature Communications","citation":{"short":"M. Šimášková, J. O’Brien, M. Khan-Djamei, G. Van Noorden, K. Ötvös, A. Vieten, I. De Clercq, J. Van Haperen, C. Cuesta, K. Hoyerová, S. Vanneste, P. Marhavý, K.T. Wabnik, F. Van Breusegem, M. Nowack, A. Murphy, J. Friml, D. Weijers, T. Beeckman, E. Benková, Nature Communications 6 (2015).","mla":"Šimášková, Mária, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” Nature Communications, vol. 6, 8717, Nature Publishing Group, 2015, doi:10.1038/ncomms9717.","chicago":"Šimášková, Mária, José O’Brien, Mamoona Khan-Djamei, Giel Van Noorden, Krisztina Ötvös, Anne Vieten, Inge De Clercq, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9717.","ama":"Šimášková M, O’Brien J, Khan-Djamei M, et al. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. 2015;6. doi:10.1038/ncomms9717","ieee":"M. Šimášková et al., “Cytokinin response factors regulate PIN-FORMED auxin transporters,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Šimášková, M., O’Brien, J., Khan-Djamei, M., Van Noorden, G., Ötvös, K., Vieten, A., … Benková, E. (2015). Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9717","ista":"Šimášková M, O’Brien J, Khan-Djamei M, Van Noorden G, Ötvös K, Vieten A, De Clercq I, Van Haperen J, Cuesta C, Hoyerová K, Vanneste S, Marhavý P, Wabnik KT, Van Breusegem F, Nowack M, Murphy A, Friml J, Weijers D, Beeckman T, Benková E. 2015. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. 6, 8717."},"date_published":"2015-01-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1"},{"department":[{"_id":"UlWa"}],"publisher":"Electronic Journal of Combinatorics","publication_status":"published","acknowledgement":"e research leading to these results has received funding fromthe People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no [291734], and ESF Eurogiga project GraDR as GAˇCRGIG/11/E023.","year":"2015","volume":22,"date_updated":"2023-02-21T16:03:02Z","date_created":"2018-12-11T11:53:12Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10793"}]},"author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"},{"full_name":"Malinovič, Igor","first_name":"Igor","last_name":"Malinovič"},{"last_name":"Pálvölgyi","first_name":"Dömötör","full_name":"Pálvölgyi, Dömötör"}],"article_number":"P4.24 ","ec_funded":1,"publist_id":"5511","file_date_updated":"2020-07-14T12:45:08Z","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","external_id":{"arxiv":["1305.4519"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.37236/5002","publication_identifier":{"eissn":["1077-8926"]},"month":"11","intvolume":" 22","status":"public","ddc":["514","516"],"title":"Clustered planarity testing revisited","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1642","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-714-v1+1_5002-15499-3-PB.pdf","creator":"system","file_size":443655,"content_type":"application/pdf","file_id":"5120","relation":"main_file","checksum":"40b5920b49ee736694f59f39588ee206","date_created":"2018-12-12T10:15:03Z","date_updated":"2020-07-14T12:45:08Z"}],"pubrep_id":"714","type":"journal_article","issue":"4","abstract":[{"text":"The Hanani-Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this result to clustered graphs with two disjoint clusters, and show that a straightforward extension to flat clustered graphs with three or more disjoint clusters is not possible. For general clustered graphs we show a variant of the Hanani-Tutte theorem in the case when each cluster induces a connected subgraph. Di Battista and Frati proved that clustered planarity of embedded clustered graphs whose every face is incident to at most five vertices can be tested in polynomial time. We give a new and short proof of this result, using the matroid intersection algorithm.","lang":"eng"}],"article_type":"original","citation":{"apa":"Fulek, R., Kynčl, J., Malinovič, I., & Pálvölgyi, D. (2015). Clustered planarity testing revisited. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/5002","ieee":"R. Fulek, J. Kynčl, I. Malinovič, and D. Pálvölgyi, “Clustered planarity testing revisited,” Electronic Journal of Combinatorics, vol. 22, no. 4. Electronic Journal of Combinatorics, 2015.","ista":"Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. 2015. Clustered planarity testing revisited. Electronic Journal of Combinatorics. 22(4), P4.24.","ama":"Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. Clustered planarity testing revisited. Electronic Journal of Combinatorics. 2015;22(4). doi:10.37236/5002","chicago":"Fulek, Radoslav, Jan Kynčl, Igor Malinovič, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2015. https://doi.org/10.37236/5002.","short":"R. Fulek, J. Kynčl, I. Malinovič, D. Pálvölgyi, Electronic Journal of Combinatorics 22 (2015).","mla":"Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” Electronic Journal of Combinatorics, vol. 22, no. 4, P4.24, Electronic Journal of Combinatorics, 2015, doi:10.37236/5002."},"publication":"Electronic Journal of Combinatorics","date_published":"2015-11-13T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"13"},{"page":"1745 - 1769","publication":"ESAIM: Mathematical Modelling and Numerical Analysis","citation":{"ista":"Maas J, Rumpf M, Schönlieb C, Simon S. 2015. A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. 49(6), 1745–1769.","ieee":"J. Maas, M. Rumpf, C. Schönlieb, and S. Simon, “A generalized model for optimal transport of images including dissipation and density modulation,” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 49, no. 6. EDP Sciences, pp. 1745–1769, 2015.","apa":"Maas, J., Rumpf, M., Schönlieb, C., & Simon, S. (2015). A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2015043","ama":"Maas J, Rumpf M, Schönlieb C, Simon S. A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. 2015;49(6):1745-1769. doi:10.1051/m2an/2015043","chicago":"Maas, Jan, Martin Rumpf, Carola Schönlieb, and Stefan Simon. “A Generalized Model for Optimal Transport of Images Including Dissipation and Density Modulation.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences, 2015. https://doi.org/10.1051/m2an/2015043.","mla":"Maas, Jan, et al. “A Generalized Model for Optimal Transport of Images Including Dissipation and Density Modulation.” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 49, no. 6, EDP Sciences, 2015, pp. 1745–69, doi:10.1051/m2an/2015043.","short":"J. Maas, M. Rumpf, C. Schönlieb, S. Simon, ESAIM: Mathematical Modelling and Numerical Analysis 49 (2015) 1745–1769."},"date_published":"2015-11-01T00:00:00Z","scopus_import":1,"day":"01","status":"public","title":"A generalized model for optimal transport of images including dissipation and density modulation","intvolume":" 49","_id":"1639","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"In this paper the optimal transport and the metamorphosis perspectives are combined. For a pair of given input images geodesic paths in the space of images are defined as minimizers of a resulting path energy. To this end, the underlying Riemannian metric measures the rate of transport cost and the rate of viscous dissipation. Furthermore, the model is capable to deal with strongly varying image contrast and explicitly allows for sources and sinks in the transport equations which are incorporated in the metric related to the metamorphosis approach by Trouvé and Younes. In the non-viscous case with source term existence of geodesic paths is proven in the space of measures. The proposed model is explored on the range from merely optimal transport to strongly dissipative dynamics. For this model a robust and effective variational time discretization of geodesic paths is proposed. This requires to minimize a discrete path energy consisting of a sum of consecutive image matching functionals. These functionals are defined on corresponding pairs of intensity functions and on associated pairwise matching deformations. Existence of time discrete geodesics is demonstrated. Furthermore, a finite element implementation is proposed and applied to instructive test cases and to real images. In the non-viscous case this is compared to the algorithm proposed by Benamou and Brenier including a discretization of the source term. Finally, the model is generalized to define discrete weighted barycentres with applications to textures and objects.","lang":"eng"}],"issue":"6","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.01988"}],"external_id":{"arxiv":["1504.01988"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1051/m2an/2015043","month":"11","publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"EDP Sciences","year":"2015","acknowledgement":"The authors acknowledge support of the Collaborative Research Centre 1060 funded by the German Science foundation. This work is further supported by the King Abdullah University for Science and Technology (KAUST) Award No. KUK-I1-007-43 and the EPSRC grant Nr. EP/M00483X/1.","date_created":"2018-12-11T11:53:11Z","date_updated":"2021-01-12T06:52:10Z","volume":49,"author":[{"full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"first_name":"Martin","last_name":"Rumpf","full_name":"Rumpf, Martin"},{"full_name":"Schönlieb, Carola","last_name":"Schönlieb","first_name":"Carola"},{"full_name":"Simon, Stefan","last_name":"Simon","first_name":"Stefan"}],"publist_id":"5514"},{"title":"A giant molecular proton pump: structure and mechanism of respiratory complex I","publication_status":"published","status":"public","publisher":"Nature Publishing Group","department":[{"_id":"LeSa"}],"intvolume":" 16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1638","year":"2015","date_created":"2018-12-11T11:53:11Z","date_updated":"2021-01-12T06:52:10Z","volume":16,"oa_version":"None","author":[{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The mitochondrial respiratory chain, also known as the electron transport chain (ETC), is crucial to life, and energy production in the form of ATP is the main mitochondrial function. Three proton-translocating enzymes of the ETC, namely complexes I, III and IV, generate proton motive force, which in turn drives ATP synthase (complex V). The atomic structures and basic mechanisms of most respiratory complexes have previously been established, with the exception of complex I, the largest complex in the ETC. Recently, the crystal structure of the entire complex I was solved using a bacterial enzyme. The structure provided novel insights into the core architecture of the complex, the electron transfer and proton translocation pathways, as well as the mechanism that couples these two processes."}],"publist_id":"5517","issue":"6","quality_controlled":"1","page":"375 - 388","publication":"Nature Reviews Molecular Cell Biology","citation":{"chicago":"Sazanov, Leonid A. “A Giant Molecular Proton Pump: Structure and Mechanism of Respiratory Complex I.” Nature Reviews Molecular Cell Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nrm3997.","mla":"Sazanov, Leonid A. “A Giant Molecular Proton Pump: Structure and Mechanism of Respiratory Complex I.” Nature Reviews Molecular Cell Biology, vol. 16, no. 6, Nature Publishing Group, 2015, pp. 375–88, doi:10.1038/nrm3997.","short":"L.A. Sazanov, Nature Reviews Molecular Cell Biology 16 (2015) 375–388.","ista":"Sazanov LA. 2015. A giant molecular proton pump: structure and mechanism of respiratory complex I. Nature Reviews Molecular Cell Biology. 16(6), 375–388.","apa":"Sazanov, L. A. (2015). A giant molecular proton pump: structure and mechanism of respiratory complex I. Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/nrm3997","ieee":"L. A. Sazanov, “A giant molecular proton pump: structure and mechanism of respiratory complex I,” Nature Reviews Molecular Cell Biology, vol. 16, no. 6. Nature Publishing Group, pp. 375–388, 2015.","ama":"Sazanov LA. A giant molecular proton pump: structure and mechanism of respiratory complex I. Nature Reviews Molecular Cell Biology. 2015;16(6):375-388. doi:10.1038/nrm3997"},"language":[{"iso":"eng"}],"date_published":"2015-05-22T00:00:00Z","doi":"10.1038/nrm3997","scopus_import":1,"month":"05","day":"22"},{"title":"Key-homomorphic constrained pseudorandom functions","status":"public","ddc":["000","004"],"intvolume":" 9015","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1646","oa_version":"Submitted Version","file":[{"creator":"system","file_size":450665,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-679-v1+1_180.pdf","checksum":"3c5093bda5783c89beaacabf1aa0e60e","date_updated":"2020-07-14T12:45:08Z","date_created":"2018-12-12T10:15:17Z","file_id":"5136","relation":"main_file"}],"pubrep_id":"679","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"A pseudorandom function (PRF) is a keyed function F : K × X → Y where, for a random key k ∈ K, the function F(k, ·) is indistinguishable from a uniformly random function, given black-box access. A key-homomorphic PRF has the additional feature that for any keys k, k' and any input x, we have F(k+k', x) = F(k, x)⊕F(k', x) for some group operations +,⊕ on K and Y, respectively. A constrained PRF for a family of setsS ⊆ P(X) has the property that, given any key k and set S ∈ S, one can efficiently compute a “constrained” key kS that enables evaluation of F(k, x) on all inputs x ∈ S, while the values F(k, x) for x /∈ S remain pseudorandom even given kS. In this paper we construct PRFs that are simultaneously constrained and key homomorphic, where the homomorphic property holds even for constrained keys. We first show that the multilinear map-based bit-fixing and circuit-constrained PRFs of Boneh and Waters (Asiacrypt 2013) can be modified to also be keyhomomorphic. We then show that the LWE-based key-homomorphic PRFs of Banerjee and Peikert (Crypto 2014) are essentially already prefix-constrained PRFs, using a (non-obvious) definition of constrained keys and associated group operation. Moreover, the constrained keys themselves are pseudorandom, and the constraining and evaluation functions can all be computed in low depth. As an application of key-homomorphic constrained PRFs,we construct a proxy re-encryption schemewith fine-grained access control. This scheme allows storing encrypted data on an untrusted server, where each file can be encrypted relative to some attributes, so that only parties whose constrained keys match the attributes can decrypt. Moreover, the server can re-key (arbitrary subsets of) the ciphertexts without learning anything about the plaintexts, thus permitting efficient and finegrained revocation.","lang":"eng"}],"page":"31 - 60","publication":"12th Theory of Cryptography Conference","citation":{"chicago":"Banerjee, Abishek, Georg Fuchsbauer, Chris Peikert, Krzysztof Z Pietrzak, and Sophie Stevens. “Key-Homomorphic Constrained Pseudorandom Functions.” In 12th Theory of Cryptography Conference, 9015:31–60. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-46497-7_2.","short":"A. Banerjee, G. Fuchsbauer, C. Peikert, K.Z. Pietrzak, S. Stevens, in:, 12th Theory of Cryptography Conference, Springer Nature, 2015, pp. 31–60.","mla":"Banerjee, Abishek, et al. “Key-Homomorphic Constrained Pseudorandom Functions.” 12th Theory of Cryptography Conference, vol. 9015, Springer Nature, 2015, pp. 31–60, doi:10.1007/978-3-662-46497-7_2.","apa":"Banerjee, A., Fuchsbauer, G., Peikert, C., Pietrzak, K. Z., & Stevens, S. (2015). Key-homomorphic constrained pseudorandom functions. In 12th Theory of Cryptography Conference (Vol. 9015, pp. 31–60). Warsaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-662-46497-7_2","ieee":"A. Banerjee, G. Fuchsbauer, C. Peikert, K. Z. Pietrzak, and S. Stevens, “Key-homomorphic constrained pseudorandom functions,” in 12th Theory of Cryptography Conference, Warsaw, Poland, 2015, vol. 9015, pp. 31–60.","ista":"Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. 2015. Key-homomorphic constrained pseudorandom functions. 12th Theory of Cryptography Conference. TCC: Theory of Cryptography Conference, LNCS, vol. 9015, 31–60.","ama":"Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. Key-homomorphic constrained pseudorandom functions. In: 12th Theory of Cryptography Conference. Vol 9015. Springer Nature; 2015:31-60. doi:10.1007/978-3-662-46497-7_2"},"date_published":"2015-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","year":"2015","date_updated":"2022-02-03T08:41:46Z","date_created":"2018-12-11T11:53:14Z","volume":9015,"author":[{"full_name":"Banerjee, Abishek","first_name":"Abishek","last_name":"Banerjee"},{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"last_name":"Peikert","first_name":"Chris","full_name":"Peikert, Chris"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Stevens","first_name":"Sophie","full_name":"Stevens, Sophie"}],"file_date_updated":"2020-07-14T12:45:08Z","publist_id":"5505","ec_funded":1,"quality_controlled":"1","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2015/180"}],"language":[{"iso":"eng"}],"conference":{"location":"Warsaw, Poland","start_date":"2015-03-23","end_date":"2015-03-25","name":"TCC: Theory of Cryptography Conference"},"doi":"10.1007/978-3-662-46497-7_2","month":"03","publication_identifier":{"isbn":["978-3-662-46496-0"]}},{"scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"ieee":"G. Fuchsbauer, Z. Jafargholi, and K. Z. Pietrzak, “A quasipolynomial reduction for generalized selective decryption on trees,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2015, vol. 9215, pp. 601–620.","apa":"Fuchsbauer, G., Jafargholi, Z., & Pietrzak, K. Z. (2015). A quasipolynomial reduction for generalized selective decryption on trees (Vol. 9215, pp. 601–620). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. https://doi.org/10.1007/978-3-662-47989-6_29","ista":"Fuchsbauer G, Jafargholi Z, Pietrzak KZ. 2015. A quasipolynomial reduction for generalized selective decryption on trees. CRYPTO: International Cryptology Conference, LNCS, vol. 9215, 601–620.","ama":"Fuchsbauer G, Jafargholi Z, Pietrzak KZ. A quasipolynomial reduction for generalized selective decryption on trees. In: Vol 9215. Springer; 2015:601-620. doi:10.1007/978-3-662-47989-6_29","chicago":"Fuchsbauer, Georg, Zahra Jafargholi, and Krzysztof Z Pietrzak. “A Quasipolynomial Reduction for Generalized Selective Decryption on Trees,” 9215:601–20. Springer, 2015. https://doi.org/10.1007/978-3-662-47989-6_29.","short":"G. Fuchsbauer, Z. Jafargholi, K.Z. Pietrzak, in:, Springer, 2015, pp. 601–620.","mla":"Fuchsbauer, Georg, et al. A Quasipolynomial Reduction for Generalized Selective Decryption on Trees. Vol. 9215, Springer, 2015, pp. 601–20, doi:10.1007/978-3-662-47989-6_29."},"page":"601 - 620","date_published":"2015-08-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Generalized Selective Decryption (GSD), introduced by Panjwani [TCC’07], is a game for a symmetric encryption scheme Enc that captures the difficulty of proving adaptive security of certain protocols, most notably the Logical Key Hierarchy (LKH) multicast encryption protocol. In the GSD game there are n keys k1,..., kn, which the adversary may adaptively corrupt (learn); moreover, it can ask for encryptions Encki (kj) of keys under other keys. The adversary’s task is to distinguish keys (which it cannot trivially compute) from random. Proving the hardness of GSD assuming only IND-CPA security of Enc is surprisingly hard. Using “complexity leveraging” loses a factor exponential in n, which makes the proof practically meaningless. We can think of the GSD game as building a graph on n vertices, where we add an edge i → j when the adversary asks for an encryption of kj under ki. If restricted to graphs of depth ℓ, Panjwani gave a reduction that loses only a factor exponential in ℓ (not n). To date, this is the only non-trivial result known for GSD. In this paper we give almost-polynomial reductions for large classes of graphs. Most importantly, we prove the security of the GSD game restricted to trees losing only a quasi-polynomial factor n3 log n+5. Trees are an important special case capturing real-world protocols like the LKH protocol. Our new bound improves upon Panjwani’s on some LKH variants proposed in the literature where the underlying tree is not balanced. Our proof builds on ideas from the “nested hybrids” technique recently introduced by Fuchsbauer et al. [Asiacrypt’14] for proving the adaptive security of constrained PRFs."}],"_id":"1648","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"title":"A quasipolynomial reduction for generalized selective decryption on trees","status":"public","intvolume":" 9215","pubrep_id":"674","oa_version":"Submitted Version","file":[{"checksum":"99b76b3263d5082554d0a9cbdeca3a22","date_created":"2018-12-12T10:13:31Z","date_updated":"2020-07-14T12:45:08Z","file_id":"5015","relation":"main_file","creator":"system","file_size":505618,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-674-v1+1_389.pdf"}],"month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"conference":{"name":"CRYPTO: International Cryptology Conference","end_date":"2015-08-20","start_date":"2015-08-16","location":"Santa Barbara, CA, USA"},"doi":"10.1007/978-3-662-47989-6_29","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:08Z","ec_funded":1,"publist_id":"5502","year":"2015","publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"author":[{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"last_name":"Jafargholi","first_name":"Zahra","full_name":"Jafargholi, Zahra"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"date_updated":"2021-01-12T06:52:14Z","date_created":"2018-12-11T11:53:14Z","volume":9215},{"citation":{"ama":"Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. Efficient zero-knowledge proofs for commitments from learning with errors over rings. 2015;9326:305-325. doi:10.1007/978-3-319-24174-6_16","ista":"Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. 2015. Efficient zero-knowledge proofs for commitments from learning with errors over rings. 9326, 305–325.","ieee":"F. Benhamouda, S. Krenn, V. Lyubashevsky, and K. Z. Pietrzak, “Efficient zero-knowledge proofs for commitments from learning with errors over rings,” vol. 9326. Springer, pp. 305–325, 2015.","apa":"Benhamouda, F., Krenn, S., Lyubashevsky, V., & Pietrzak, K. Z. (2015). Efficient zero-knowledge proofs for commitments from learning with errors over rings. Presented at the ESORICS: European Symposium on Research in Computer Security, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-24174-6_16","mla":"Benhamouda, Fabrice, et al. Efficient Zero-Knowledge Proofs for Commitments from Learning with Errors over Rings. Vol. 9326, Springer, 2015, pp. 305–25, doi:10.1007/978-3-319-24174-6_16.","short":"F. Benhamouda, S. Krenn, V. Lyubashevsky, K.Z. Pietrzak, 9326 (2015) 305–325.","chicago":"Benhamouda, Fabrice, Stephan Krenn, Vadim Lyubashevsky, and Krzysztof Z Pietrzak. “Efficient Zero-Knowledge Proofs for Commitments from Learning with Errors over Rings.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-24174-6_16."},"page":"305 - 325","date_published":"2015-01-01T00:00:00Z","scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"01","has_accepted_license":"1","_id":"1649","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Efficient zero-knowledge proofs for commitments from learning with errors over rings","ddc":["000","004"],"status":"public","intvolume":" 9326","pubrep_id":"678","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":494239,"access_level":"open_access","file_name":"IST-2016-678-v1+1_889.pdf","checksum":"6eac4a485b2aa644b2d3f753ed0b280b","date_updated":"2020-07-14T12:45:08Z","date_created":"2018-12-12T10:11:28Z","file_id":"4883","relation":"main_file"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We extend a commitment scheme based on the learning with errors over rings (RLWE) problem, and present efficient companion zeroknowledge proofs of knowledge. Our scheme maps elements from the ring (or equivalently, n elements from ","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"conference":{"name":"ESORICS: European Symposium on Research in Computer Security","end_date":"2015-09-25","location":"Vienna, Austria","start_date":"2015-09-21"},"doi":"10.1007/978-3-319-24174-6_16","language":[{"iso":"eng"}],"month":"01","year":"2015","publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"author":[{"last_name":"Benhamouda","first_name":"Fabrice","full_name":"Benhamouda, Fabrice"},{"last_name":"Krenn","first_name":"Stephan","full_name":"Krenn, Stephan"},{"first_name":"Vadim","last_name":"Lyubashevsky","full_name":"Lyubashevsky, Vadim"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"date_created":"2018-12-11T11:53:15Z","date_updated":"2021-01-12T06:52:14Z","volume":9326,"file_date_updated":"2020-07-14T12:45:08Z","ec_funded":1,"publist_id":"5501","license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"month":"01","conference":{"location":"Lugano, Switzerland","start_date":"2015-05-02","end_date":"2015-05-05","name":"ICITS: International Conference on Information Theoretic Security"},"doi":"10.1007/978-3-319-17470-9_10","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2015/315"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"publist_id":"5507","ec_funded":1,"author":[{"full_name":"Demay, Grégory","last_name":"Demay","first_name":"Grégory"},{"full_name":"Gazi, Peter","last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ueli","last_name":"Maurer","full_name":"Maurer, Ueli"},{"full_name":"Tackmann, Björn","first_name":"Björn","last_name":"Tackmann"}],"date_updated":"2021-01-12T06:52:13Z","date_created":"2018-12-11T11:53:13Z","volume":9063,"year":"2015","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","day":"01","scopus_import":1,"date_published":"2015-01-01T00:00:00Z","citation":{"chicago":"Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Query-Complexity Amplification for Random Oracles,” 9063:159–80. Springer, 2015. https://doi.org/10.1007/978-3-319-17470-9_10.","mla":"Demay, Grégory, et al. Query-Complexity Amplification for Random Oracles. Vol. 9063, Springer, 2015, pp. 159–80, doi:10.1007/978-3-319-17470-9_10.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, Springer, 2015, pp. 159–180.","ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2015. Query-complexity amplification for random oracles. ICITS: International Conference on Information Theoretic Security, LNCS, vol. 9063, 159–180.","apa":"Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2015). Query-complexity amplification for random oracles (Vol. 9063, pp. 159–180). Presented at the ICITS: International Conference on Information Theoretic Security, Lugano, Switzerland: Springer. https://doi.org/10.1007/978-3-319-17470-9_10","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Query-complexity amplification for random oracles,” presented at the ICITS: International Conference on Information Theoretic Security, Lugano, Switzerland, 2015, vol. 9063, pp. 159–180.","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Query-complexity amplification for random oracles. In: Vol 9063. Springer; 2015:159-180. doi:10.1007/978-3-319-17470-9_10"},"page":"159 - 180","abstract":[{"text":"Increasing the computational complexity of evaluating a hash function, both for the honest users as well as for an adversary, is a useful technique employed for example in password-based cryptographic schemes to impede brute-force attacks, and also in so-called proofs of work (used in protocols like Bitcoin) to show that a certain amount of computation was performed by a legitimate user. A natural approach to adjust the complexity of a hash function is to iterate it c times, for some parameter c, in the hope that any query to the scheme requires c evaluations of the underlying hash function. However, results by Dodis et al. (Crypto 2012) imply that plain iteration falls short of achieving this goal, and designing schemes which provably have such a desirable property remained an open problem. This paper formalizes explicitly what it means for a given scheme to amplify the query complexity of a hash function. In the random oracle model, the goal of a secure query-complexity amplifier (QCA) scheme is captured as transforming, in the sense of indifferentiability, a random oracle allowing R queries (for the adversary) into one provably allowing only r < R queries. Turned around, this means that making r queries to the scheme requires at least R queries to the actual random oracle. Second, a new scheme, called collision-free iteration, is proposed and proven to achieve c-fold QCA for both the honest parties and the adversary, for any fixed parameter c.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1644","title":"Query-complexity amplification for random oracles","status":"public","intvolume":" 9063"},{"abstract":[{"lang":"eng","text":"Round-optimal blind signatures are notoriously hard to construct in the standard model, especially in the malicious-signer model, where blindness must hold under adversarially chosen keys. This is substantiated by several impossibility results. The only construction that can be termed theoretically efficient, by Garg and Gupta (Eurocrypt’14), requires complexity leveraging, inducing an exponential security loss. We present a construction of practically efficient round-optimal blind signatures in the standard model. It is conceptually simple and builds on the recent structure-preserving signatures on equivalence classes (SPSEQ) from Asiacrypt’14. While the traditional notion of blindness follows from standard assumptions, we prove blindness under adversarially chosen keys under an interactive variant of DDH. However, we neither require non-uniform assumptions nor complexity leveraging. We then show how to extend our construction to partially blind signatures and to blind signatures on message vectors, which yield a construction of one-show anonymous credentials à la “anonymous credentials light” (CCS’13) in the standard model. Furthermore, we give the first SPS-EQ construction under noninteractive assumptions and show how SPS-EQ schemes imply conventional structure-preserving signatures, which allows us to apply optimality results for the latter to SPS-EQ."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","title":"Practical round-optimal blind signatures in the standard model","status":"public","intvolume":" 9216","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1647","day":"01","article_processing_charge":"No","scopus_import":1,"date_published":"2015-08-01T00:00:00Z","page":"233 - 253","citation":{"chicago":"Fuchsbauer, Georg, Christian Hanser, and Daniel Slamanig. “Practical Round-Optimal Blind Signatures in the Standard Model,” 9216:233–53. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_12.","mla":"Fuchsbauer, Georg, et al. Practical Round-Optimal Blind Signatures in the Standard Model. Vol. 9216, Springer, 2015, pp. 233–53, doi:10.1007/978-3-662-48000-7_12.","short":"G. Fuchsbauer, C. Hanser, D. Slamanig, in:, Springer, 2015, pp. 233–253.","ista":"Fuchsbauer G, Hanser C, Slamanig D. 2015. Practical round-optimal blind signatures in the standard model. CRYPTO: International Cryptology Conference, LNCS, vol. 9216, 233–253.","ieee":"G. Fuchsbauer, C. Hanser, and D. Slamanig, “Practical round-optimal blind signatures in the standard model,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 233–253.","apa":"Fuchsbauer, G., Hanser, C., & Slamanig, D. (2015). Practical round-optimal blind signatures in the standard model (Vol. 9216, pp. 233–253). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_12","ama":"Fuchsbauer G, Hanser C, Slamanig D. Practical round-optimal blind signatures in the standard model. In: Vol 9216. Springer; 2015:233-253. doi:10.1007/978-3-662-48000-7_12"},"publist_id":"5503","ec_funded":1,"date_updated":"2023-02-21T16:44:51Z","date_created":"2018-12-11T11:53:14Z","volume":9216,"author":[{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"last_name":"Hanser","first_name":"Christian","full_name":"Hanser, Christian"},{"full_name":"Slamanig, Daniel","first_name":"Daniel","last_name":"Slamanig"}],"related_material":{"record":[{"id":"1225","status":"public","relation":"later_version"}]},"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","year":"2015","month":"08","language":[{"iso":"eng"}],"conference":{"name":"CRYPTO: International Cryptology Conference","start_date":"2015-08-16","location":"Santa Barbara, CA, United States","end_date":"2015-08-20"},"doi":"10.1007/978-3-662-48000-7_12","quality_controlled":"1","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2015/626.pdf"}]},{"scopus_import":1,"month":"06","day":"24","citation":{"ama":"Gazi P, Tessaro S. Secret-key cryptography from ideal primitives: A systematic verview. In: 2015 IEEE Information Theory Workshop. IEEE; 2015. doi:10.1109/ITW.2015.7133163","ista":"Gazi P, Tessaro S. 2015. Secret-key cryptography from ideal primitives: A systematic verview. 2015 IEEE Information Theory Workshop. ITW 2015: IEEE Information Theory Workshop, 7133163.","apa":"Gazi, P., & Tessaro, S. (2015). Secret-key cryptography from ideal primitives: A systematic verview. In 2015 IEEE Information Theory Workshop. Jerusalem, Israel: IEEE. https://doi.org/10.1109/ITW.2015.7133163","ieee":"P. Gazi and S. Tessaro, “Secret-key cryptography from ideal primitives: A systematic verview,” in 2015 IEEE Information Theory Workshop, Jerusalem, Israel, 2015.","mla":"Gazi, Peter, and Stefano Tessaro. “Secret-Key Cryptography from Ideal Primitives: A Systematic Verview.” 2015 IEEE Information Theory Workshop, 7133163, IEEE, 2015, doi:10.1109/ITW.2015.7133163.","short":"P. Gazi, S. Tessaro, in:, 2015 IEEE Information Theory Workshop, IEEE, 2015.","chicago":"Gazi, Peter, and Stefano Tessaro. “Secret-Key Cryptography from Ideal Primitives: A Systematic Verview.” In 2015 IEEE Information Theory Workshop. IEEE, 2015. https://doi.org/10.1109/ITW.2015.7133163."},"publication":"2015 IEEE Information Theory Workshop","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1109/ITW.2015.7133163","date_published":"2015-06-24T00:00:00Z","conference":{"location":"Jerusalem, Israel","start_date":"2015-04-26","end_date":"2015-05-01","name":"ITW 2015: IEEE Information Theory Workshop"},"language":[{"iso":"eng"}],"type":"conference","article_number":"7133163","ec_funded":1,"publist_id":"5506","abstract":[{"text":"Secret-key constructions are often proved secure in a model where one or more underlying components are replaced by an idealized oracle accessible to the attacker. This model gives rise to information-theoretic security analyses, and several advances have been made in this area over the last few years. This paper provides a systematic overview of what is achievable in this model, and how existing works fit into this view.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1645","year":"2015","publisher":"IEEE","department":[{"_id":"KrPi"}],"publication_status":"published","status":"public","title":"Secret-key cryptography from ideal primitives: A systematic verview","author":[{"full_name":"Gazi, Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Gazi"},{"full_name":"Tessaro, Stefano","last_name":"Tessaro","first_name":"Stefano"}],"oa_version":"None","date_created":"2018-12-11T11:53:13Z","date_updated":"2021-01-12T06:52:13Z"},{"file_date_updated":"2020-07-14T12:45:08Z","ec_funded":1,"publist_id":"5496","year":"2015","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","author":[{"full_name":"Gazi, Peter","last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"first_name":"Stefano","last_name":"Tessaro","full_name":"Tessaro, Stefano"}],"date_updated":"2021-01-12T06:52:16Z","date_created":"2018-12-11T11:53:17Z","volume":9453,"month":"12","oa":1,"quality_controlled":"1","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"ASIACRYPT: Theory and Application of Cryptology and Information Security","location":"Auckland, New Zealand","start_date":"2015-11-29","end_date":"2015-12-03"},"doi":"10.1007/978-3-662-48800-3_4","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"HMAC and its variant NMAC are the most popular approaches to deriving a MAC (and more generally, a PRF) from a cryptographic hash function. Despite nearly two decades of research, their exact security still remains far from understood in many different contexts. Indeed, recent works have re-surfaced interest for {\\em generic} attacks, i.e., attacks that treat the compression function of the underlying hash function as a black box.\r\n\r\nGeneric security can be proved in a model where the underlying compression function is modeled as a random function -- yet, to date, the question of proving tight, non-trivial bounds on the generic security of HMAC/NMAC even as a PRF remains a challenging open question.\r\n\r\nIn this paper, we ask the question of whether a small modification to HMAC and NMAC can allow us to exactly characterize the security of the resulting constructions, while only incurring little penalty with respect to efficiency. To this end, we present simple variants of NMAC and HMAC, for which we prove tight bounds on the generic PRF security, expressed in terms of numbers of construction and compression function queries necessary to break the construction. All of our constructions are obtained via a (near) {\\em black-box} modification of NMAC and HMAC, which can be interpreted as an initial step of key-dependent message pre-processing.\r\n\r\nWhile our focus is on PRF security, a further attractive feature of our new constructions is that they clearly defeat all recent generic attacks against properties such as state recovery and universal forgery. These exploit properties of the so-called ``functional graph'' which are not directly accessible in our new constructions. ","lang":"eng"}],"_id":"1654","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004","005"],"status":"public","title":"Generic security of NMAC and HMAC with input whitening","intvolume":" 9453","pubrep_id":"676","oa_version":"Submitted Version","file":[{"file_id":"4732","relation":"main_file","checksum":"d1e53203db2d8573a560995ccdffac62","date_updated":"2020-07-14T12:45:08Z","date_created":"2018-12-12T10:09:09Z","access_level":"open_access","file_name":"IST-2016-676-v1+1_881.pdf","creator":"system","file_size":512071,"content_type":"application/pdf"}],"scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"30","has_accepted_license":"1","citation":{"ista":"Gazi P, Pietrzak KZ, Tessaro S. 2015. Generic security of NMAC and HMAC with input whitening. 9453, 85–109.","ieee":"P. Gazi, K. Z. Pietrzak, and S. Tessaro, “Generic security of NMAC and HMAC with input whitening,” vol. 9453. Springer, pp. 85–109, 2015.","apa":"Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). Generic security of NMAC and HMAC with input whitening. Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48800-3_4","ama":"Gazi P, Pietrzak KZ, Tessaro S. Generic security of NMAC and HMAC with input whitening. 2015;9453:85-109. doi:10.1007/978-3-662-48800-3_4","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “Generic Security of NMAC and HMAC with Input Whitening.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48800-3_4.","mla":"Gazi, Peter, et al. Generic Security of NMAC and HMAC with Input Whitening. Vol. 9453, Springer, 2015, pp. 85–109, doi:10.1007/978-3-662-48800-3_4.","short":"P. Gazi, K.Z. Pietrzak, S. Tessaro, 9453 (2015) 85–109."},"page":"85 - 109","date_published":"2015-12-30T00:00:00Z"},{"month":"06","doi":"10.1007/978-3-662-47672-7_85","conference":{"name":"ICALP: Automata, Languages and Programming","location":"Kyoto, Japan","start_date":"2015-07-06","end_date":"2015-07-10"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"quality_controlled":"1","ec_funded":1,"publist_id":"5500","file_date_updated":"2020-07-14T12:45:08Z","author":[{"full_name":"Skórski, Maciej","last_name":"Skórski","first_name":"Maciej"},{"full_name":"Golovnev, Alexander","first_name":"Alexander","last_name":"Golovnev"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"volume":9134,"date_created":"2018-12-11T11:53:15Z","date_updated":"2021-01-12T06:52:15Z","year":"2015","department":[{"_id":"KrPi"}],"publisher":"Springer","publication_status":"published","has_accepted_license":"1","day":"20","scopus_import":1,"date_published":"2015-06-20T00:00:00Z","citation":{"ama":"Skórski M, Golovnev A, Pietrzak KZ. Condensed unpredictability . In: Vol 9134. Springer; 2015:1046-1057. doi:10.1007/978-3-662-47672-7_85","apa":"Skórski, M., Golovnev, A., & Pietrzak, K. Z. (2015). Condensed unpredictability (Vol. 9134, pp. 1046–1057). Presented at the ICALP: Automata, Languages and Programming, Kyoto, Japan: Springer. https://doi.org/10.1007/978-3-662-47672-7_85","ieee":"M. Skórski, A. Golovnev, and K. Z. Pietrzak, “Condensed unpredictability ,” presented at the ICALP: Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 1046–1057.","ista":"Skórski M, Golovnev A, Pietrzak KZ. 2015. Condensed unpredictability . ICALP: Automata, Languages and Programming, LNCS, vol. 9134, 1046–1057.","short":"M. Skórski, A. Golovnev, K.Z. Pietrzak, in:, Springer, 2015, pp. 1046–1057.","mla":"Skórski, Maciej, et al. Condensed Unpredictability . Vol. 9134, Springer, 2015, pp. 1046–57, doi:10.1007/978-3-662-47672-7_85.","chicago":"Skórski, Maciej, Alexander Golovnev, and Krzysztof Z Pietrzak. “Condensed Unpredictability ,” 9134:1046–57. Springer, 2015. https://doi.org/10.1007/978-3-662-47672-7_85."},"page":"1046 - 1057","abstract":[{"text":"We consider the task of deriving a key with high HILL entropy (i.e., being computationally indistinguishable from a key with high min-entropy) from an unpredictable source.\r\n\r\nPrevious to this work, the only known way to transform unpredictability into a key that was ϵ indistinguishable from having min-entropy was via pseudorandomness, for example by Goldreich-Levin (GL) hardcore bits. This approach has the inherent limitation that from a source with k bits of unpredictability entropy one can derive a key of length (and thus HILL entropy) at most k−2log(1/ϵ) bits. In many settings, e.g. when dealing with biometric data, such a 2log(1/ϵ) bit entropy loss in not an option. Our main technical contribution is a theorem that states that in the high entropy regime, unpredictability implies HILL entropy. Concretely, any variable K with |K|−d bits of unpredictability entropy has the same amount of so called metric entropy (against real-valued, deterministic distinguishers), which is known to imply the same amount of HILL entropy. The loss in circuit size in this argument is exponential in the entropy gap d, and thus this result only applies for small d (i.e., where the size of distinguishers considered is exponential in d).\r\n\r\nTo overcome the above restriction, we investigate if it’s possible to first “condense” unpredictability entropy and make the entropy gap small. We show that any source with k bits of unpredictability can be condensed into a source of length k with k−3 bits of unpredictability entropy. Our condenser simply “abuses" the GL construction and derives a k bit key from a source with k bits of unpredicatibily. The original GL theorem implies nothing when extracting that many bits, but we show that in this regime, GL still behaves like a “condenser" for unpredictability. This result comes with two caveats (1) the loss in circuit size is exponential in k and (2) we require that the source we start with has no HILL entropy (equivalently, one can efficiently check if a guess is correct). We leave it as an intriguing open problem to overcome these restrictions or to prove they’re inherent.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"pubrep_id":"675","file":[{"access_level":"open_access","file_name":"IST-2016-675-v1+1_384.pdf","content_type":"application/pdf","file_size":525503,"creator":"system","relation":"main_file","file_id":"4693","checksum":"e808c7eecb631336fc9f9bf2e8d4ecae","date_created":"2018-12-12T10:08:32Z","date_updated":"2020-07-14T12:45:08Z"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1650","intvolume":" 9134","title":"Condensed unpredictability ","status":"public","ddc":["000","005"]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-662-46447-2_5"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"conference":{"end_date":"2015-04-01","start_date":"2015-03-30","location":"Gaithersburg, MD, United States","name":"PKC: Public Key Crypography"},"doi":"10.1007/978-3-662-46447-2_5","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"isbn":["978-3-662-46446-5"]},"year":"2015","acknowledgement":"Work done as an intern in Microsoft Research Redmond and as a student at Brown University, where supported by NSF grant 0964379. Supported by the European Research Council, ERC Starting Grant (259668-PSPC).","publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"author":[{"full_name":"Baldimtsi, Foteini","first_name":"Foteini","last_name":"Baldimtsi"},{"full_name":"Chase, Melissa","first_name":"Melissa","last_name":"Chase"},{"first_name":"Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"full_name":"Kohlweiss, Markulf","last_name":"Kohlweiss","first_name":"Markulf"}],"date_updated":"2022-05-23T10:08:37Z","date_created":"2018-12-11T11:53:15Z","volume":9020,"ec_funded":1,"publist_id":"5499","publication":"Public-Key Cryptography - PKC 2015","citation":{"short":"F. Baldimtsi, M. Chase, G. Fuchsbauer, M. Kohlweiss, in:, Public-Key Cryptography - PKC 2015, Springer, 2015, pp. 101–124.","mla":"Baldimtsi, Foteini, et al. “Anonymous Transferable E-Cash.” Public-Key Cryptography - PKC 2015, vol. 9020, Springer, 2015, pp. 101–24, doi:10.1007/978-3-662-46447-2_5.","chicago":"Baldimtsi, Foteini, Melissa Chase, Georg Fuchsbauer, and Markulf Kohlweiss. “Anonymous Transferable E-Cash.” In Public-Key Cryptography - PKC 2015, 9020:101–24. Springer, 2015. https://doi.org/10.1007/978-3-662-46447-2_5.","ama":"Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. Anonymous transferable e-cash. In: Public-Key Cryptography - PKC 2015. Vol 9020. Springer; 2015:101-124. doi:10.1007/978-3-662-46447-2_5","apa":"Baldimtsi, F., Chase, M., Fuchsbauer, G., & Kohlweiss, M. (2015). Anonymous transferable e-cash. In Public-Key Cryptography - PKC 2015 (Vol. 9020, pp. 101–124). Gaithersburg, MD, United States: Springer. https://doi.org/10.1007/978-3-662-46447-2_5","ieee":"F. Baldimtsi, M. Chase, G. Fuchsbauer, and M. Kohlweiss, “Anonymous transferable e-cash,” in Public-Key Cryptography - PKC 2015, Gaithersburg, MD, United States, 2015, vol. 9020, pp. 101–124.","ista":"Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. 2015. Anonymous transferable e-cash. Public-Key Cryptography - PKC 2015. PKC: Public Key Crypography, LNCS, vol. 9020, 101–124."},"page":"101 - 124","date_published":"2015-03-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1651","status":"public","title":"Anonymous transferable e-cash","intvolume":" 9020","oa_version":"Published Version","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Cryptographic e-cash allows off-line electronic transactions between a bank, users and merchants in a secure and anonymous fashion. A plethora of e-cash constructions has been proposed in the literature; however, these traditional e-cash schemes only allow coins to be transferred once between users and merchants. Ideally, we would like users to be able to transfer coins between each other multiple times before deposit, as happens with physical cash. “Transferable” e-cash schemes are the solution to this problem. Unfortunately, the currently proposed schemes are either completely impractical or do not achieve the desirable anonymity properties without compromises, such as assuming the existence of a trusted “judge” who can trace all coins and users in the system. This paper presents the first efficient and fully anonymous transferable e-cash scheme without any trusted third parties. We start by revising the security and anonymity properties of transferable e-cash to capture issues that were previously overlooked. For our construction we use the recently proposed malleable signatures by Chase et al. to allow the secure and anonymous transfer of coins, combined with a new efficient double-spending detection mechanism. Finally, we discuss an instantiation of our construction.","lang":"eng"}]},{"year":"2015","_id":"1652","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"publisher":"ACM","status":"public","publication_status":"published","title":"High parallel complexity graphs and memory-hard functions","author":[{"full_name":"Alwen, Joel F","first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Serbinenko","first_name":"Vladimir","full_name":"Serbinenko, Vladimir"}],"oa_version":"Submitted Version","date_updated":"2021-01-12T06:52:16Z","date_created":"2018-12-11T11:53:16Z","type":"conference","ec_funded":1,"publist_id":"5498","abstract":[{"text":"We develop new theoretical tools for proving lower-bounds on the (amortized) complexity of certain functions in models of parallel computation. We apply the tools to construct a class of functions with high amortized memory complexity in the parallel Random Oracle Model (pROM); a variant of the standard ROM allowing for batches of simultaneous queries. In particular we obtain a new, more robust, type of Memory-Hard Functions (MHF); a security primitive which has recently been gaining acceptance in practice as an effective means of countering brute-force attacks on security relevant functions. Along the way we also demonstrate an important shortcoming of previous definitions of MHFs and give a new definition addressing the problem. The tools we develop represent an adaptation of the powerful pebbling paradigm (initially introduced by Hewitt and Paterson [HP70] and Cook [Coo73]) to a simple and intuitive parallel setting. We define a simple pebbling game Gp over graphs which aims to abstract parallel computation in an intuitive way. As a conceptual contribution we define a measure of pebbling complexity for graphs called cumulative complexity (CC) and show how it overcomes a crucial shortcoming (in the parallel setting) exhibited by more traditional complexity measures used in the past. As a main technical contribution we give an explicit construction of a constant in-degree family of graphs whose CC in Gp approaches maximality to within a polylogarithmic factor for any graph of equal size (analogous to the graphs of Tarjan et. al. [PTC76, LT82] for sequential pebbling games). Finally, for a given graph G and related function fG, we derive a lower-bound on the amortized memory complexity of fG in the pROM in terms of the CC of G in the game Gp.","lang":"eng"}],"citation":{"ama":"Alwen JF, Serbinenko V. High parallel complexity graphs and memory-hard functions. In: Proceedings of the 47th Annual ACM Symposium on Theory of Computing. ACM; 2015:595-603. doi:10.1145/2746539.2746622","ista":"Alwen JF, Serbinenko V. 2015. High parallel complexity graphs and memory-hard functions. Proceedings of the 47th annual ACM symposium on Theory of computing. STOC: Symposium on the Theory of Computing, 595–603.","ieee":"J. F. Alwen and V. Serbinenko, “High parallel complexity graphs and memory-hard functions,” in Proceedings of the 47th annual ACM symposium on Theory of computing, Portland, OR, United States, 2015, pp. 595–603.","apa":"Alwen, J. F., & Serbinenko, V. (2015). High parallel complexity graphs and memory-hard functions. In Proceedings of the 47th annual ACM symposium on Theory of computing (pp. 595–603). Portland, OR, United States: ACM. https://doi.org/10.1145/2746539.2746622","mla":"Alwen, Joel F., and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” Proceedings of the 47th Annual ACM Symposium on Theory of Computing, ACM, 2015, pp. 595–603, doi:10.1145/2746539.2746622.","short":"J.F. Alwen, V. Serbinenko, in:, Proceedings of the 47th Annual ACM Symposium on Theory of Computing, ACM, 2015, pp. 595–603.","chicago":"Alwen, Joel F, and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” In Proceedings of the 47th Annual ACM Symposium on Theory of Computing, 595–603. ACM, 2015. https://doi.org/10.1145/2746539.2746622."},"main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2014/238"}],"oa":1,"publication":"Proceedings of the 47th annual ACM symposium on Theory of computing","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"page":"595 - 603","quality_controlled":"1","date_published":"2015-06-01T00:00:00Z","doi":"10.1145/2746539.2746622","conference":{"name":"STOC: Symposium on the Theory of Computing","location":"Portland, OR, United States","start_date":"2015-06-14","end_date":"2015-06-17"},"language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"06"},{"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-23401-4_8","conference":{"location":"Nantes, France","start_date":"2015-09-16","end_date":"2015-09-18","name":"CMSB: Computational Methods in Systems Biology"},"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","ec_funded":1,"publist_id":"5492","volume":9308,"date_updated":"2023-02-21T16:17:24Z","date_created":"2018-12-11T11:53:18Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"1148"}]},"author":[{"full_name":"Bogomolov, Sergiy","first_name":"Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Andreas","last_name":"Podelski","full_name":"Podelski, Andreas"},{"full_name":"Ruess, Jakob","first_name":"Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling"}],"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publisher":"Springer","publication_status":"published","year":"2015","day":"01","series_title":"Lecture Notes in Computer Science","scopus_import":1,"date_published":"2015-09-01T00:00:00Z","page":"77 - 89","citation":{"chicago":"Bogomolov, Sergiy, Thomas A Henzinger, Andreas Podelski, Jakob Ruess, and Christian Schilling. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-23401-4_8.","mla":"Bogomolov, Sergiy, et al. Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks. Vol. 9308, Springer, 2015, pp. 77–89, doi:10.1007/978-3-319-23401-4_8.","short":"S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, C. Schilling, 9308 (2015) 77–89.","ista":"Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. 2015. Adaptive moment closure for parameter inference of biochemical reaction networks. 9308, 77–89.","ieee":"S. Bogomolov, T. A. Henzinger, A. Podelski, J. Ruess, and C. Schilling, “Adaptive moment closure for parameter inference of biochemical reaction networks,” vol. 9308. Springer, pp. 77–89, 2015.","apa":"Bogomolov, S., Henzinger, T. A., Podelski, A., Ruess, J., & Schilling, C. (2015). Adaptive moment closure for parameter inference of biochemical reaction networks. Presented at the CMSB: Computational Methods in Systems Biology, Nantes, France: Springer. https://doi.org/10.1007/978-3-319-23401-4_8","ama":"Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. Adaptive moment closure for parameter inference of biochemical reaction networks. 2015;9308:77-89. doi:10.1007/978-3-319-23401-4_8"},"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."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"None","intvolume":" 9308","status":"public","title":"Adaptive moment closure for parameter inference of biochemical reaction networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1658"},{"publist_id":"5490","ec_funded":1,"abstract":[{"lang":"eng","text":"We study the pattern frequency vector for runs in probabilistic Vector Addition Systems with States (pVASS). Intuitively, each configuration of a given pVASS is assigned one of finitely many patterns, and every run can thus be seen as an infinite sequence of these patterns. The pattern frequency vector assigns to each run the limit of pattern frequencies computed for longer and longer prefixes of the run. If the limit does not exist, then the vector is undefined. We show that for one-counter pVASS, the pattern frequency vector is defined and takes one of finitely many values for almost all runs. Further, these values and their associated probabilities can be approximated up to an arbitrarily small relative error in polynomial time. For stable two-counter pVASS, we show the same result, but we do not provide any upper complexity bound. As a byproduct of our study, we discover counterexamples falsifying some classical results about stochastic Petri nets published in the 80s."}],"type":"conference","alternative_title":["LICS"],"author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"first_name":"Stefan","last_name":"Kiefer","full_name":"Kiefer, Stefan"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"},{"full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny"}],"oa_version":"Preprint","date_created":"2018-12-11T11:53:19Z","date_updated":"2021-01-12T06:52:20Z","_id":"1660","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"publisher":"IEEE","title":"Long-run average behaviour of probabilistic vector addition systems","status":"public","publication_status":"published","month":"07","day":"01","scopus_import":1,"date_published":"2015-07-01T00:00:00Z","doi":"10.1109/LICS.2015.15","conference":{"name":"LICS: Logic in Computer Science","location":"Kyoto, Japan","start_date":"2015-07-06","end_date":"2015-07-10"},"language":[{"iso":"eng"}],"citation":{"ama":"Brázdil T, Kiefer S, Kučera A, Novotný P. Long-run average behaviour of probabilistic vector addition systems. In: IEEE; 2015:44-55. doi:10.1109/LICS.2015.15","ieee":"T. Brázdil, S. Kiefer, A. Kučera, and P. Novotný, “Long-run average behaviour of probabilistic vector addition systems,” presented at the LICS: Logic in Computer Science, Kyoto, Japan, 2015, pp. 44–55.","apa":"Brázdil, T., Kiefer, S., Kučera, A., & Novotný, P. (2015). Long-run average behaviour of probabilistic vector addition systems (pp. 44–55). Presented at the LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.15","ista":"Brázdil T, Kiefer S, Kučera A, Novotný P. 2015. Long-run average behaviour of probabilistic vector addition systems. LICS: Logic in Computer Science, LICS, , 44–55.","short":"T. Brázdil, S. Kiefer, A. Kučera, P. Novotný, in:, IEEE, 2015, pp. 44–55.","mla":"Brázdil, Tomáš, et al. Long-Run Average Behaviour of Probabilistic Vector Addition Systems. IEEE, 2015, pp. 44–55, doi:10.1109/LICS.2015.15.","chicago":"Brázdil, Tomáš, Stefan Kiefer, Antonín Kučera, and Petr Novotný. “Long-Run Average Behaviour of Probabilistic Vector Addition Systems,” 44–55. IEEE, 2015. https://doi.org/10.1109/LICS.2015.15."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.02655"}],"oa":1,"page":"44 - 55","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1"},{"date_created":"2018-12-11T11:53:21Z","date_updated":"2021-01-12T06:52:23Z","volume":526,"author":[{"last_name":"Landau","first_name":"Dan","full_name":"Landau, Dan"},{"full_name":"Tausch, Eugen","first_name":"Eugen","last_name":"Tausch"},{"last_name":"Taylor Weiner","first_name":"Amaro","full_name":"Taylor Weiner, Amaro"},{"full_name":"Stewart, Chip","first_name":"Chip","last_name":"Stewart"},{"full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","first_name":"Johannes"},{"full_name":"Bahlo, Jasmin","last_name":"Bahlo","first_name":"Jasmin"},{"last_name":"Kluth","first_name":"Sandra","full_name":"Kluth, Sandra"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"full_name":"Lawrence, Michael","first_name":"Michael","last_name":"Lawrence"},{"full_name":"Böttcher, Sebastian","last_name":"Böttcher","first_name":"Sebastian"},{"full_name":"Carter, Scott","last_name":"Carter","first_name":"Scott"},{"full_name":"Cibulskis, Kristian","first_name":"Kristian","last_name":"Cibulskis"},{"last_name":"Mertens","first_name":"Daniel","full_name":"Mertens, Daniel"},{"full_name":"Sougnez, Carrie","last_name":"Sougnez","first_name":"Carrie"},{"first_name":"Mara","last_name":"Rosenberg","full_name":"Rosenberg, Mara"},{"first_name":"Julian","last_name":"Hess","full_name":"Hess, Julian"},{"full_name":"Edelmann, Jennifer","last_name":"Edelmann","first_name":"Jennifer"},{"last_name":"Kless","first_name":"Sabrina","full_name":"Kless, Sabrina"},{"last_name":"Kneba","first_name":"Michael","full_name":"Kneba, Michael"},{"full_name":"Ritgen, Matthias","first_name":"Matthias","last_name":"Ritgen"},{"first_name":"Anna","last_name":"Fink","full_name":"Fink, Anna"},{"last_name":"Fischer","first_name":"Kirsten","full_name":"Fischer, Kirsten"},{"full_name":"Gabriel, Stacey","first_name":"Stacey","last_name":"Gabriel"},{"full_name":"Lander, Eric","first_name":"Eric","last_name":"Lander"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"last_name":"Döhner","first_name":"Hartmut","full_name":"Döhner, Hartmut"},{"first_name":"Michael","last_name":"Hallek","full_name":"Hallek, Michael"},{"last_name":"Neuberg","first_name":"Donna","full_name":"Neuberg, Donna"},{"first_name":"Gad","last_name":"Getz","full_name":"Getz, Gad"},{"full_name":"Stilgenbauer, Stephan","first_name":"Stephan","last_name":"Stilgenbauer"},{"last_name":"Wu","first_name":"Catherine","full_name":"Wu, Catherine"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"year":"2015","pmid":1,"publist_id":"5484","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1038/nature15395","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"pmid":["26466571"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815041/","open_access":"1"}],"month":"10","oa_version":"Submitted Version","status":"public","title":"Mutations driving CLL and their evolution in progression and relapse","intvolume":" 526","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1665","abstract":[{"text":"Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signalling as central pathways involved in CLL. Clonality analysis of this large data set further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing data sets of clinically informative samples enable the discovery of novel genes associated with cancer, the network of relationships between the driver events, and their impact on disease relapse and clinical outcome.","lang":"eng"}],"issue":"7574","type":"journal_article","date_published":"2015-10-22T00:00:00Z","article_type":"original","page":"525 - 530","publication":"Nature","citation":{"ista":"Landau D, Tausch E, Taylor Weiner A, Stewart C, Reiter J, Bahlo J, Kluth S, Božić I, Lawrence M, Böttcher S, Carter S, Cibulskis K, Mertens D, Sougnez C, Rosenberg M, Hess J, Edelmann J, Kless S, Kneba M, Ritgen M, Fink A, Fischer K, Gabriel S, Lander E, Nowak M, Döhner H, Hallek M, Neuberg D, Getz G, Stilgenbauer S, Wu C. 2015. Mutations driving CLL and their evolution in progression and relapse. Nature. 526(7574), 525–530.","apa":"Landau, D., Tausch, E., Taylor Weiner, A., Stewart, C., Reiter, J., Bahlo, J., … Wu, C. (2015). Mutations driving CLL and their evolution in progression and relapse. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15395","ieee":"D. Landau et al., “Mutations driving CLL and their evolution in progression and relapse,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 525–530, 2015.","ama":"Landau D, Tausch E, Taylor Weiner A, et al. Mutations driving CLL and their evolution in progression and relapse. Nature. 2015;526(7574):525-530. doi:10.1038/nature15395","chicago":"Landau, Dan, Eugen Tausch, Amaro Taylor Weiner, Chip Stewart, Johannes Reiter, Jasmin Bahlo, Sandra Kluth, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15395.","mla":"Landau, Dan, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 525–30, doi:10.1038/nature15395.","short":"D. Landau, E. Tausch, A. Taylor Weiner, C. Stewart, J. Reiter, J. Bahlo, S. Kluth, I. Božić, M. Lawrence, S. Böttcher, S. Carter, K. Cibulskis, D. Mertens, C. Sougnez, M. Rosenberg, J. Hess, J. Edelmann, S. Kless, M. Kneba, M. Ritgen, A. Fink, K. Fischer, S. Gabriel, E. Lander, M. Nowak, H. Döhner, M. Hallek, D. Neuberg, G. Getz, S. Stilgenbauer, C. Wu, Nature 526 (2015) 525–530."},"day":"22","article_processing_charge":"No","scopus_import":1},{"month":"11","doi":"10.1016/j.cellsig.2015.08.001","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"file_date_updated":"2020-07-14T12:45:10Z","ec_funded":1,"publist_id":"5487","author":[{"id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","last_name":"Kovács","first_name":"Krisztián","full_name":"Kovács, Krisztián"},{"full_name":"Steinmann, Myriam","last_name":"Steinmann","first_name":"Myriam"},{"last_name":"Halfon","first_name":"Olivier","full_name":"Halfon, Olivier"},{"last_name":"Magistretti","first_name":"Pierre","full_name":"Magistretti, Pierre"},{"last_name":"Cardinaux","first_name":"Jean","full_name":"Cardinaux, Jean"}],"date_created":"2018-12-11T11:53:20Z","date_updated":"2021-01-12T06:52:22Z","volume":27,"year":"2015","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JoCs"}],"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2015-11-01T00:00:00Z","publication":"Cellular Signalling","citation":{"chicago":"Kovács, Krisztián, Myriam Steinmann, Olivier Halfon, Pierre Magistretti, and Jean Cardinaux. “Complex Regulation of CREB-Binding Protein by Homeodomain-Interacting Protein Kinase 2.” Cellular Signalling. Elsevier, 2015. https://doi.org/10.1016/j.cellsig.2015.08.001.","mla":"Kovács, Krisztián, et al. “Complex Regulation of CREB-Binding Protein by Homeodomain-Interacting Protein Kinase 2.” Cellular Signalling, vol. 27, no. 11, Elsevier, 2015, pp. 2252–60, doi:10.1016/j.cellsig.2015.08.001.","short":"K. Kovács, M. Steinmann, O. Halfon, P. Magistretti, J. Cardinaux, Cellular Signalling 27 (2015) 2252–2260.","ista":"Kovács K, Steinmann M, Halfon O, Magistretti P, Cardinaux J. 2015. Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. 27(11), 2252–2260.","ieee":"K. Kovács, M. Steinmann, O. Halfon, P. Magistretti, and J. Cardinaux, “Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2,” Cellular Signalling, vol. 27, no. 11. Elsevier, pp. 2252–2260, 2015.","apa":"Kovács, K., Steinmann, M., Halfon, O., Magistretti, P., & Cardinaux, J. (2015). Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. Elsevier. https://doi.org/10.1016/j.cellsig.2015.08.001","ama":"Kovács K, Steinmann M, Halfon O, Magistretti P, Cardinaux J. Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. 2015;27(11):2252-2260. doi:10.1016/j.cellsig.2015.08.001"},"page":"2252 - 2260","abstract":[{"lang":"eng","text":"CREB-binding protein (CBP) and p300 are transcriptional coactivators involved in numerous biological processes that affect cell growth, transformation, differentiation, and development. In this study, we provide evidence of the involvement of homeodomain-interacting protein kinase 2 (HIPK2) in the regulation of CBP activity. We show that HIPK2 interacts with and phosphorylates several regions of CBP. We demonstrate that serines 2361, 2363, 2371, 2376, and 2381 are responsible for the HIPK2-induced mobility shift of CBP C-terminal activation domain. Moreover, we show that HIPK2 strongly potentiates the transcriptional activity of CBP. However, our data suggest that HIPK2 activates CBP mainly by counteracting the repressive action of cell cycle regulatory domain 1 (CRD1), located between amino acids 977 and 1076, independently of CBP phosphorylation. Our findings thus highlight a complex regulation of CBP activity by HIPK2, which might be relevant for the control of specific sets of target genes involved in cellular proliferation, differentiation and apoptosis."}],"issue":"11","type":"journal_article","pubrep_id":"578","oa_version":"Published Version","file":[{"file_id":"5321","relation":"main_file","checksum":"4ee690b6444b7a43523237f0941457d1","date_updated":"2020-07-14T12:45:10Z","date_created":"2018-12-12T10:18:03Z","access_level":"local","file_name":"IST-2016-578-v1+1_CLS-D-15-00072R1_.pdf","creator":"system","content_type":"application/pdf","file_size":1735337}],"_id":"1663","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2","status":"public","intvolume":" 27"},{"page":"141 - 159","citation":{"chicago":"Brázdil, Tomáš, L’Uboš Korenčiak, Jan Krčál, Petr Novotný, and Vojtěch Řehák. “Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22264-6_10.","mla":"Brázdil, Tomáš, et al. Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis. Vol. 9259, Springer, 2015, pp. 141–59, doi:10.1007/978-3-319-22264-6_10.","short":"T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, V. Řehák, 9259 (2015) 141–159.","ista":"Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. 2015. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 9259, 141–159.","apa":"Brázdil, T., Korenčiak, L., Krčál, J., Novotný, P., & Řehák, V. (2015). Optimizing performance of continuous-time stochastic systems using timeout synthesis. Presented at the QEST: Quantitative Evaluation of Systems, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-22264-6_10","ieee":"T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, and V. Řehák, “Optimizing performance of continuous-time stochastic systems using timeout synthesis,” vol. 9259. Springer, pp. 141–159, 2015.","ama":"Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 2015;9259:141-159. doi:10.1007/978-3-319-22264-6_10"},"date_published":"2015-08-22T00:00:00Z","series_title":"Lecture Notes in Computer Science","scopus_import":1,"day":"22","intvolume":" 9259","title":"Optimizing performance of continuous-time stochastic systems using timeout synthesis","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1667","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We consider parametric version of fixed-delay continuoustime Markov chains (or equivalently deterministic and stochastic Petri nets, DSPN) where fixed-delay transitions are specified by parameters, rather than concrete values. Our goal is to synthesize values of these parameters that, for a given cost function, minimise expected total cost incurred before reaching a given set of target states. We show that under mild assumptions, optimal values of parameters can be effectively approximated using translation to a Markov decision process (MDP) whose actions correspond to discretized values of these parameters. To this end we identify and overcome several interesting phenomena arising in systems with fixed delays.","lang":"eng"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1407.4777","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-22264-6_10","conference":{"name":"QEST: Quantitative Evaluation of Systems","start_date":"2015-09-01","location":"Madrid, Spain","end_date":"2015-09-03"},"month":"08","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n∘ [291734]. This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the Czech Science Foundation, grant No. 15-17564S, and by the CAS/SAFEA International Partnership Program for Creative Research Teams.","year":"2015","volume":9259,"date_updated":"2021-01-12T06:52:24Z","date_created":"2018-12-11T11:53:22Z","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"full_name":"Korenčiak, L'Uboš","last_name":"Korenčiak","first_name":"L'Uboš"},{"first_name":"Jan","last_name":"Krčál","full_name":"Krčál, Jan"},{"first_name":"Petr","last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr"},{"first_name":"Vojtěch","last_name":"Řehák","full_name":"Řehák, Vojtěch"}],"publist_id":"5482","ec_funded":1},{"oa_version":"Preprint","intvolume":" 526","title":"The rise of fully turbulent flow","status":"public","_id":"1664","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7574","abstract":[{"text":"Over a century of research into the origin of turbulence in wall-bounded shear flows has resulted in a puzzling picture in which turbulence appears in a variety of different states competing with laminar background flow. At moderate flow speeds, turbulence is confined to localized patches; it is only at higher speeds that the entire flow becomes turbulent. The origin of the different states encountered during this transition, the front dynamics of the turbulent regions and the transformation to full turbulence have yet to be explained. By combining experiments, theory and computer simulations, here we uncover a bifurcation scenario that explains the transformation to fully turbulent pipe flow and describe the front dynamics of the different states encountered in the process. Key to resolving this problem is the interpretation of the flow as a bistable system with nonlinear propagation (advection) of turbulent fronts. These findings bridge the gap between our understanding of the onset of turbulence and fully turbulent flows.","lang":"eng"}],"type":"journal_article","date_published":"2015-10-21T00:00:00Z","page":"550 - 553","citation":{"ieee":"D. Barkley, B. Song, M. Vasudevan, G. M. Lemoult, M. Avila, and B. Hof, “The rise of fully turbulent flow,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 550–553, 2015.","apa":"Barkley, D., Song, B., Vasudevan, M., Lemoult, G. M., Avila, M., & Hof, B. (2015). The rise of fully turbulent flow. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15701","ista":"Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. 2015. The rise of fully turbulent flow. Nature. 526(7574), 550–553.","ama":"Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. The rise of fully turbulent flow. Nature. 2015;526(7574):550-553. doi:10.1038/nature15701","chicago":"Barkley, Dwight, Baofang Song, Mukund Vasudevan, Grégoire M Lemoult, Marc Avila, and Björn Hof. “The Rise of Fully Turbulent Flow.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15701.","short":"D. Barkley, B. Song, M. Vasudevan, G.M. Lemoult, M. Avila, B. Hof, Nature 526 (2015) 550–553.","mla":"Barkley, Dwight, et al. “The Rise of Fully Turbulent Flow.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 550–53, doi:10.1038/nature15701."},"publication":"Nature","day":"21","scopus_import":1,"volume":526,"date_created":"2018-12-11T11:53:20Z","date_updated":"2021-01-12T06:52:22Z","author":[{"full_name":"Barkley, Dwight","first_name":"Dwight","last_name":"Barkley"},{"first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang"},{"id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","first_name":"Mukund","last_name":"Vasudevan","full_name":"Vasudevan, Mukund"},{"first_name":"Grégoire M","last_name":"Lemoult","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","full_name":"Lemoult, Grégoire M"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"publisher":"Nature Publishing Group","department":[{"_id":"BjHo"}],"publication_status":"published","acknowledgement":"We acknowledge the Deutsche Forschungsgemeinschaft (Project No. FOR 1182), and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589 for financial support. B.S. acknowledges financial support from the Chinese State Scholarship Fund under grant number 2010629145. B.S. acknowledges support from the International Max Planck Research School for the Physics of Biological and Complex Systems and the Göttingen Graduate School for Neurosciences and Molecular Biosciences. We acknowledge computing resources from GWDG (Gesellschaft für wissenschaftliche Datenverarbeitung Göttingen) and the Jülich Supercomputing Centre (grant HGU16) where the simulations were performed.","year":"2015","publist_id":"5485","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1038/nature15701","project":[{"call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1510.09143","open_access":"1"}],"month":"10"},{"abstract":[{"text":"Composable notions of incoercibility aim to forbid a coercer from using anything beyond the coerced parties’ inputs and outputs to catch them when they try to deceive him. Existing definitions are restricted to weak coercion types, and/or are not universally composable. Furthermore, they often make too strong assumptions on the knowledge of coerced parties—e.g., they assume they known the identities and/or the strategies of other coerced parties, or those of corrupted parties— which makes them unsuitable for applications of incoercibility such as e-voting, where colluding adversarial parties may attempt to coerce honest voters, e.g., by offering them money for a promised vote, and use their own view to check that the voter keeps his end of the bargain. In this work we put forward the first universally composable notion of incoercible multi-party computation, which satisfies the above intuition and does not assume collusions among coerced parties or knowledge of the corrupted set. We define natural notions of UC incoercibility corresponding to standard coercion-types, i.e., receipt-freeness and resistance to full-active coercion. Importantly, our suggested notion has the unique property that it builds on top of the well studied UC framework by Canetti instead of modifying it. This guarantees backwards compatibility, and allows us to inherit results from the rich UC literature. We then present MPC protocols which realize our notions of UC incoercibility given access to an arguably minimal setup—namely honestly generate tamper-proof hardware performing a very simple cryptographic operation—e.g., a smart card. This is, to our knowledge, the first proposed construction of an MPC protocol (for more than two parties) that is incoercibly secure and universally composable, and therefore the first construction of a universally composable receipt-free e-voting protocol.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":397363,"access_level":"open_access","file_name":"2015_CRYPTO_Alwen.pdf","checksum":"5b6649e80d1f781a8910f7cce6427f78","date_updated":"2020-07-14T12:45:11Z","date_created":"2020-05-15T08:55:29Z","file_id":"7853","relation":"main_file"}],"intvolume":" 9216","status":"public","ddc":["000"],"title":"Incoercible multi-party computation and universally composable receipt-free voting","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1672","has_accepted_license":"1","article_processing_charge":"No","day":"01","series_title":"Lecture Notes in Computer Science","scopus_import":"1","date_published":"2015-08-01T00:00:00Z","page":"763 - 780","citation":{"chicago":"Alwen, Joel F, Rafail Ostrovsky, Hongsheng Zhou, and Vassilis Zikas. “Incoercible Multi-Party Computation and Universally Composable Receipt-Free Voting.” In Advances in Cryptology - CRYPTO 2015, 9216:763–80. Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_37.","mla":"Alwen, Joel F., et al. “Incoercible Multi-Party Computation and Universally Composable Receipt-Free Voting.” Advances in Cryptology - CRYPTO 2015, vol. 9216, Springer, 2015, pp. 763–80, doi:10.1007/978-3-662-48000-7_37.","short":"J.F. Alwen, R. Ostrovsky, H. Zhou, V. Zikas, in:, Advances in Cryptology - CRYPTO 2015, Springer, 2015, pp. 763–780.","ista":"Alwen JF, Ostrovsky R, Zhou H, Zikas V. 2015. Incoercible multi-party computation and universally composable receipt-free voting. Advances in Cryptology - CRYPTO 2015. CRYPTO: International Cryptology ConferenceLecture Notes in Computer Science, LNCS, vol. 9216, 763–780.","apa":"Alwen, J. F., Ostrovsky, R., Zhou, H., & Zikas, V. (2015). Incoercible multi-party computation and universally composable receipt-free voting. In Advances in Cryptology - CRYPTO 2015 (Vol. 9216, pp. 763–780). Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_37","ieee":"J. F. Alwen, R. Ostrovsky, H. Zhou, and V. Zikas, “Incoercible multi-party computation and universally composable receipt-free voting,” in Advances in Cryptology - CRYPTO 2015, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 763–780.","ama":"Alwen JF, Ostrovsky R, Zhou H, Zikas V. Incoercible multi-party computation and universally composable receipt-free voting. In: Advances in Cryptology - CRYPTO 2015. Vol 9216. Lecture Notes in Computer Science. Springer; 2015:763-780. doi:10.1007/978-3-662-48000-7_37"},"publication":"Advances in Cryptology - CRYPTO 2015","publist_id":"5476","ec_funded":1,"file_date_updated":"2020-07-14T12:45:11Z","volume":9216,"date_created":"2018-12-11T11:53:23Z","date_updated":"2022-06-07T09:51:55Z","author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F","full_name":"Alwen, Joel F"},{"full_name":"Ostrovsky, Rafail","first_name":"Rafail","last_name":"Ostrovsky"},{"last_name":"Zhou","first_name":"Hongsheng","full_name":"Zhou, Hongsheng"},{"last_name":"Zikas","first_name":"Vassilis","full_name":"Zikas, Vassilis"}],"department":[{"_id":"KrPi"}],"publisher":"Springer","publication_status":"published","acknowledgement":"Joël Alwen was supported by the ERC starting grant (259668-PSPC). Rafail Ostrovsky was supported in part by NSF grants 09165174, 1065276, 1118126 and 1136174, US-Israel BSF grant 2008411, OKAWA Foundation Research Award, IBM Faculty Research Award, Xerox Faculty Research Award, B. John Garrick Foundation Award, Teradata Research Award, Lockheed-Martin Corporation Research Award, and the Defense Advanced Research Projects Agency through the U.S. Office of Naval Research under Contract N00014 -11 -1-0392. The views expressed are those of the author and do not reflect the official policy or position of the Department of Defense or the U.S. Government. Vassilis Zikas was supported in part by the Swiss National Science Foundation (SNF) via the Ambizione grant PZ00P-2142549.","year":"2015","publication_identifier":{"isbn":["978-3-662-47999-5"],"eisbn":["978-3-662-48000-7"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-48000-7_37","conference":{"start_date":"2015-08-16","location":"Santa Barbara, CA, United States","end_date":"2015-08-20","name":"CRYPTO: International Cryptology Conference"},"project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1},{"publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2015","volume":9230,"date_created":"2018-12-11T11:53:22Z","date_updated":"2021-01-12T06:52:24Z","author":[{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Skórski, Maciej","last_name":"Skórski","first_name":"Maciej"}],"ec_funded":1,"publist_id":"5480","file_date_updated":"2020-07-14T12:45:11Z","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-22174-8_5","conference":{"location":"Guadalajara, Mexico","start_date":"2015-08-23","end_date":"2015-08-26","name":"LATINCRYPT: Cryptology and Information Security in Latin America"},"month":"08","intvolume":" 9230","status":"public","ddc":["005"],"title":"The chain rule for HILL pseudoentropy, revisited","_id":"1669","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:11Z","date_created":"2018-12-12T10:18:29Z","checksum":"8cd4215b83efba720e8cf27c23ff4781","file_id":"5351","relation":"main_file","creator":"system","file_size":443340,"content_type":"application/pdf","file_name":"IST-2016-669-v1+1_599.pdf","access_level":"open_access"}],"pubrep_id":"669","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Computational notions of entropy (a.k.a. pseudoentropy) have found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The most important tools to argue about pseudoentropy are chain rules, which quantify by how much (in terms of quantity and quality) the pseudoentropy of a given random variable X decreases when conditioned on some other variable Z (think for example of X as a secret key and Z as information leaked by a side-channel). In this paper we give a very simple and modular proof of the chain rule for HILL pseudoentropy, improving best known parameters. Our version allows for increasing the acceptable length of leakage in applications up to a constant factor compared to the best previous bounds. As a contribution of independent interest, we provide a comprehensive study of all known versions of the chain rule, comparing their worst-case strength and limitations."}],"page":"81 - 98","citation":{"ama":"Pietrzak KZ, Skórski M. The chain rule for HILL pseudoentropy, revisited. 2015;9230:81-98. doi:10.1007/978-3-319-22174-8_5","apa":"Pietrzak, K. Z., & Skórski, M. (2015). The chain rule for HILL pseudoentropy, revisited. Presented at the LATINCRYPT: Cryptology and Information Security in Latin America, Guadalajara, Mexico: Springer. https://doi.org/10.1007/978-3-319-22174-8_5","ieee":"K. Z. Pietrzak and M. Skórski, “The chain rule for HILL pseudoentropy, revisited,” vol. 9230. Springer, pp. 81–98, 2015.","ista":"Pietrzak KZ, Skórski M. 2015. The chain rule for HILL pseudoentropy, revisited. 9230, 81–98.","short":"K.Z. Pietrzak, M. Skórski, 9230 (2015) 81–98.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. The Chain Rule for HILL Pseudoentropy, Revisited. Vol. 9230, Springer, 2015, pp. 81–98, doi:10.1007/978-3-319-22174-8_5.","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “The Chain Rule for HILL Pseudoentropy, Revisited.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22174-8_5."},"date_published":"2015-08-15T00:00:00Z","series_title":"Lecture Notes in Computer Science","scopus_import":1,"has_accepted_license":"1","day":"15"},{"intvolume":" 9215","ddc":["004","005"],"title":"The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1671","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2016-673-v1+1_053.pdf","content_type":"application/pdf","file_size":592296,"creator":"system","relation":"main_file","file_id":"4827","checksum":"17d854227b3b753fd34f5d29e5b5a32e","date_created":"2018-12-12T10:10:38Z","date_updated":"2020-07-14T12:45:11Z"}],"pubrep_id":"673","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"This paper studies the concrete security of PRFs and MACs obtained by keying hash functions based on the sponge paradigm. One such hash function is KECCAK, selected as NIST’s new SHA-3 standard. In contrast to other approaches like HMAC, the exact security of keyed sponges is not well understood. Indeed, recent security analyses delivered concrete security bounds which are far from existing attacks. This paper aims to close this gap. We prove (nearly) exact bounds on the concrete PRF security of keyed sponges using a random permutation. These bounds are tight for the most relevant ranges of parameters, i.e., for messages of length (roughly) l ≤ min{2n/4, 2r} blocks, where n is the state size and r is the desired output length; and for l ≤ q queries (to the construction or the underlying permutation). Moreover, we also improve standard-model bounds. As an intermediate step of independent interest, we prove tight bounds on the PRF security of the truncated CBC-MAC construction, which operates as plain CBC-MAC, but only returns a prefix of the output."}],"page":"368 - 387","citation":{"short":"P. Gazi, K.Z. Pietrzak, S. Tessaro, in:, Springer, 2015, pp. 368–387.","mla":"Gazi, Peter, et al. The Exact PRF Security of Truncation: Tight Bounds for Keyed Sponges and Truncated CBC. Vol. 9215, Springer, 2015, pp. 368–87, doi:10.1007/978-3-662-47989-6_18.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “The Exact PRF Security of Truncation: Tight Bounds for Keyed Sponges and Truncated CBC,” 9215:368–87. Springer, 2015. https://doi.org/10.1007/978-3-662-47989-6_18.","ama":"Gazi P, Pietrzak KZ, Tessaro S. The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC. In: Vol 9215. Springer; 2015:368-387. doi:10.1007/978-3-662-47989-6_18","ieee":"P. Gazi, K. Z. Pietrzak, and S. Tessaro, “The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9215, pp. 368–387.","apa":"Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC (Vol. 9215, pp. 368–387). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-47989-6_18","ista":"Gazi P, Pietrzak KZ, Tessaro S. 2015. The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC. CRYPTO: International Cryptology Conference, LNCS, vol. 9215, 368–387."},"date_published":"2015-08-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2015","volume":9215,"date_updated":"2021-01-12T06:52:25Z","date_created":"2018-12-11T11:53:23Z","author":[{"full_name":"Gazi, Peter","first_name":"Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Tessaro, Stefano","last_name":"Tessaro","first_name":"Stefano"}],"ec_funded":1,"publist_id":"5478","file_date_updated":"2020-07-14T12:45:11Z","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-47989-6_18","conference":{"location":"Santa Barbara, CA, United States","start_date":"2015-08-16","end_date":"2015-08-20","name":"CRYPTO: International Cryptology Conference"},"month":"08"},{"has_accepted_license":"1","day":"08","scopus_import":1,"date_published":"2015-09-08T00:00:00Z","citation":{"chicago":"Adlam, Ben, Krishnendu Chatterjee, and Martin Nowak. “Amplifiers of Selection.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2015. https://doi.org/10.1098/rspa.2015.0114.","mla":"Adlam, Ben, et al. “Amplifiers of Selection.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 471, no. 2181, 20150114, Royal Society of London, 2015, doi:10.1098/rspa.2015.0114.","short":"B. Adlam, K. Chatterjee, M. Nowak, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 471 (2015).","ista":"Adlam B, Chatterjee K, Nowak M. 2015. Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 471(2181), 20150114.","ieee":"B. Adlam, K. Chatterjee, and M. Nowak, “Amplifiers of selection,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 471, no. 2181. Royal Society of London, 2015.","apa":"Adlam, B., Chatterjee, K., & Nowak, M. (2015). Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2015.0114","ama":"Adlam B, Chatterjee K, Nowak M. Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2015;471(2181). doi:10.1098/rspa.2015.0114"},"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","issue":"2181","abstract":[{"text":"When a new mutant arises in a population, there is a probability it outcompetes the residents and fixes. The structure of the population can affect this fixation probability. Suppressing population structures reduce the difference between two competing variants, while amplifying population structures enhance the difference. Suppressors are ubiquitous and easy to construct, but amplifiers for the large population limit are more elusive and only a few examples have been discovered. Whether or not a population structure is an amplifier of selection depends on the probability distribution for the placement of the invading mutant. First, we prove that there exist only bounded amplifiers for adversarial placement-that is, for arbitrary initial conditions. Next, we show that the Star population structure, which is known to amplify for mutants placed uniformly at random, does not amplify for mutants that arise through reproduction and are therefore placed proportional to the temperatures of the vertices. Finally, we construct population structures that amplify for all mutational events that arise through reproduction, uniformly at random, or through some combination of the two. ","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"6342","date_created":"2019-04-18T12:39:56Z","date_updated":"2020-07-14T12:45:11Z","checksum":"e613d94d283c776322403a28aad11bdd","file_name":"2015_rspa_Adlam.pdf","access_level":"open_access","content_type":"application/pdf","file_size":391466,"creator":"kschuh"}],"oa_version":"Published Version","_id":"1673","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 471","status":"public","ddc":["000"],"title":"Amplifiers of selection","month":"09","doi":"10.1098/rspa.2015.0114","language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publist_id":"5477","ec_funded":1,"file_date_updated":"2020-07-14T12:45:11Z","article_number":"20150114","author":[{"full_name":"Adlam, Ben","first_name":"Ben","last_name":"Adlam"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"volume":471,"date_created":"2018-12-11T11:53:24Z","date_updated":"2021-01-12T06:52:26Z","year":"2015","acknowledgement":"K.C. gratefully acknowledges support from ERC Start grant no. (279307: Graph Games), Austrian Science Fund (FWF) grant no. P23499-N23, and FWF NFN grant no. S11407-N23 (RiSE). ","department":[{"_id":"KrCh"}],"publisher":"Royal Society of London","publication_status":"published"},{"day":"12","scopus_import":1,"series_title":"Lecture Notes in Computer Science","date_published":"2015-08-12T00:00:00Z","citation":{"ieee":"P. Gazi, J. Lee, Y. Seurin, J. Steinberger, and S. Tessaro, “Relaxing full-codebook security: A refined analysis of key-length extension schemes,” vol. 9054. Springer, pp. 319–341, 2015.","apa":"Gazi, P., Lee, J., Seurin, Y., Steinberger, J., & Tessaro, S. (2015). Relaxing full-codebook security: A refined analysis of key-length extension schemes. Presented at the FSE: Fast Software Encryption, Istanbul, Turkey: Springer. https://doi.org/10.1007/978-3-662-48116-5_16","ista":"Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. 2015. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 9054, 319–341.","ama":"Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 2015;9054:319-341. doi:10.1007/978-3-662-48116-5_16","chicago":"Gazi, Peter, Jooyoung Lee, Yannick Seurin, John Steinberger, and Stefano Tessaro. “Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48116-5_16.","short":"P. Gazi, J. Lee, Y. Seurin, J. Steinberger, S. Tessaro, 9054 (2015) 319–341.","mla":"Gazi, Peter, et al. Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes. Vol. 9054, Springer, 2015, pp. 319–41, doi:10.1007/978-3-662-48116-5_16."},"page":"319 - 341","abstract":[{"text":"We revisit the security (as a pseudorandom permutation) of cascading-based constructions for block-cipher key-length extension. Previous works typically considered the extreme case where the adversary is given the entire codebook of the construction, the only complexity measure being the number qe of queries to the underlying ideal block cipher, representing adversary’s secret-key-independent computation. Here, we initiate a systematic study of the more natural case of an adversary restricted to adaptively learning a number qc of plaintext/ciphertext pairs that is less than the entire codebook. For any such qc, we aim to determine the highest number of block-cipher queries qe the adversary can issue without being able to successfully distinguish the construction (under a secret key) from a random permutation.\r\nMore concretely, we show the following results for key-length extension schemes using a block cipher with n-bit blocks and κ-bit keys:\r\nPlain cascades of length ℓ=2r+1 are secure whenever qcqre≪2r(κ+n), qc≪2κ and qe≪22κ. The bound for r=1 also applies to two-key triple encryption (as used within Triple DES).\r\nThe r-round XOR-cascade is secure as long as qcqre≪2r(κ+n), matching an attack by Gaži (CRYPTO 2013).\r\nWe fully characterize the security of Gaži and Tessaro’s two-call ","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1668","intvolume":" 9054","status":"public","title":"Relaxing full-codebook security: A refined analysis of key-length extension schemes","month":"08","doi":"10.1007/978-3-662-48116-5_16","conference":{"name":"FSE: Fast Software Encryption","start_date":"2015-03-08","location":"Istanbul, Turkey","end_date":"2015-03-11"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"http://eprint.iacr.org/2015/397","open_access":"1"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","ec_funded":1,"publist_id":"5481","author":[{"full_name":"Gazi, Peter","last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lee","first_name":"Jooyoung","full_name":"Lee, Jooyoung"},{"first_name":"Yannick","last_name":"Seurin","full_name":"Seurin, Yannick"},{"full_name":"Steinberger, John","first_name":"John","last_name":"Steinberger"},{"first_name":"Stefano","last_name":"Tessaro","full_name":"Tessaro, Stefano"}],"volume":9054,"date_created":"2018-12-11T11:53:22Z","date_updated":"2020-08-11T10:09:26Z","year":"2015","publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published"},{"_id":"1670","year":"2015","acknowledgement":"This 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 AVACS, http://www.avacs.org/), by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the Swiss National Science Foundation (SNSF) as part of the project “Automated Reformulation and Pruning in Factored State Spaces (ARAP)”.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"PDDL+ planning with hybrid automata: Foundations of translating must behavior","publication_status":"published","status":"public","publisher":"AAAI Press","department":[{"_id":"ToHe"}],"author":[{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"last_name":"Magazzeni","first_name":"Daniele","full_name":"Magazzeni, Daniele"},{"last_name":"Minopoli","first_name":"Stefano","full_name":"Minopoli, Stefano"},{"last_name":"Wehrle","first_name":"Martin","full_name":"Wehrle, Martin"}],"date_created":"2018-12-11T11:53:23Z","date_updated":"2021-01-12T06:52:25Z","oa_version":"None","type":"conference","abstract":[{"lang":"eng","text":"Planning in hybrid domains poses a special challenge due to the involved mixed discrete-continuous dynamics. A recent solving approach for such domains is based on applying model checking techniques on a translation of PDDL+ planning problems to hybrid automata. However, the proposed translation is limited because must behavior is only overapproximated, and hence, processes and events are not reflected exactly. In this paper, we present the theoretical foundation of an exact PDDL+ translation. We propose a schema to convert a hybrid automaton with must transitions into an equivalent hybrid automaton featuring only may transitions."}],"ec_funded":1,"publist_id":"5479","citation":{"ama":"Bogomolov S, Magazzeni D, Minopoli S, Wehrle M. PDDL+ planning with hybrid automata: Foundations of translating must behavior. In: AAAI Press; 2015:42-46.","apa":"Bogomolov, S., Magazzeni, D., Minopoli, S., & Wehrle, M. (2015). PDDL+ planning with hybrid automata: Foundations of translating must behavior (pp. 42–46). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Jerusalem, Israel: AAAI Press.","ieee":"S. Bogomolov, D. Magazzeni, S. Minopoli, and M. Wehrle, “PDDL+ planning with hybrid automata: Foundations of translating must behavior,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Jerusalem, Israel, 2015, pp. 42–46.","ista":"Bogomolov S, Magazzeni D, Minopoli S, Wehrle M. 2015. PDDL+ planning with hybrid automata: Foundations of translating must behavior. ICAPS: International Conference on Automated Planning and Scheduling, 42–46.","short":"S. Bogomolov, D. Magazzeni, S. Minopoli, M. Wehrle, in:, AAAI Press, 2015, pp. 42–46.","mla":"Bogomolov, Sergiy, et al. PDDL+ Planning with Hybrid Automata: Foundations of Translating Must Behavior. AAAI Press, 2015, pp. 42–46.","chicago":"Bogomolov, Sergiy, Daniele Magazzeni, Stefano Minopoli, and Martin Wehrle. “PDDL+ Planning with Hybrid Automata: Foundations of Translating Must Behavior,” 42–46. AAAI Press, 2015."},"main_file_link":[{"url":"https://www.aaai.org/ocs/index.php/ICAPS/ICAPS15/paper/view/10606/10394"}],"quality_controlled":"1","page":"42 - 46","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","end_date":"2015-06-11","location":"Jerusalem, Israel","start_date":"2015-06-07"},"date_published":"2015-06-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"month":"06","day":"01"},{"article_number":"1550018","type":"journal_article","abstract":[{"text":"We consider N × N random matrices of the form H = W + V where W is a real symmetric Wigner matrix and V a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W and we choose V so that the eigenvalues of W and V are typically of the same order. For a large class of diagonal matrices V, we show that the rescaled distribution of the extremal eigenvalues is given by the Tracy-Widom distribution F1 in the limit of large N. Our proofs also apply to the complex Hermitian setting, i.e. when W is a complex Hermitian Wigner matrix.","lang":"eng"}],"issue":"8","publist_id":"5475","publication_status":"published","title":"Edge universality for deformed Wigner matrices","status":"public","publisher":"World Scientific Publishing","intvolume":" 27","department":[{"_id":"LaEr"}],"year":"2015","_id":"1674","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:26Z","date_created":"2018-12-11T11:53:24Z","oa_version":"Preprint","volume":27,"author":[{"full_name":"Lee, Jioon","first_name":"Jioon","last_name":"Lee"},{"full_name":"Schnelli, Kevin","first_name":"Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231"}],"scopus_import":1,"month":"09","day":"01","quality_controlled":"1","publication":"Reviews in Mathematical Physics","citation":{"ama":"Lee J, Schnelli K. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 2015;27(8). doi:10.1142/S0129055X1550018X","ista":"Lee J, Schnelli K. 2015. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 27(8), 1550018.","apa":"Lee, J., & Schnelli, K. (2015). Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X1550018X","ieee":"J. Lee and K. Schnelli, “Edge universality for deformed Wigner matrices,” Reviews in Mathematical Physics, vol. 27, no. 8. World Scientific Publishing, 2015.","mla":"Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner Matrices.” Reviews in Mathematical Physics, vol. 27, no. 8, 1550018, World Scientific Publishing, 2015, doi:10.1142/S0129055X1550018X.","short":"J. Lee, K. Schnelli, Reviews in Mathematical Physics 27 (2015).","chicago":"Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner Matrices.” Reviews in Mathematical Physics. World Scientific Publishing, 2015. https://doi.org/10.1142/S0129055X1550018X."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.8015"}],"oa":1,"language":[{"iso":"eng"}],"date_published":"2015-09-01T00:00:00Z","doi":"10.1142/S0129055X1550018X"},{"citation":{"mla":"Lemoult, Grégoire M., et al. “Taylor’s Forest.” Physics of Fluids, vol. 27, no. 9, 091102, American Institute of Physics, 2015, doi:10.1063/1.4930850.","short":"G.M. Lemoult, P. Maier, B. Hof, Physics of Fluids 27 (2015).","chicago":"Lemoult, Grégoire M, Philipp Maier, and Björn Hof. “Taylor’s Forest.” Physics of Fluids. American Institute of Physics, 2015. https://doi.org/10.1063/1.4930850.","ama":"Lemoult GM, Maier P, Hof B. Taylor’s Forest. Physics of Fluids. 2015;27(9). doi:10.1063/1.4930850","ista":"Lemoult GM, Maier P, Hof B. 2015. Taylor’s Forest. Physics of Fluids. 27(9), 091102.","ieee":"G. M. Lemoult, P. Maier, and B. Hof, “Taylor’s Forest,” Physics of Fluids, vol. 27, no. 9. American Institute of Physics, 2015.","apa":"Lemoult, G. M., Maier, P., & Hof, B. (2015). Taylor’s Forest. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4930850"},"publication":"Physics of Fluids","date_published":"2015-09-24T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"24","_id":"1679","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 27","status":"public","ddc":["532"],"title":"Taylor's Forest","pubrep_id":"748","file":[{"date_updated":"2020-07-14T12:45:12Z","date_created":"2018-12-12T10:13:35Z","checksum":"604bba3c2496aadb3efcff77de01ce6c","relation":"main_file","file_id":"5019","content_type":"application/pdf","file_size":872366,"creator":"system","file_name":"IST-2017-748-v1+1_1.4930850.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"9","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1063/1.4930850","language":[{"iso":"eng"}],"month":"09","year":"2015","department":[{"_id":"BjHo"}],"publisher":"American Institute of Physics","publication_status":"published","author":[{"first_name":"Grégoire M","last_name":"Lemoult","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","full_name":"Lemoult, Grégoire M"},{"full_name":"Maier, Philipp","id":"384F7C04-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Maier"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"}],"volume":27,"date_updated":"2021-01-12T06:52:28Z","date_created":"2018-12-11T11:53:26Z","article_number":"091102","publist_id":"5469","file_date_updated":"2020-07-14T12:45:12Z"},{"type":"journal_article","publist_id":"5473","issue":"10","publisher":"Elsevier","department":[{"_id":"MiSi"}],"intvolume":" 36","status":"public","publication_status":"published","title":"Editorial overview: Cell adhesion and migration","_id":"1676","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","oa_version":"None","volume":36,"date_created":"2018-12-11T11:53:25Z","date_updated":"2021-01-12T06:52:27Z","author":[{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Raz, Erez","last_name":"Raz","first_name":"Erez"}],"scopus_import":1,"day":"01","month":"10","page":"4 - 6","citation":{"short":"M.K. Sixt, E. Raz, Current Opinion in Cell Biology 36 (2015) 4–6.","mla":"Sixt, Michael K., and Erez Raz. “Editorial Overview: Cell Adhesion and Migration.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 4–6, doi:10.1016/j.ceb.2015.09.004.","chicago":"Sixt, Michael K, and Erez Raz. “Editorial Overview: Cell Adhesion and Migration.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.09.004.","ama":"Sixt MK, Raz E. Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. 2015;36(10):4-6. doi:10.1016/j.ceb.2015.09.004","ieee":"M. K. Sixt and E. Raz, “Editorial overview: Cell adhesion and migration,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 4–6, 2015.","apa":"Sixt, M. K., & Raz, E. (2015). Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.09.004","ista":"Sixt MK, Raz E. 2015. Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. 36(10), 4–6."},"publication":"Current Opinion in Cell Biology","language":[{"iso":"eng"}],"doi":"10.1016/j.ceb.2015.09.004","date_published":"2015-10-01T00:00:00Z"},{"page":"93 - 102","citation":{"chicago":"Sarris, Milka, and Michael K Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.08.001.","mla":"Sarris, Milka, and Michael K. Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 93–102, doi:10.1016/j.ceb.2015.08.001.","short":"M. Sarris, M.K. Sixt, Current Opinion in Cell Biology 36 (2015) 93–102.","ista":"Sarris M, Sixt MK. 2015. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 36(10), 93–102.","apa":"Sarris, M., & Sixt, M. K. (2015). Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.08.001","ieee":"M. Sarris and M. K. Sixt, “Navigating in tissue mazes: Chemoattractant interpretation in complex environments,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 93–102, 2015.","ama":"Sarris M, Sixt MK. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 2015;36(10):93-102. doi:10.1016/j.ceb.2015.08.001"},"publication":"Current Opinion in Cell Biology","date_published":"2015-10-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 36","ddc":["570"],"title":"Navigating in tissue mazes: Chemoattractant interpretation in complex environments","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1687","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4875","date_created":"2018-12-12T10:11:21Z","date_updated":"2020-07-14T12:45:12Z","checksum":"c29973924b790aab02fdd91857759cfb","file_name":"IST-2016-445-v1+1_1-s2.0-S0955067415001064-main.pdf","access_level":"open_access","content_type":"application/pdf","file_size":797964,"creator":"system"}],"pubrep_id":"445","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"Guided cell movement is essential for development and integrity of animals and crucially involved in cellular immune responses. Leukocytes are professional migratory cells that can navigate through most types of tissues and sense a wide range of directional cues. The responses of these cells to attractants have been mainly explored in tissue culture settings. How leukocytes make directional decisions in situ, within the challenging environment of a tissue maze, is less understood. Here we review recent advances in how leukocytes sense chemical cues in complex tissue settings and make links with paradigms of directed migration in development and Dictyostelium discoideum amoebae."}],"project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.ceb.2015.08.001","month":"10","department":[{"_id":"MiSi"}],"publisher":"Elsevier","publication_status":"published","year":"2015","volume":36,"date_updated":"2021-01-12T06:52:31Z","date_created":"2018-12-11T11:53:28Z","author":[{"first_name":"Milka","last_name":"Sarris","full_name":"Sarris, Milka"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"ec_funded":1,"publist_id":"5458","file_date_updated":"2020-07-14T12:45:12Z"},{"date_published":"2015-09-01T00:00:00Z","page":"386 - 398","citation":{"mla":"Cohen Addad, Vincent, and Arnaud N. de Mesmay. A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface. Vol. 9294, Springer, 2015, pp. 386–98, doi:10.1007/978-3-662-48350-3_33.","short":"V. Cohen Addad, A.N. de Mesmay, in:, Springer, 2015, pp. 386–398.","chicago":"Cohen Addad, Vincent, and Arnaud N de Mesmay. “A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface,” 9294:386–98. Springer, 2015. https://doi.org/10.1007/978-3-662-48350-3_33.","ama":"Cohen Addad V, de Mesmay AN. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. In: Vol 9294. Springer; 2015:386-398. doi:10.1007/978-3-662-48350-3_33","ista":"Cohen Addad V, de Mesmay AN. 2015. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. ESA: European Symposium on Algorithms, LNCS, vol. 9294, 386–398.","apa":"Cohen Addad, V., & de Mesmay, A. N. (2015). A fixed parameter tractable approximation scheme for the optimal cut graph of a surface (Vol. 9294, pp. 386–398). Presented at the ESA: European Symposium on Algorithms, Patras, Greece: Springer. https://doi.org/10.1007/978-3-662-48350-3_33","ieee":"V. Cohen Addad and A. N. de Mesmay, “A fixed parameter tractable approximation scheme for the optimal cut graph of a surface,” presented at the ESA: European Symposium on Algorithms, Patras, Greece, 2015, vol. 9294, pp. 386–398."},"day":"01","scopus_import":1,"oa_version":"Preprint","intvolume":" 9294","status":"public","title":"A fixed parameter tractable approximation scheme for the optimal cut graph of a surface","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1685","abstract":[{"lang":"eng","text":"Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph is a subgraph of G such that cutting Σ along G yields a topological disk. We provide a fixed parameter tractable approximation scheme for the problem of computing the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε) approximation of the shortest cut graph in time f(ε, g)n3.\r\nOur techniques first rely on the computation of a spanner for the problem using the technique of brick decompositions, to reduce the problem to the case of bounded tree-width. Then, to solve the bounded tree-width case, we introduce a variant of the surface-cut decomposition of Rué, Sau and Thilikos, which may be of independent interest."}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-48350-3_33","conference":{"location":"Patras, Greece","start_date":"2015-09-14","end_date":"2015-09-16","name":"ESA: European Symposium on Algorithms"},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1507.01688"}],"oa":1,"month":"09","volume":9294,"date_updated":"2021-01-12T06:52:31Z","date_created":"2018-12-11T11:53:27Z","author":[{"full_name":"Cohen Addad, Vincent","first_name":"Vincent","last_name":"Cohen Addad"},{"first_name":"Arnaud N","last_name":"De Mesmay","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","full_name":"De Mesmay, Arnaud N"}],"publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2015","publist_id":"5462","ec_funded":1},{"oa_version":"Preprint","_id":"1688","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Bounds for Pach's selection theorem and for the minimum solid angle in a simplex","intvolume":" 54","abstract":[{"lang":"eng","text":"We estimate the selection constant in the following geometric selection theorem by Pach: For every positive integer d, there is a constant (Formula presented.) such that whenever (Formula presented.) are n-element subsets of (Formula presented.), we can find a point (Formula presented.) and subsets (Formula presented.) for every i∈[d+1], each of size at least cdn, such that p belongs to all rainbowd-simplices determined by (Formula presented.) simplices with one vertex in each Yi. We show a super-exponentially decreasing upper bound (Formula presented.). The ideas used in the proof of the upper bound also help us to prove Pach’s theorem with (Formula presented.), which is a lower bound doubly exponentially decreasing in d (up to some polynomial in the exponent). For comparison, Pach’s original approach yields a triply exponentially decreasing lower bound. On the other hand, Fox, Pach, and Suk recently obtained a hypergraph density result implying a proof of Pach’s theorem with (Formula presented.). In our construction for the upper bound, we use the fact that the minimum solid angle of every d-simplex is super-exponentially small. This fact was previously unknown and might be of independent interest. For the lower bound, we improve the ‘separation’ part of the argument by showing that in one of the key steps only d+1 separations are necessary, compared to 2d separations in the original proof. We also provide a measure version of Pach’s theorem."}],"issue":"3","type":"journal_article","date_published":"2015-10-01T00:00:00Z","publication":"Discrete & Computational Geometry","citation":{"chicago":"Karasev, Roman, Jan Kynčl, Pavel Paták, Zuzana Patakova, and Martin Tancer. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9720-z.","short":"R. Karasev, J. Kynčl, P. Paták, Z. Patakova, M. Tancer, Discrete & Computational Geometry 54 (2015) 610–636.","mla":"Karasev, Roman, et al. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry, vol. 54, no. 3, Springer, 2015, pp. 610–36, doi:10.1007/s00454-015-9720-z.","ieee":"R. Karasev, J. Kynčl, P. Paták, Z. Patakova, and M. Tancer, “Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex,” Discrete & Computational Geometry, vol. 54, no. 3. Springer, pp. 610–636, 2015.","apa":"Karasev, R., Kynčl, J., Paták, P., Patakova, Z., & Tancer, M. (2015). Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9720-z","ista":"Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. 2015. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 54(3), 610–636.","ama":"Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 2015;54(3):610-636. doi:10.1007/s00454-015-9720-z"},"page":"610 - 636","day":"01","scopus_import":1,"author":[{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"},{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"},{"last_name":"Paták","first_name":"Pavel","full_name":"Paták, Pavel"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova","first_name":"Zuzana"},{"full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","last_name":"Tancer","first_name":"Martin"}],"date_created":"2018-12-11T11:53:28Z","date_updated":"2021-01-12T06:52:32Z","volume":54,"acknowledgement":"R. K. was supported by the Russian Foundation for Basic Research Grant 15-31-20403 (mol_a_ved) and grant 15-01-99563. J. K., Z. P., and M. T. were partially supported by ERC Advanced Research Grant No. 267165 (DISCONV) and by the project CE-ITI (GAČR P202/12/G061) of the Czech Science Foundation. J. K. was also partially supported by Swiss National Science Foundation Grants 200021-137574 and 200020-14453. P. P., Z. P., and M. T. were partially supported by the Charles University Grant GAUK 421511. P. P. was also partially supported by the Charles University Grant SVV-2014-260107. Z. P. was also partially supported by the Charles University Grant SVV-2014-260103.","year":"2015","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"publist_id":"5457","doi":"10.1007/s00454-015-9720-z","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1403.8147","open_access":"1"}],"oa":1,"quality_controlled":"1","month":"10"},{"article_number":"2","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the satisfiability problem for modal logic over first-order definable classes of frames.We confirm the conjecture from Hemaspaandra and Schnoor [2008] that modal logic is decidable over classes definable by universal Horn formulae. We provide a full classification of Horn formulae with respect to the complexity of the corresponding satisfiability problem. It turns out, that except for the trivial case of inconsistent formulae, local satisfiability is eitherNP-complete or PSPACE-complete, and global satisfiability is NP-complete, PSPACE-complete, or ExpTime-complete. We also show that the finite satisfiability problem for modal logic over Horn definable classes of frames is decidable. On the negative side, we show undecidability of two related problems. First, we exhibit a simple universal three-variable formula defining the class of frames over which modal logic is undecidable. Second, we consider the satisfiability problem of bimodal logic over Horn definable classes of frames, and also present a formula leading to undecidability."}],"ec_funded":1,"publist_id":"5468","issue":"1","title":"On the decidability of elementary modal logics","status":"public","publication_status":"published","intvolume":" 17","department":[{"_id":"ToHe"}],"publisher":"ACM","_id":"1680","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:29Z","date_created":"2018-12-11T11:53:26Z","oa_version":"None","volume":17,"author":[{"last_name":"Michaliszyn","first_name":"Jakub","full_name":"Michaliszyn, Jakub"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"},{"first_name":"Emanuel","last_name":"Kieroňski","full_name":"Kieroňski, Emanuel"}],"day":"01","month":"09","quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"publication":"ACM Transactions on Computational Logic","citation":{"chicago":"Michaliszyn, Jakub, Jan Otop, and Emanuel Kieroňski. “On the Decidability of Elementary Modal Logics.” ACM Transactions on Computational Logic. ACM, 2015. https://doi.org/10.1145/2817825.","short":"J. Michaliszyn, J. Otop, E. Kieroňski, ACM Transactions on Computational Logic 17 (2015).","mla":"Michaliszyn, Jakub, et al. “On the Decidability of Elementary Modal Logics.” ACM Transactions on Computational Logic, vol. 17, no. 1, 2, ACM, 2015, doi:10.1145/2817825.","ieee":"J. Michaliszyn, J. Otop, and E. Kieroňski, “On the decidability of elementary modal logics,” ACM Transactions on Computational Logic, vol. 17, no. 1. ACM, 2015.","apa":"Michaliszyn, J., Otop, J., & Kieroňski, E. (2015). On the decidability of elementary modal logics. ACM Transactions on Computational Logic. ACM. https://doi.org/10.1145/2817825","ista":"Michaliszyn J, Otop J, Kieroňski E. 2015. On the decidability of elementary modal logics. ACM Transactions on Computational Logic. 17(1), 2.","ama":"Michaliszyn J, Otop J, Kieroňski E. On the decidability of elementary modal logics. ACM Transactions on Computational Logic. 2015;17(1). doi:10.1145/2817825"},"language":[{"iso":"eng"}],"date_published":"2015-09-01T00:00:00Z","doi":"10.1145/2817825"},{"quality_controlled":"1","publication":"Journal of the ACM","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1402.0858","open_access":"1"}],"citation":{"chicago":"Franek, Peter, and Marek Krcál. “Robust Satisfiability of Systems of Equations.” Journal of the ACM. ACM, 2015. https://doi.org/10.1145/2751524.","mla":"Franek, Peter, and Marek Krcál. “Robust Satisfiability of Systems of Equations.” Journal of the ACM, vol. 62, no. 4, 26, ACM, 2015, doi:10.1145/2751524.","short":"P. Franek, M. Krcál, Journal of the ACM 62 (2015).","ista":"Franek P, Krcál M. 2015. Robust satisfiability of systems of equations. Journal of the ACM. 62(4), 26.","apa":"Franek, P., & Krcál, M. (2015). Robust satisfiability of systems of equations. Journal of the ACM. ACM. https://doi.org/10.1145/2751524","ieee":"P. Franek and M. Krcál, “Robust satisfiability of systems of equations,” Journal of the ACM, vol. 62, no. 4. ACM, 2015.","ama":"Franek P, Krcál M. Robust satisfiability of systems of equations. Journal of the ACM. 2015;62(4). doi:10.1145/2751524"},"language":[{"iso":"eng"}],"date_published":"2015-08-01T00:00:00Z","doi":"10.1145/2751524","scopus_import":1,"day":"01","month":"08","title":"Robust satisfiability of systems of equations","status":"public","publication_status":"published","intvolume":" 62","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publisher":"ACM","_id":"1682","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:53:27Z","date_updated":"2021-01-12T06:52:30Z","volume":62,"oa_version":"Preprint","author":[{"full_name":"Franek, Peter","first_name":"Peter","last_name":"Franek"},{"full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Krcál"}],"article_number":"26","type":"journal_article","abstract":[{"lang":"eng","text":"We study the problem of robust satisfiability of systems of nonlinear equations, namely, whether for a given continuous function f:K→ ℝn on a finite simplicial complex K and α > 0, it holds that each function g: K → ℝn such that ||g - f || ∞ < α, has a root in K. Via a reduction to the extension problem of maps into a sphere, we particularly show that this problem is decidable in polynomial time for every fixed n, assuming dimK ≤ 2n - 3. This is a substantial extension of previous computational applications of topological degree and related concepts in numerical and interval analysis. Via a reverse reduction, we prove that the problem is undecidable when dim K > 2n - 2, where the threshold comes from the stable range in homotopy theory. For the lucidity of our exposition, we focus on the setting when f is simplexwise linear. Such functions can approximate general continuous functions, and thus we get approximation schemes and undecidability of the robust satisfiability in other possible settings."}],"publist_id":"5466","issue":"4"},{"date_published":"2015-08-01T00:00:00Z","doi":"10.1016/j.sbi.2015.08.008","language":[{"iso":"eng"}],"publication":"Current Opinion in Structural Biology","citation":{"ista":"Letts JA, Sazanov LA. 2015. Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. 33(8), 135–145.","apa":"Letts, J. A., & Sazanov, L. A. (2015). Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2015.08.008","ieee":"J. A. Letts and L. A. Sazanov, “Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions,” Current Opinion in Structural Biology, vol. 33, no. 8. Elsevier, pp. 135–145, 2015.","ama":"Letts JA, Sazanov LA. Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. 2015;33(8):135-145. doi:10.1016/j.sbi.2015.08.008","chicago":"Letts, James A, and Leonid A Sazanov. “Gaining Mass: The Structure of Respiratory Complex I-from Bacterial towards Mitochondrial Versions.” Current Opinion in Structural Biology. Elsevier, 2015. https://doi.org/10.1016/j.sbi.2015.08.008.","mla":"Letts, James A., and Leonid A. Sazanov. “Gaining Mass: The Structure of Respiratory Complex I-from Bacterial towards Mitochondrial Versions.” Current Opinion in Structural Biology, vol. 33, no. 8, Elsevier, 2015, pp. 135–45, doi:10.1016/j.sbi.2015.08.008.","short":"J.A. Letts, L.A. Sazanov, Current Opinion in Structural Biology 33 (2015) 135–145."},"quality_controlled":"1","page":"135 - 145","day":"01","month":"08","scopus_import":1,"author":[{"full_name":"Letts, Jame A","first_name":"Jame A","last_name":"Letts","id":"322DA418-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9864-3586"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"}],"date_updated":"2021-01-12T06:52:30Z","date_created":"2018-12-11T11:53:27Z","oa_version":"None","volume":33,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1683","year":"2015","status":"public","title":"Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions","publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Elsevier","intvolume":" 33","abstract":[{"text":"The 1 MDa, 45-subunit proton-pumping NADH-ubiquinone oxidoreductase (complex I) is the largest complex of the mitochondrial electron transport chain. The molecular mechanism of complex I is central to the metabolism of cells, but has yet to be fully characterized. The last two years have seen steady progress towards this goal with the first atomic-resolution structure of the entire bacterial complex I, a 5 Å cryo-electron microscopy map of bovine mitochondrial complex I and a ∼3.8 Å resolution X-ray crystallographic study of mitochondrial complex I from yeast Yarrowia lipotytica. In this review we will discuss what we have learned from these studies and what remains to be elucidated.","lang":"eng"}],"publist_id":"5465","issue":"8","type":"journal_article"},{"type":"journal_article","issue":"6252","publist_id":"5459","year":"2015","_id":"1686","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection","intvolume":" 349","department":[{"_id":"MiSi"}],"publisher":"American Association for the Advancement of Science","author":[{"orcid":"0000-0001-6165-5738","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","last_name":"Kiermaier","first_name":"Eva","full_name":"Kiermaier, Eva"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"date_updated":"2021-01-12T06:52:31Z","date_created":"2018-12-11T11:53:28Z","volume":349,"oa_version":"None","scopus_import":1,"day":"04","month":"09","publication":"Science","citation":{"short":"E. Kiermaier, M.K. Sixt, Science 349 (2015) 1055–1056.","mla":"Kiermaier, Eva, and Michael K. Sixt. “Fragmented Communication between Immune Cells: Neutrophils Blaze a Trail with Migratory Cues for T Cells to Follow to Sites of Infection.” Science, vol. 349, no. 6252, American Association for the Advancement of Science, 2015, pp. 1055–56, doi:10.1126/science.aad0867.","chicago":"Kiermaier, Eva, and Michael K Sixt. “Fragmented Communication between Immune Cells: Neutrophils Blaze a Trail with Migratory Cues for T Cells to Follow to Sites of Infection.” Science. American Association for the Advancement of Science, 2015. https://doi.org/10.1126/science.aad0867.","ama":"Kiermaier E, Sixt MK. Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. 2015;349(6252):1055-1056. doi:10.1126/science.aad0867","apa":"Kiermaier, E., & Sixt, M. K. (2015). Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aad0867","ieee":"E. Kiermaier and M. K. Sixt, “Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection,” Science, vol. 349, no. 6252. American Association for the Advancement of Science, pp. 1055–1056, 2015.","ista":"Kiermaier E, Sixt MK. 2015. Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. 349(6252), 1055–1056."},"quality_controlled":"1","page":"1055 - 1056","date_published":"2015-09-04T00:00:00Z","doi":"10.1126/science.aad0867","language":[{"iso":"eng"}]},{"doi":"10.1145/2728606.2728622","date_published":"2015-04-14T00:00:00Z","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2015-04-16","location":"Seattle, WA, United States","start_date":"2015-04-14"},"language":[{"iso":"eng"}],"citation":{"ama":"Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. Eliminating spurious transitions in reachability with support functions. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:149-158. doi:10.1145/2728606.2728622","ista":"Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. 2015. Eliminating spurious transitions in reachability with support functions. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 149–158.","ieee":"G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, and A. Podelski, “Eliminating spurious transitions in reachability with support functions,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 149–158.","apa":"Frehse, G., Bogomolov, S., Greitschus, M., Strump, T., & Podelski, A. (2015). Eliminating spurious transitions in reachability with support functions. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 149–158). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728622","mla":"Frehse, Goran, et al. “Eliminating Spurious Transitions in Reachability with Support Functions.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 149–58, doi:10.1145/2728606.2728622.","short":"G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, A. Podelski, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 149–158.","chicago":"Frehse, Goran, Sergiy Bogomolov, Marius Greitschus, Thomas Strump, and Andreas Podelski. “Eliminating Spurious Transitions in Reachability with Support Functions.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 149–58. ACM, 2015. https://doi.org/10.1145/2728606.2728622."},"publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","page":"149 - 158","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-1-4503-3433-4"]},"month":"04","day":"14","scopus_import":1,"author":[{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"first_name":"Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"first_name":"Marius","last_name":"Greitschus","full_name":"Greitschus, Marius"},{"first_name":"Thomas","last_name":"Strump","full_name":"Strump, Thomas"},{"last_name":"Podelski","first_name":"Andreas","full_name":"Podelski, Andreas"}],"oa_version":"None","date_created":"2018-12-11T11:53:30Z","date_updated":"2021-01-12T06:52:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1692","year":"2015","department":[{"_id":"ToHe"}],"publisher":"ACM","status":"public","title":"Eliminating spurious transitions in reachability with support functions","publication_status":"published","ec_funded":1,"publist_id":"5452","abstract":[{"text":"Computing an approximation of the reachable states of a hybrid system is a challenge, mainly because overapproximating the solutions of ODEs with a finite number of sets does not scale well. Using template polyhedra can greatly reduce the computational complexity, since it replaces complex operations on sets with a small number of optimization problems. However, the use of templates may make the over-approximation too conservative. Spurious transitions, which are falsely considered reachable, are particularly detrimental to performance and accuracy, and may exacerbate the state explosion problem. In this paper, we examine how spurious transitions can be avoided with minimal computational effort. To this end, detecting spurious transitions is reduced to the well-known problem of showing that two convex sets are disjoint by finding a hyperplane that separates them. We generalize this to owpipes by considering hyperplanes that evolve with time in correspondence to the dynamics of the system. The approach is implemented in the model checker SpaceEx and demonstrated on examples.","lang":"eng"}],"type":"conference"},{"month":"08","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.92.022514","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1506.02734"}],"ec_funded":1,"publist_id":"5451","article_number":"022514","volume":92,"date_updated":"2021-01-12T06:52:34Z","date_created":"2018-12-11T11:53:30Z","author":[{"full_name":"Amaro, Pedro","first_name":"Pedro","last_name":"Amaro"},{"full_name":"Franke, Beatrice","last_name":"Franke","first_name":"Beatrice"},{"last_name":"Krauth","first_name":"Julian","full_name":"Krauth, Julian"},{"full_name":"Diepold, Marc","last_name":"Diepold","first_name":"Marc"},{"full_name":"Fratini, Filippo","first_name":"Filippo","last_name":"Fratini"},{"full_name":"Safari, Laleh","last_name":"Safari","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jorge","last_name":"Machado","full_name":"Machado, Jorge"},{"first_name":"Aldo","last_name":"Antognini","full_name":"Antognini, Aldo"},{"first_name":"Franz","last_name":"Kottmann","full_name":"Kottmann, Franz"},{"last_name":"Indelicato","first_name":"Paul","full_name":"Indelicato, Paul"},{"first_name":"Randolf","last_name":"Pohl","full_name":"Pohl, Randolf"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"}],"department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2015","day":"28","scopus_import":1,"date_published":"2015-08-28T00:00:00Z","citation":{"short":"P. Amaro, B. Franke, J. Krauth, M. Diepold, F. Fratini, L. Safari, J. Machado, A. Antognini, F. Kottmann, P. Indelicato, R. Pohl, J. Santos, Physical Review A 92 (2015).","mla":"Amaro, Pedro, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” Physical Review A, vol. 92, no. 2, 022514, American Physical Society, 2015, doi:10.1103/PhysRevA.92.022514.","chicago":"Amaro, Pedro, Beatrice Franke, Julian Krauth, Marc Diepold, Filippo Fratini, Laleh Safari, Jorge Machado, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.022514.","ama":"Amaro P, Franke B, Krauth J, et al. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. 2015;92(2). doi:10.1103/PhysRevA.92.022514","ieee":"P. Amaro et al., “Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3,” Physical Review A, vol. 92, no. 2. American Physical Society, 2015.","apa":"Amaro, P., Franke, B., Krauth, J., Diepold, M., Fratini, F., Safari, L., … Santos, J. (2015). Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.92.022514","ista":"Amaro P, Franke B, Krauth J, Diepold M, Fratini F, Safari L, Machado J, Antognini A, Kottmann F, Indelicato P, Pohl R, Santos J. 2015. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. 92(2), 022514."},"publication":"Physical Review A","issue":"2","abstract":[{"text":"Quantum interference between energetically close states is theoretically investigated, with the state structure being observed via laser spectroscopy. In this work, we focus on hyperfine states of selected hydrogenic muonic isotopes, and on how quantum interference affects the measured Lamb shift. The process of photon excitation and subsequent photon decay is implemented within the framework of nonrelativistic second-order perturbation theory. Due to its experimental interest, calculations are performed for muonic hydrogen, deuterium, and helium-3. We restrict our analysis to the case of photon scattering by incident linear polarized photons and the polarization of the scattered photons not being observed. We conclude that while quantum interference effects can be safely neglected in muonic hydrogen and helium-3, in the case of muonic deuterium there are resonances with close proximity, where quantum interference effects can induce shifts up to a few percent of the linewidth, assuming a pointlike detector. However, by taking into account the geometry of the setup used by the CREMA collaboration, this effect is reduced to less than 0.2% of the linewidth in all possible cases, which makes it irrelevant at the present level of accuracy. © 2015 American Physical Society.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 92","status":"public","title":"Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3","_id":"1693","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"conference","publist_id":"5454","ec_funded":1,"abstract":[{"text":"A number of powerful and scalable hybrid systems model checkers have recently emerged. Although all of them honor roughly the same hybrid systems semantics, they have drastically different model description languages. This situation (a) makes it difficult to quickly evaluate a specific hybrid automaton model using the different tools, (b) obstructs comparisons of reachability approaches, and (c) impedes the widespread application of research results that perform model modification and could benefit many of the tools. In this paper, we present Hyst, a Hybrid Source Transformer. Hyst is a source-to-source translation tool, currently taking input in the SpaceEx model format, and translating to the formats of HyCreate, Flow∗, or dReach. Internally, the tool supports generic model-to-model transformation passes that serve to both ease the translation and potentially improve reachability results for the supported tools. Although these model transformation passes could be implemented within each tool, the Hyst approach provides a single place for model modification, generating modified input sources for the unmodified target tools. Our evaluation demonstrates Hyst is capable of automatically translating benchmarks in several classes (including affine and nonlinear hybrid automata) to the input formats of several tools. Additionally, we illustrate a general model transformation pass based on pseudo-invariants implemented in Hyst that illustrates the reachability improvement.","lang":"eng"}],"_id":"1690","year":"2015","acknowledgement":"The material presented in this paper is based upon work sup-ported by the Air Force Research Laboratory’s Information Directorate (AFRL/RI) through the Visiting Faculty Research Program (VFRP) under contract number FA8750-13-2-0115 and the Air Force Office of Scientific Research (AFOSR). Any opinions,findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the AFRL/RI or AFOSR. This work was also partly supported in part by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR14 AVACS, http://www.avacs.org/), 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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","department":[{"_id":"ToHe"}],"title":"HYST: A source transformation and translation tool for hybrid automaton models","status":"public","publication_status":"published","author":[{"first_name":"Stanley","last_name":"Bak","full_name":"Bak, Stanley"},{"full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov"},{"full_name":"Johnson, Taylor","last_name":"Johnson","first_name":"Taylor"}],"oa_version":"None","date_created":"2018-12-11T11:53:29Z","date_updated":"2021-01-12T06:52:33Z","month":"04","day":"14","citation":{"apa":"Bak, S., Bogomolov, S., & Johnson, T. (2015). HYST: A source transformation and translation tool for hybrid automaton models (pp. 128–133). Presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States: Springer. https://doi.org/10.1145/2728606.2728630","ieee":"S. Bak, S. Bogomolov, and T. Johnson, “HYST: A source transformation and translation tool for hybrid automaton models,” presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States, 2015, pp. 128–133.","ista":"Bak S, Bogomolov S, Johnson T. 2015. HYST: A source transformation and translation tool for hybrid automaton models. HSCC: Hybrid Systems - Computation and Control, 128–133.","ama":"Bak S, Bogomolov S, Johnson T. HYST: A source transformation and translation tool for hybrid automaton models. In: Springer; 2015:128-133. doi:10.1145/2728606.2728630","chicago":"Bak, Stanley, Sergiy Bogomolov, and Taylor Johnson. “HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models,” 128–33. Springer, 2015. https://doi.org/10.1145/2728606.2728630.","short":"S. Bak, S. Bogomolov, T. Johnson, in:, Springer, 2015, pp. 128–133.","mla":"Bak, Stanley, et al. HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models. Springer, 2015, pp. 128–33, doi:10.1145/2728606.2728630."},"page":"128 - 133","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","date_published":"2015-04-14T00:00:00Z","doi":"10.1145/2728606.2728630","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2015-04-16","start_date":"2015-04-14","location":"Seattle, WA, United States"},"language":[{"iso":"eng"}]},{"doi":"10.1145/2728606.2728617","date_published":"2015-04-14T00:00:00Z","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","location":"Seattle, WA, United States","start_date":"2015-04-14","end_date":"2015-04-16"},"language":[{"iso":"eng"}],"citation":{"ama":"Svoreňová M, Chmelik M, Leahy K, et al. Temporal logic motion planning using POMDPs with parity objectives: Case study paper. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:233-238. doi:10.1145/2728606.2728617","ieee":"M. Svoreňová et al., “Temporal logic motion planning using POMDPs with parity objectives: Case study paper,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 233–238.","apa":"Svoreňová, M., Chmelik, M., Leahy, K., Eniser, H., Chatterjee, K., Cěrná, I., & Belta, C. (2015). Temporal logic motion planning using POMDPs with parity objectives: Case study paper. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 233–238). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728617","ista":"Svoreňová M, Chmelik M, Leahy K, Eniser H, Chatterjee K, Cěrná I, Belta C. 2015. Temporal logic motion planning using POMDPs with parity objectives: Case study paper. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 233–238.","short":"M. Svoreňová, M. Chmelik, K. Leahy, H. Eniser, K. Chatterjee, I. Cěrná, C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 233–238.","mla":"Svoreňová, Mária, et al. “Temporal Logic Motion Planning Using POMDPs with Parity Objectives: Case Study Paper.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 233–38, doi:10.1145/2728606.2728617.","chicago":"Svoreňová, Mária, Martin Chmelik, Kevin Leahy, Hasan Eniser, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Motion Planning Using POMDPs with Parity Objectives: Case Study Paper.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 233–38. ACM, 2015. https://doi.org/10.1145/2728606.2728617."},"publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","page":"233 - 238","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"month":"04","day":"14","scopus_import":1,"author":[{"first_name":"Mária","last_name":"Svoreňová","full_name":"Svoreňová, Mária"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kevin","last_name":"Leahy","full_name":"Leahy, Kevin"},{"first_name":"Hasan","last_name":"Eniser","full_name":"Eniser, Hasan"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Cěrná, Ivana","last_name":"Cěrná","first_name":"Ivana"},{"last_name":"Belta","first_name":"Cǎlin","full_name":"Belta, Cǎlin"}],"oa_version":"None","date_updated":"2021-01-12T06:52:33Z","date_created":"2018-12-11T11:53:29Z","_id":"1691","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","department":[{"_id":"KrCh"}],"title":"Temporal logic motion planning using POMDPs with parity objectives: Case study paper","status":"public","publication_status":"published","publist_id":"5453","ec_funded":1,"abstract":[{"lang":"eng","text":"We consider a case study of the problem of deploying an autonomous air vehicle in a partially observable, dynamic, indoor environment from a specification given as a linear temporal logic (LTL) formula over regions of interest. We model the motion and sensing capabilities of the vehicle as a partially observable Markov decision process (POMDP). We adapt recent results for solving POMDPs with parity objectives to generate a control policy. We also extend the existing framework with a policy minimization technique to obtain a better implementable policy, while preserving its correctness. The proposed techniques are illustrated in an experimental setup involving an autonomous quadrotor performing surveillance in a dynamic environment."}],"type":"conference"},{"type":"journal_article","ec_funded":1,"publist_id":"5450","issue":"9","abstract":[{"lang":"eng","text":"\r\nWe introduce quantitative timed refinement and timed simulation (directed) metrics, incorporating zenoness checks, for timed systems. These metrics assign positive real numbers which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximal timing mismatch that can arise, (2) the “steady-state” maximal timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation distances to within any desired degree of accuracy. In order to compute the values of the quantitative simulation distances, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite-state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives in graph games, and then use these algorithms to compute the values of the timed simulation distances over timed automata.\r\n"}],"year":"2015","_id":"1694","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"publisher":"IEEE","intvolume":" 60","title":"Quantitative temporal simulation and refinement distances for timed systems","publication_status":"published","status":"public","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Vinayak","last_name":"Prabhu","full_name":"Prabhu, Vinayak"}],"oa_version":"None","volume":60,"date_created":"2018-12-11T11:53:30Z","date_updated":"2021-01-12T06:52:34Z","scopus_import":1,"day":"24","month":"02","citation":{"chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation and Refinement Distances for Timed Systems.” IEEE Transactions on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2015.2404612.","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation and Refinement Distances for Timed Systems.” IEEE Transactions on Automatic Control, vol. 60, no. 9, IEEE, 2015, pp. 2291–306, doi:10.1109/TAC.2015.2404612.","short":"K. Chatterjee, V. Prabhu, IEEE Transactions on Automatic Control 60 (2015) 2291–2306.","ista":"Chatterjee K, Prabhu V. 2015. Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. 60(9), 2291–2306.","apa":"Chatterjee, K., & Prabhu, V. (2015). Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. IEEE. https://doi.org/10.1109/TAC.2015.2404612","ieee":"K. Chatterjee and V. Prabhu, “Quantitative temporal simulation and refinement distances for timed systems,” IEEE Transactions on Automatic Control, vol. 60, no. 9. IEEE, pp. 2291–2306, 2015.","ama":"Chatterjee K, Prabhu V. Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. 2015;60(9):2291-2306. doi:10.1109/TAC.2015.2404612"},"publication":"IEEE Transactions on Automatic Control","page":"2291 - 2306","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","doi":"10.1109/TAC.2015.2404612","date_published":"2015-02-24T00:00:00Z","language":[{"iso":"eng"}]},{"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1503.03738"}],"language":[{"iso":"eng"}],"doi":"10.1002/pssb.201552082","month":"09","publisher":"Wiley","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2015","volume":252,"date_updated":"2021-01-12T06:52:34Z","date_created":"2018-12-11T11:53:31Z","author":[{"full_name":"Kaczmarczyk, Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1629-3675","first_name":"Jan","last_name":"Kaczmarczyk"},{"full_name":"Schickling, Tobias","last_name":"Schickling","first_name":"Tobias"},{"full_name":"Bünemann, Jörg","first_name":"Jörg","last_name":"Bünemann"}],"publist_id":"5449","ec_funded":1,"page":"2059 - 2071","citation":{"ama":"Kaczmarczyk J, Schickling T, Bünemann J. Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. 2015;252(9):2059-2071. doi:10.1002/pssb.201552082","ieee":"J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Evaluation techniques for Gutzwiller wave functions in finite dimensions,” Physica Status Solidi (B): Basic Solid State Physics, vol. 252, no. 9. Wiley, pp. 2059–2071, 2015.","apa":"Kaczmarczyk, J., Schickling, T., & Bünemann, J. (2015). Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. Wiley. https://doi.org/10.1002/pssb.201552082","ista":"Kaczmarczyk J, Schickling T, Bünemann J. 2015. Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. 252(9), 2059–2071.","short":"J. Kaczmarczyk, T. Schickling, J. Bünemann, Physica Status Solidi (B): Basic Solid State Physics 252 (2015) 2059–2071.","mla":"Kaczmarczyk, Jan, et al. “Evaluation Techniques for Gutzwiller Wave Functions in Finite Dimensions.” Physica Status Solidi (B): Basic Solid State Physics, vol. 252, no. 9, Wiley, 2015, pp. 2059–71, doi:10.1002/pssb.201552082.","chicago":"Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Evaluation Techniques for Gutzwiller Wave Functions in Finite Dimensions.” Physica Status Solidi (B): Basic Solid State Physics. Wiley, 2015. https://doi.org/10.1002/pssb.201552082."},"publication":"Physica Status Solidi (B): Basic Solid State Physics","date_published":"2015-09-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 252","title":"Evaluation techniques for Gutzwiller wave functions in finite dimensions","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1695","oa_version":"Preprint","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"We give a comprehensive introduction into a diagrammatic method that allows for the evaluation of Gutzwiller wave functions in finite spatial dimensions. We discuss in detail some numerical schemes that turned out to be useful in the real-space evaluation of the diagrams. The method is applied to the problem of d-wave superconductivity in a two-dimensional single-band Hubbard model. Here, we discuss in particular the role of long-range contributions in our diagrammatic expansion. We further reconsider our previous analysis on the kinetic energy gain in the superconducting state."}]},{"pubrep_id":"455","file":[{"file_name":"IST-2016-455-v1+1_journal.pcbi.1004304.pdf","access_level":"open_access","file_size":4673930,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5212","date_created":"2018-12-12T10:16:25Z","date_updated":"2020-07-14T12:45:12Z","checksum":"472b979f3f1cffb37b3e503f085115ca"}],"oa_version":"Published Version","_id":"1697","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 11","status":"public","ddc":["570"],"title":"High accuracy decoding of dynamical motion from a large retinal population","issue":"7","abstract":[{"text":"Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits.","lang":"eng"}],"type":"journal_article","date_published":"2015-07-01T00:00:00Z","citation":{"short":"O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015).","mla":"Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.","chicago":"Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gašper Tkačik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004304.","ama":"Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 2015;11(7). doi:10.1371/journal.pcbi.1004304","ieee":"O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015.","apa":"Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkačik, G., & Berry, M. (2015). High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004304","ista":"Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. 2015. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 11(7), e1004304."},"publication":"PLoS Computational Biology","has_accepted_license":"1","day":"01","scopus_import":1,"author":[{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"orcid":"0000-0002-8790-1914","id":"421234E8-F248-11E8-B48F-1D18A9856A87","last_name":"Botella Soler","first_name":"Vicente","full_name":"Botella Soler, Vicente"},{"full_name":"Simmons, Kristina","last_name":"Simmons","first_name":"Kristina"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"volume":11,"date_created":"2018-12-11T11:53:31Z","date_updated":"2021-01-12T06:52:35Z","acknowledgement":"This work was supported by grants EY 014196 and EY 017934 to MJB, ANR OPTIMA, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche [LIFESENSES: ANR-10-LABX-65], and by a EC grant from the Human Brain Project (CLAP) to OM, the Austrian Research Foundation FWF P25651 to VBS and GT. VBS is partially supported by contracts MEC, Spain (Grant No. AYA2010- 22111-C03-02, Grant No. AYA2013-48623-C2-2 and FEDER Funds).","year":"2015","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","publist_id":"5447","file_date_updated":"2020-07-14T12:45:12Z","article_number":"e1004304","doi":"10.1371/journal.pcbi.1004304","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26"}],"quality_controlled":"1","month":"07"},{"month":"06","doi":"10.1007/s00285-014-0802-y","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"L'OREAL Fellowship","_id":"25B67606-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publist_id":"5442","file_date_updated":"2020-07-14T12:45:12Z","author":[{"full_name":"Uecker, Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","first_name":"Hildegard","last_name":"Uecker"},{"first_name":"Derek","last_name":"Setter","full_name":"Setter, Derek"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"}],"volume":70,"date_created":"2018-12-11T11:53:32Z","date_updated":"2023-02-23T10:10:36Z","acknowledgement":"This work was made possible with financial support by the Vienna Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG), Research Unit 1078 Natural selection in structured populations, by the Austrian Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics, and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria).","year":"2015","department":[{"_id":"NiBa"}],"publisher":"Springer","publication_status":"published","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2015-06-01T00:00:00Z","citation":{"ieee":"H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer, pp. 1523–1580, 2015.","apa":"Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y","ista":"Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580.","ama":"Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y","chicago":"Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology. Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y.","short":"H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580.","mla":"Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80, doi:10.1007/s00285-014-0802-y."},"publication":"Journal of Mathematical Biology","page":"1523 - 1580","issue":"7","abstract":[{"text":"By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.","lang":"eng"}],"type":"journal_article","pubrep_id":"458","file":[{"content_type":"application/pdf","file_size":1321527,"creator":"system","access_level":"open_access","file_name":"IST-2016-458-v1+1_s00285-014-0802-y.pdf","checksum":"00e3a67bda05d4cc165b3a48b41ef9ad","date_created":"2018-12-12T10:14:27Z","date_updated":"2020-07-14T12:45:12Z","relation":"main_file","file_id":"5079"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1699","intvolume":" 70","title":"Adaptive gene introgression after secondary contact","ddc":["576"],"status":"public"},{"publication":"Physical Review B","citation":{"mla":"Wysokiński, Marcin, et al. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” Physical Review B, vol. 92, no. 12, 125135, American Physical Society, 2015, doi:10.1103/PhysRevB.92.125135.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B 92 (2015).","chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” Physical Review B. American Physical Society, 2015. https://doi.org/10.1103/PhysRevB.92.125135.","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. 2015;92(12). doi:10.1103/PhysRevB.92.125135","ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2015. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. 92(12), 125135.","apa":"Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2015). Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.92.125135","ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states,” Physical Review B, vol. 92, no. 12. American Physical Society, 2015."},"date_published":"2015-09-18T00:00:00Z","scopus_import":1,"day":"18","title":"Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states","status":"public","intvolume":" 92","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1696","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The recently proposed diagrammatic expansion (DE) technique for the full Gutzwiller wave function (GWF) is applied to the Anderson lattice model. This approach allows for a systematic evaluation of the expectation values with full Gutzwiller wave function in finite-dimensional systems. It introduces results extending in an essential manner those obtained by means of the standard Gutzwiller approximation (GA), which is variationally exact only in infinite dimensions. Within the DE-GWF approach we discuss the principal paramagnetic properties and their relevance to heavy-fermion systems. We demonstrate the formation of an effective, narrow f band originating from atomic f-electron states and subsequently interpret this behavior as a direct itineracy of f electrons; it represents a combined effect of both the hybridization and the correlations induced by the Coulomb repulsive interaction. Such a feature is absent on the level of GA, which is equivalent to the zeroth order of our expansion. Formation of the hybridization- and electron-concentration-dependent narrow f band rationalizes the common assumption of such dispersion of f levels in the phenomenological modeling of the band structure of CeCoIn5. Moreover, it is shown that the emerging f-electron direct itineracy leads in a natural manner to three physically distinct regimes within a single model that are frequently discussed for 4f- or 5f-electron compounds as separate model situations. We identify these regimes as (i) the mixed-valence regime, (ii) Kondo/almost-Kondo insulating regime, and (iii) the Kondo-lattice limit when the f-electron occupancy is very close to the f-state half filling, ⟨nˆf⟩→1. The nonstandard features of the emerging correlated quantum liquid state are stressed.","lang":"eng"}],"issue":"12","quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.07003"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.92.125135","month":"09","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2015","acknowledgement":"The work was partly supported by the National Science Centre (NCN) under MAESTRO, Grant No. DEC-2012/04/A/ST3/00342. M.W. acknowledges the hospitality of the Institute of Science and Technology Austria during the final stage of development of the present work, as well as partial financial support from the Society-Environment-Technology project of the Jagiellonian University for that stay. J.K. 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 ].","date_created":"2018-12-11T11:53:31Z","date_updated":"2021-01-12T06:52:35Z","volume":92,"author":[{"last_name":"Wysokiński","first_name":"Marcin","full_name":"Wysokiński, Marcin"},{"first_name":"Jan","last_name":"Kaczmarczyk","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1629-3675","full_name":"Kaczmarczyk, Jan"},{"first_name":"Jozef","last_name":"Spałek","full_name":"Spałek, Jozef"}],"article_number":"125135","publist_id":"5448","ec_funded":1},{"publist_id":"5440","pmid":1,"year":"2015","acknowledgement":"Research was supported in part by National Science Foundation Grants PHY-1305525, PHY-1451171, and CCF-0939370, by National Institutes of Health Grant R01 EY14196, and by Austrian Science Foundation Grant FWF P25651. Additional support was provided by the\r\nFannie and John Hertz Foundation, by the Swartz Foundation, by the W. M. Keck Foundation, and by the Simons Foundation.","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","publication_status":"published","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"last_name":"Mora","first_name":"Thierry","full_name":"Mora, Thierry"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"last_name":"Amodei","first_name":"Dario","full_name":"Amodei, Dario"},{"first_name":"Stephanie","last_name":"Palmer","full_name":"Palmer, Stephanie"},{"first_name":"Michael","last_name":"Berry Ii","full_name":"Berry Ii, Michael"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"}],"volume":112,"date_created":"2018-12-11T11:53:33Z","date_updated":"2021-01-12T06:52:37Z","month":"09","external_id":{"pmid":["26330611"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577210/"}],"oa":1,"project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26"}],"quality_controlled":"1","doi":"10.1073/pnas.1514188112","language":[{"iso":"eng"}],"type":"journal_article","issue":"37","abstract":[{"lang":"eng","text":"The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but, with more spikes, the number of possible patterns increases. This tradeoff between probability and numerosity is mathematically equivalent to the relationship between entropy and energy in statistical physics. We construct this relationship for populations of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination of direct and model-based analyses of experiments on the response of this network to naturalistic movies. We see signs of a thermodynamic limit, where the entropy per neuron approaches a smooth function of the energy per neuron as N increases. The form of this function corresponds to the distribution of activity being poised near an unusual kind of critical point. We suggest further tests of criticality, and give a brief discussion of its functional significance. "}],"_id":"1701","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 112","status":"public","title":"Thermodynamics and signatures of criticality in a network of neurons","oa_version":"Submitted Version","scopus_import":1,"day":"15","citation":{"mla":"Tkačik, Gašper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112.","short":"G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.","chicago":"Tkačik, Gašper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1514188112.","ama":"Tkačik G, Mora T, Marre O, et al. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 2015;112(37):11508-11513. doi:10.1073/pnas.1514188112","ista":"Tkačik G, Mora T, Marre O, Amodei D, Palmer S, Berry Ii M, Bialek W. 2015. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 112(37), 11508–11513.","ieee":"G. Tkačik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015.","apa":"Tkačik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., & Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of neurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1514188112"},"publication":"PNAS","page":"11508 - 11513","date_published":"2015-09-15T00:00:00Z"},{"month":"04","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.3234"}],"oa":1,"quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"doi":"10.1016/j.ic.2015.03.001","language":[{"iso":"eng"}],"publist_id":"5443","ec_funded":1,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 and S11402-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (267989: Quantitative Reactive Modeling), European project Cassting (FP7-601148), ERC Start grant (279499: inVEST).","year":"2015","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Elsevier","author":[{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Rabinovich","first_name":"Alexander","full_name":"Rabinovich, Alexander"},{"first_name":"Jean","last_name":"Raskin","full_name":"Raskin, Jean"}],"date_created":"2018-12-11T11:53:32Z","date_updated":"2021-01-12T06:52:36Z","volume":241,"scopus_import":1,"day":"01","publication":"Information and Computation","citation":{"chicago":"Velner, Yaron, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger, Alexander Rabinovich, and Jean Raskin. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.001.","short":"Y. Velner, K. Chatterjee, L. Doyen, T.A. Henzinger, A. Rabinovich, J. Raskin, Information and Computation 241 (2015) 177–196.","mla":"Velner, Yaron, et al. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” Information and Computation, vol. 241, no. 4, Elsevier, 2015, pp. 177–96, doi:10.1016/j.ic.2015.03.001.","ieee":"Y. Velner, K. Chatterjee, L. Doyen, T. A. Henzinger, A. Rabinovich, and J. Raskin, “The complexity of multi-mean-payoff and multi-energy games,” Information and Computation, vol. 241, no. 4. Elsevier, pp. 177–196, 2015.","apa":"Velner, Y., Chatterjee, K., Doyen, L., Henzinger, T. A., Rabinovich, A., & Raskin, J. (2015). The complexity of multi-mean-payoff and multi-energy games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.001","ista":"Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. 2015. The complexity of multi-mean-payoff and multi-energy games. Information and Computation. 241(4), 177–196.","ama":"Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. The complexity of multi-mean-payoff and multi-energy games. Information and Computation. 2015;241(4):177-196. doi:10.1016/j.ic.2015.03.001"},"page":"177 - 196","date_published":"2015-04-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Multi-mean-payoff and multi-energy games replace individual weights by tuples, and the limit average (resp., running sum) of each coordinate must be (resp., remain) nonnegative. We prove finite-memory determinacy of multi-energy games and show inter-reducibility of multi-mean-payoff and multi-energy games for finite-memory strategies. We improve the computational complexity for solving both classes with finite-memory strategies: we prove coNP-completeness improving the previous known EXPSPACE bound. For memoryless strategies, we show that deciding the existence of a winning strategy for the protagonist is NP-complete. We present the first solution of multi-mean-payoff games with infinite-memory strategies: we show that mean-payoff-sup objectives can be decided in NP∩coNP, whereas mean-payoff-inf objectives are coNP-complete."}],"issue":"4","_id":"1698","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The complexity of multi-mean-payoff and multi-energy games","status":"public","intvolume":" 241","oa_version":"Preprint"}]