[{"status":"public","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"conference":{"location":"Kyoto, Japan","end_date":"2015-07-10","start_date":"2015-07-06","name":"LICS: Logic in Computer Science"},"type":"conference","_id":"1660","title":"Long-run average behaviour of probabilistic vector addition systems","department":[{"_id":"KrCh"}],"publist_id":"5490","author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"last_name":"Kiefer","full_name":"Kiefer, Stefan","first_name":"Stefan"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"T. Brázdil, S. Kiefer, A. Kučera, P. Novotný, in:, IEEE, 2015, pp. 44–55.","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","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","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."},"date_updated":"2021-01-12T06:52:20Z","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.02655"}],"oa":1,"scopus_import":1,"quality_controlled":"1","alternative_title":["LICS"],"publisher":"IEEE","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T11:53:19Z","ec_funded":1,"date_published":"2015-07-01T00:00:00Z","doi":"10.1109/LICS.2015.15","page":"44 - 55","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015"},{"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"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815041/","open_access":"1"}],"scopus_import":1,"intvolume":" 526","month":"10","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":526,"issue":"7574","_id":"1665","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T06:52:23Z","department":[{"_id":"KrCh"}],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2015","publication":"Nature","day":"22","page":"525 - 530","date_created":"2018-12-11T11:53:21Z","doi":"10.1038/nature15395","date_published":"2015-10-22T00:00:00Z","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"citation":{"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.","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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["26466571"]},"publist_id":"5484","author":[{"full_name":"Landau, Dan","last_name":"Landau","first_name":"Dan"},{"first_name":"Eugen","full_name":"Tausch, Eugen","last_name":"Tausch"},{"first_name":"Amaro","full_name":"Taylor Weiner, Amaro","last_name":"Taylor Weiner"},{"first_name":"Chip","last_name":"Stewart","full_name":"Stewart, Chip"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Reiter","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"first_name":"Jasmin","last_name":"Bahlo","full_name":"Bahlo, Jasmin"},{"last_name":"Kluth","full_name":"Kluth, Sandra","first_name":"Sandra"},{"last_name":"Božić","full_name":"Božić, Ivana","first_name":"Ivana"},{"first_name":"Michael","last_name":"Lawrence","full_name":"Lawrence, Michael"},{"last_name":"Böttcher","full_name":"Böttcher, Sebastian","first_name":"Sebastian"},{"first_name":"Scott","full_name":"Carter, Scott","last_name":"Carter"},{"last_name":"Cibulskis","full_name":"Cibulskis, Kristian","first_name":"Kristian"},{"last_name":"Mertens","full_name":"Mertens, Daniel","first_name":"Daniel"},{"first_name":"Carrie","last_name":"Sougnez","full_name":"Sougnez, Carrie"},{"first_name":"Mara","last_name":"Rosenberg","full_name":"Rosenberg, Mara"},{"last_name":"Hess","full_name":"Hess, Julian","first_name":"Julian"},{"first_name":"Jennifer","last_name":"Edelmann","full_name":"Edelmann, Jennifer"},{"first_name":"Sabrina","last_name":"Kless","full_name":"Kless, Sabrina"},{"first_name":"Michael","full_name":"Kneba, Michael","last_name":"Kneba"},{"last_name":"Ritgen","full_name":"Ritgen, Matthias","first_name":"Matthias"},{"full_name":"Fink, Anna","last_name":"Fink","first_name":"Anna"},{"first_name":"Kirsten","last_name":"Fischer","full_name":"Fischer, Kirsten"},{"last_name":"Gabriel","full_name":"Gabriel, Stacey","first_name":"Stacey"},{"first_name":"Eric","last_name":"Lander","full_name":"Lander, Eric"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"first_name":"Hartmut","last_name":"Döhner","full_name":"Döhner, Hartmut"},{"first_name":"Michael","full_name":"Hallek, Michael","last_name":"Hallek"},{"first_name":"Donna","full_name":"Neuberg, Donna","last_name":"Neuberg"},{"last_name":"Getz","full_name":"Getz, Gad","first_name":"Gad"},{"first_name":"Stephan","last_name":"Stilgenbauer","full_name":"Stilgenbauer, Stephan"},{"first_name":"Catherine","full_name":"Wu, Catherine","last_name":"Wu"}],"title":"Mutations driving CLL and their evolution in progression and relapse"},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"author":[{"first_name":"Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","full_name":"Kovács, Krisztián","last_name":"Kovács"},{"last_name":"Steinmann","full_name":"Steinmann, Myriam","first_name":"Myriam"},{"first_name":"Olivier","last_name":"Halfon","full_name":"Halfon, Olivier"},{"full_name":"Magistretti, Pierre","last_name":"Magistretti","first_name":"Pierre"},{"full_name":"Cardinaux, Jean","last_name":"Cardinaux","first_name":"Jean"}],"publist_id":"5487","title":"Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2","citation":{"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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","page":"2252 - 2260","date_published":"2015-11-01T00:00:00Z","doi":"10.1016/j.cellsig.2015.08.001","date_created":"2018-12-11T11:53:20Z","has_accepted_license":"1","year":"2015","day":"01","publication":"Cellular Signalling","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"578","_id":"1663","department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:45:10Z","date_updated":"2021-01-12T06:52:22Z","ddc":["570"],"scopus_import":1,"month":"11","intvolume":" 27","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","issue":"11","volume":27,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"local","checksum":"4ee690b6444b7a43523237f0941457d1","file_id":"5321","file_size":1735337,"date_updated":"2020-07-14T12:45:10Z","creator":"system","file_name":"IST-2016-578-v1+1_CLS-D-15-00072R1_.pdf","date_created":"2018-12-12T10:18:03Z"}],"language":[{"iso":"eng"}]},{"ec_funded":1,"volume":9259,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 9259","month":"08","main_file_link":[{"url":"http://arxiv.org/abs/1407.4777","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T06:52:24Z","status":"public","conference":{"name":"QEST: Quantitative Evaluation of Systems","end_date":"2015-09-03","location":"Madrid, Spain","start_date":"2015-09-01"},"type":"conference","_id":"1667","series_title":"Lecture Notes in Computer Science","date_created":"2018-12-11T11:53:22Z","date_published":"2015-08-22T00:00:00Z","doi":"10.1007/978-3-319-22264-6_10","page":"141 - 159","day":"22","year":"2015","oa":1,"quality_controlled":"1","publisher":"Springer","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.","title":"Optimizing performance of continuous-time stochastic systems using timeout synthesis","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"first_name":"L'Uboš","last_name":"Korenčiak","full_name":"Korenčiak, L'Uboš"},{"full_name":"Krčál, Jan","last_name":"Krčál","first_name":"Jan"},{"last_name":"Novotny","full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"full_name":"Řehák, Vojtěch","last_name":"Řehák","first_name":"Vojtěch"}],"publist_id":"5482","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","short":"T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, V. Řehák, 9259 (2015) 141–159.","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.","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."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"year":"2015","day":"21","publication":"Nature","page":"550 - 553","date_published":"2015-10-21T00:00:00Z","doi":"10.1038/nature15701","date_created":"2018-12-11T11:53:20Z","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.","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"citation":{"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.","short":"D. Barkley, B. Song, M. Vasudevan, G.M. Lemoult, M. Avila, B. Hof, Nature 526 (2015) 550–553.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Barkley","full_name":"Barkley, Dwight","first_name":"Dwight"},{"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","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","last_name":"Lemoult","full_name":"Lemoult, Grégoire M"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"publist_id":"5485","title":"The rise of fully turbulent flow","project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589"}],"publication_status":"published","language":[{"iso":"eng"}],"volume":526,"issue":"7574","ec_funded":1,"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"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.09143"}],"month":"10","intvolume":" 526","date_updated":"2021-01-12T06:52:22Z","department":[{"_id":"BjHo"}],"_id":"1664","type":"journal_article","status":"public"},{"publist_id":"5476","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ostrovsky, Rafail","last_name":"Ostrovsky","first_name":"Rafail"},{"last_name":"Zhou","full_name":"Zhou, Hongsheng","first_name":"Hongsheng"},{"full_name":"Zikas, Vassilis","last_name":"Zikas","first_name":"Vassilis"}],"article_processing_charge":"No","title":"Incoercible multi-party computation and universally composable receipt-free voting","citation":{"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.","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.","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","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","short":"J.F. Alwen, R. Ostrovsky, H. Zhou, V. Zikas, in:, Advances in Cryptology - CRYPTO 2015, Springer, 2015, pp. 763–780.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"page":"763 - 780","doi":"10.1007/978-3-662-48000-7_37","date_published":"2015-08-01T00:00:00Z","date_created":"2018-12-11T11:53:23Z","has_accepted_license":"1","year":"2015","day":"01","publication":"Advances in Cryptology - CRYPTO 2015","quality_controlled":"1","publisher":"Springer","oa":1,"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.","department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:45:11Z","date_updated":"2022-06-07T09:51:55Z","ddc":["000"],"type":"conference","conference":{"start_date":"2015-08-16","end_date":"2015-08-20","location":"Santa Barbara, CA, United States","name":"CRYPTO: International Cryptology Conference"},"status":"public","_id":"1672","series_title":"Lecture Notes in Computer Science","volume":9216,"ec_funded":1,"publication_identifier":{"eisbn":["978-3-662-48000-7"],"isbn":["978-3-662-47999-5"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:45:11Z","file_size":397363,"date_created":"2020-05-15T08:55:29Z","file_name":"2015_CRYPTO_Alwen.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"5b6649e80d1f781a8910f7cce6427f78","file_id":"7853"}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":"1","month":"08","intvolume":" 9216","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version"},{"project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"citation":{"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.","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","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","short":"K.Z. Pietrzak, M. Skórski, 9230 (2015) 81–98.","ieee":"K. Z. Pietrzak and M. Skórski, “The chain rule for HILL pseudoentropy, revisited,” vol. 9230. Springer, pp. 81–98, 2015.","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.","ista":"Pietrzak KZ, Skórski M. 2015. The chain rule for HILL pseudoentropy, revisited. 9230, 81–98."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"last_name":"Skórski","full_name":"Skórski, Maciej","first_name":"Maciej"}],"publist_id":"5480","title":"The chain rule for HILL pseudoentropy, revisited","quality_controlled":"1","publisher":"Springer","oa":1,"has_accepted_license":"1","year":"2015","day":"15","page":"81 - 98","doi":"10.1007/978-3-319-22174-8_5","date_published":"2015-08-15T00:00:00Z","date_created":"2018-12-11T11:53:22Z","series_title":"Lecture Notes in Computer Science","_id":"1669","type":"conference","conference":{"name":"LATINCRYPT: Cryptology and Information Security in Latin America","location":"Guadalajara, Mexico","end_date":"2015-08-26","start_date":"2015-08-23"},"status":"public","pubrep_id":"669","date_updated":"2021-01-12T06:52:24Z","ddc":["005"],"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:45:11Z","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."}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"month":"08","intvolume":" 9230","publication_status":"published","file":[{"file_size":443340,"date_updated":"2020-07-14T12:45:11Z","creator":"system","file_name":"IST-2016-669-v1+1_599.pdf","date_created":"2018-12-12T10:18:29Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5351","checksum":"8cd4215b83efba720e8cf27c23ff4781"}],"language":[{"iso":"eng"}],"volume":9230,"ec_funded":1},{"year":"2015","has_accepted_license":"1","day":"01","page":"368 - 387","date_created":"2018-12-11T11:53:23Z","doi":"10.1007/978-3-662-47989-6_18","date_published":"2015-08-01T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"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.","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.","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.","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","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","short":"P. Gazi, K.Z. Pietrzak, S. Tessaro, in:, Springer, 2015, pp. 368–387.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5478","author":[{"first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter","last_name":"Gazi"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tessaro","full_name":"Tessaro, Stefano","first_name":"Stefano"}],"title":"The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC","project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":592296,"date_updated":"2020-07-14T12:45:11Z","creator":"system","file_name":"IST-2016-673-v1+1_053.pdf","date_created":"2018-12-12T10:10:38Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"17d854227b3b753fd34f5d29e5b5a32e","file_id":"4827"}],"ec_funded":1,"volume":9215,"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."}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 9215","month":"08","date_updated":"2021-01-12T06:52:25Z","ddc":["004","005"],"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:45:11Z","_id":"1671","conference":{"location":"Santa Barbara, CA, United States","end_date":"2015-08-20","start_date":"2015-08-16","name":"CRYPTO: International Cryptology Conference"},"type":"conference","pubrep_id":"673","status":"public"},{"ddc":["000"],"date_updated":"2021-01-12T06:52:26Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:11Z","_id":"1673","status":"public","type":"journal_article","file":[{"file_id":"6342","checksum":"e613d94d283c776322403a28aad11bdd","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2015_rspa_Adlam.pdf","date_created":"2019-04-18T12:39:56Z","creator":"kschuh","file_size":391466,"date_updated":"2020-07-14T12:45:11Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":471,"issue":"2181","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"month":"09","intvolume":" 471","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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.","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.","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).","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"},"title":"Amplifiers of selection","publist_id":"5477","author":[{"full_name":"Adlam, Ben","last_name":"Adlam","first_name":"Ben"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"article_number":"20150114","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"day":"08","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","has_accepted_license":"1","year":"2015","date_published":"2015-09-08T00:00:00Z","doi":"10.1098/rspa.2015.0114","date_created":"2018-12-11T11:53:24Z","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). ","publisher":"Royal Society of London","quality_controlled":"1","oa":1},{"project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"title":"Relaxing full-codebook security: A refined analysis of key-length extension schemes","author":[{"first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter","last_name":"Gazi"},{"full_name":"Lee, Jooyoung","last_name":"Lee","first_name":"Jooyoung"},{"last_name":"Seurin","full_name":"Seurin, Yannick","first_name":"Yannick"},{"full_name":"Steinberger, John","last_name":"Steinberger","first_name":"John"},{"first_name":"Stefano","full_name":"Tessaro, Stefano","last_name":"Tessaro"}],"publist_id":"5481","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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.","short":"P. Gazi, J. Lee, Y. Seurin, J. Steinberger, S. Tessaro, 9054 (2015) 319–341."},"quality_controlled":"1","publisher":"Springer","oa":1,"doi":"10.1007/978-3-662-48116-5_16","date_published":"2015-08-12T00:00:00Z","date_created":"2018-12-11T11:53:22Z","page":"319 - 341","day":"12","year":"2015","status":"public","type":"conference","conference":{"start_date":"2015-03-08","location":"Istanbul, Turkey","end_date":"2015-03-11","name":"FSE: Fast Software Encryption"},"_id":"1668","series_title":"Lecture Notes in Computer Science","department":[{"_id":"KrPi"}],"date_updated":"2020-08-11T10:09:26Z","month":"08","intvolume":" 9054","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2015/397"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","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 "}],"volume":9054,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"type":"conference","conference":{"location":"Jerusalem, Israel","end_date":"2015-06-11","start_date":"2015-06-07","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"status":"public","_id":"1670","author":[{"last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"full_name":"Magazzeni, Daniele","last_name":"Magazzeni","first_name":"Daniele"},{"last_name":"Minopoli","full_name":"Minopoli, Stefano","first_name":"Stefano"},{"full_name":"Wehrle, Martin","last_name":"Wehrle","first_name":"Martin"}],"publist_id":"5479","department":[{"_id":"ToHe"}],"title":"PDDL+ planning with hybrid automata: Foundations of translating must behavior","citation":{"mla":"Bogomolov, Sergiy, et al. PDDL+ Planning with Hybrid Automata: Foundations of Translating Must Behavior. AAAI Press, 2015, pp. 42–46.","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.","short":"S. Bogomolov, D. Magazzeni, S. Minopoli, M. Wehrle, in:, AAAI Press, 2015, pp. 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.","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.","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.","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."},"date_updated":"2021-01-12T06:52:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"AAAI Press","scopus_import":1,"quality_controlled":"1","main_file_link":[{"url":"https://www.aaai.org/ocs/index.php/ICAPS/ICAPS15/paper/view/10606/10394"}],"month":"06","abstract":[{"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.","lang":"eng"}],"oa_version":"None","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)”.","page":"42 - 46","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:53:23Z","ec_funded":1,"year":"2015","publication_status":"published","day":"01","language":[{"iso":"eng"}]},{"intvolume":" 27","month":"09","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1407.8015","open_access":"1"}],"publisher":"World Scientific Publishing","scopus_import":1,"quality_controlled":"1","oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"date_created":"2018-12-11T11:53:24Z","doi":"10.1142/S0129055X1550018X","date_published":"2015-09-01T00:00:00Z","issue":"8","volume":27,"publication":"Reviews in Mathematical Physics","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","status":"public","type":"journal_article","article_number":"1550018","_id":"1674","department":[{"_id":"LaEr"}],"title":"Edge universality for deformed Wigner matrices","author":[{"last_name":"Lee","full_name":"Lee, Jioon","first_name":"Jioon"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin"}],"publist_id":"5475","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Lee J, Schnelli K. 2015. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 27(8), 1550018.","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.","ama":"Lee J, Schnelli K. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 2015;27(8). doi:10.1142/S0129055X1550018X","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.","short":"J. Lee, K. Schnelli, Reviews in Mathematical Physics 27 (2015)."},"date_updated":"2021-01-12T06:52:26Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","ieee":"G. M. Lemoult, P. Maier, and B. Hof, “Taylor’s Forest,” Physics of Fluids, vol. 27, no. 9. American Institute of Physics, 2015.","short":"G.M. Lemoult, P. Maier, B. Hof, Physics of Fluids 27 (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","ama":"Lemoult GM, Maier P, Hof B. Taylor’s Forest. Physics of Fluids. 2015;27(9). doi:10.1063/1.4930850","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.","ista":"Lemoult GM, Maier P, Hof B. 2015. Taylor’s Forest. Physics of Fluids. 27(9), 091102."},"title":"Taylor's Forest","author":[{"first_name":"Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","full_name":"Lemoult, Grégoire M","last_name":"Lemoult"},{"id":"384F7C04-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Maier","full_name":"Maier, Philipp"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"publist_id":"5469","article_number":"091102","publication":"Physics of Fluids","day":"24","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:53:26Z","doi":"10.1063/1.4930850","date_published":"2015-09-24T00:00:00Z","oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","ddc":["532"],"date_updated":"2021-01-12T06:52:28Z","department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:12Z","_id":"1679","pubrep_id":"748","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_size":872366,"date_updated":"2020-07-14T12:45:12Z","creator":"system","file_name":"IST-2017-748-v1+1_1.4930850.pdf","date_created":"2018-12-12T10:13:35Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"604bba3c2496aadb3efcff77de01ce6c","file_id":"5019"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","volume":27,"issue":"9","oa_version":"Published Version","intvolume":" 27","month":"09","scopus_import":1},{"status":"public","type":"journal_article","_id":"1676","department":[{"_id":"MiSi"}],"title":"Editorial overview: Cell adhesion and migration","author":[{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Erez","last_name":"Raz","full_name":"Raz, Erez"}],"publist_id":"5473","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"M.K. Sixt, E. Raz, Current Opinion in Cell Biology 36 (2015) 4–6.","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.","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","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","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.","ista":"Sixt MK, Raz E. 2015. Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. 36(10), 4–6."},"date_updated":"2021-01-12T06:52:27Z","month":"10","intvolume":" 36","publisher":"Elsevier","scopus_import":1,"oa_version":"None","doi":"10.1016/j.ceb.2015.09.004","issue":"10","date_published":"2015-10-01T00:00:00Z","volume":36,"date_created":"2018-12-11T11:53:25Z","page":"4 - 6","day":"01","language":[{"iso":"eng"}],"publication":"Current Opinion in Cell Biology","publication_status":"published","year":"2015"},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","date_created":"2018-12-11T11:53:28Z","doi":"10.1016/j.ceb.2015.08.001","date_published":"2015-10-01T00:00:00Z","page":"93 - 102","publication":"Current Opinion in Cell Biology","day":"01","year":"2015","has_accepted_license":"1","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"title":"Navigating in tissue mazes: Chemoattractant interpretation in complex environments","publist_id":"5458","author":[{"full_name":"Sarris, Milka","last_name":"Sarris","first_name":"Milka"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","short":"M. Sarris, M.K. Sixt, Current Opinion in Cell Biology 36 (2015) 93–102.","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.","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.","ista":"Sarris M, Sixt MK. 2015. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 36(10), 93–102.","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."},"intvolume":" 36","month":"10","scopus_import":1,"oa_version":"Published Version","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."}],"ec_funded":1,"issue":"10","volume":36,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4875","checksum":"c29973924b790aab02fdd91857759cfb","creator":"system","file_size":797964,"date_updated":"2020-07-14T12:45:12Z","file_name":"IST-2016-445-v1+1_1-s2.0-S0955067415001064-main.pdf","date_created":"2018-12-12T10:11:21Z"}],"publication_status":"published","pubrep_id":"445","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1687","file_date_updated":"2020-07-14T12:45:12Z","department":[{"_id":"MiSi"}],"ddc":["570"],"date_updated":"2021-01-12T06:52:31Z"},{"doi":"10.1007/978-3-662-48350-3_33","date_published":"2015-09-01T00:00:00Z","date_created":"2018-12-11T11:53:27Z","page":"386 - 398","day":"01","year":"2015","quality_controlled":"1","publisher":"Springer","oa":1,"title":"A fixed parameter tractable approximation scheme for the optimal cut graph of a surface","author":[{"last_name":"Cohen Addad","full_name":"Cohen Addad, Vincent","first_name":"Vincent"},{"first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","last_name":"De Mesmay","full_name":"De Mesmay, Arnaud N"}],"publist_id":"5462","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"V. Cohen Addad, A.N. de Mesmay, in:, Springer, 2015, pp. 386–398.","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.","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","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","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."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"volume":9294,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 9294","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1507.01688"}],"oa_version":"Preprint","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."}],"department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T06:52:31Z","status":"public","type":"conference","conference":{"name":"ESA: European Symposium on Algorithms","start_date":"2015-09-14","location":"Patras, Greece","end_date":"2015-09-16"},"_id":"1685"},{"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.","publisher":"Springer","quality_controlled":"1","oa":1,"day":"01","publication":"Discrete & Computational Geometry","year":"2015","date_published":"2015-10-01T00:00:00Z","doi":"10.1007/s00454-015-9720-z","date_created":"2018-12-11T11:53:28Z","page":"610 - 636","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Karasev, J. Kynčl, P. Paták, Z. Patakova, M. Tancer, Discrete & Computational Geometry 54 (2015) 610–636.","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.","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","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","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.","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.","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."},"title":"Bounds for Pach's selection theorem and for the minimum solid angle in a simplex","publist_id":"5457","author":[{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"},{"last_name":"Kynčl","full_name":"Kynčl, Jan","first_name":"Jan"},{"last_name":"Paták","full_name":"Paták, Pavel","first_name":"Pavel"},{"first_name":"Zuzana","last_name":"Patakova","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683"},{"full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer","first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","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."}],"month":"10","intvolume":" 54","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1403.8147"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":54,"_id":"1688","status":"public","type":"journal_article","date_updated":"2021-01-12T06:52:32Z","department":[{"_id":"UlWa"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:29Z","citation":{"ista":"Michaliszyn J, Otop J, Kieroňski E. 2015. On the decidability of elementary modal logics. ACM Transactions on Computational Logic. 17(1), 2.","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.","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","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","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.","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."},"department":[{"_id":"ToHe"}],"title":"On the decidability of elementary modal logics","author":[{"first_name":"Jakub","full_name":"Michaliszyn, Jakub","last_name":"Michaliszyn"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop"},{"first_name":"Emanuel","full_name":"Kieroňski, Emanuel","last_name":"Kieroňski"}],"publist_id":"5468","article_number":"2","_id":"1680","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"status":"public","type":"journal_article","publication":"ACM Transactions on Computational Logic","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","ec_funded":1,"date_created":"2018-12-11T11:53:26Z","issue":"1","doi":"10.1145/2817825","date_published":"2015-09-01T00:00:00Z","volume":17,"oa_version":"None","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."}],"intvolume":" 17","month":"09","publisher":"ACM","quality_controlled":"1"},{"oa_version":"Preprint","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."}],"month":"08","intvolume":" 62","scopus_import":1,"quality_controlled":"1","publisher":"ACM","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0858"}],"day":"01","language":[{"iso":"eng"}],"publication":"Journal of the ACM","year":"2015","publication_status":"published","volume":62,"date_published":"2015-08-01T00:00:00Z","issue":"4","doi":"10.1145/2751524","date_created":"2018-12-11T11:53:27Z","article_number":"26","_id":"1682","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Franek P, Krcál M. 2015. Robust satisfiability of systems of equations. Journal of the ACM. 62(4), 26.","chicago":"Franek, Peter, and Marek Krcál. “Robust Satisfiability of Systems of Equations.” Journal of the ACM. ACM, 2015. https://doi.org/10.1145/2751524.","ama":"Franek P, Krcál M. Robust satisfiability of systems of equations. Journal of the ACM. 2015;62(4). doi:10.1145/2751524","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.","short":"P. Franek, M. Krcál, Journal of the ACM 62 (2015).","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."},"date_updated":"2021-01-12T06:52:30Z","title":"Robust satisfiability of systems of equations","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publist_id":"5466","author":[{"full_name":"Franek, Peter","last_name":"Franek","first_name":"Peter"},{"last_name":"Krcál","full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"}]},{"page":"135 - 145","date_created":"2018-12-11T11:53:27Z","issue":"8","doi":"10.1016/j.sbi.2015.08.008","volume":33,"date_published":"2015-08-01T00:00:00Z","publication_status":"published","year":"2015","language":[{"iso":"eng"}],"publication":"Current Opinion in Structural Biology","day":"01","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"intvolume":" 33","month":"08","abstract":[{"lang":"eng","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."}],"oa_version":"None","publist_id":"5465","author":[{"full_name":"Letts, Jame A","orcid":"0000-0002-9864-3586","last_name":"Letts","first_name":"Jame A","id":"322DA418-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"title":"Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions","department":[{"_id":"LeSa"}],"date_updated":"2021-01-12T06:52:30Z","citation":{"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.","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.","short":"J.A. Letts, L.A. Sazanov, Current Opinion in Structural Biology 33 (2015) 135–145.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1683"},{"publist_id":"5459","author":[{"last_name":"Kiermaier","full_name":"Kiermaier, Eva","orcid":"0000-0001-6165-5738","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"title":"Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection","department":[{"_id":"MiSi"}],"citation":{"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.","short":"E. Kiermaier, M.K. Sixt, Science 349 (2015) 1055–1056.","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","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.","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.","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."},"date_updated":"2021-01-12T06:52:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1686","page":"1055 - 1056","doi":"10.1126/science.aad0867","date_published":"2015-09-04T00:00:00Z","volume":349,"issue":"6252","date_created":"2018-12-11T11:53:28Z","year":"2015","publication_status":"published","day":"04","language":[{"iso":"eng"}],"publication":"Science","scopus_import":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","month":"09","intvolume":" 349","oa_version":"None"},{"status":"public","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"type":"conference","conference":{"start_date":"2015-04-14","end_date":"2015-04-16","location":"Seattle, WA, United States","name":"HSCC: Hybrid Systems - Computation and Control"},"_id":"1692","department":[{"_id":"ToHe"}],"title":"Eliminating spurious transitions in reachability with support functions","publist_id":"5452","author":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","last_name":"Bogomolov"},{"full_name":"Greitschus, Marius","last_name":"Greitschus","first_name":"Marius"},{"first_name":"Thomas","full_name":"Strump, Thomas","last_name":"Strump"},{"first_name":"Andreas","last_name":"Podelski","full_name":"Podelski, Andreas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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.","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."},"date_updated":"2021-01-12T06:52:33Z","month":"04","quality_controlled":"1","publisher":"ACM","scopus_import":1,"oa_version":"None","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"}],"date_published":"2015-04-14T00:00:00Z","doi":"10.1145/2728606.2728622","ec_funded":1,"date_created":"2018-12-11T11:53:30Z","page":"149 - 158","day":"14","publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-3433-4"]},"year":"2015","publication_status":"published"},{"status":"public","type":"journal_article","_id":"1693","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:52:34Z","month":"08","intvolume":" 92","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1506.02734","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"issue":"2","volume":92,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_number":"022514","title":"Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3","publist_id":"5451","author":[{"last_name":"Amaro","full_name":"Amaro, Pedro","first_name":"Pedro"},{"full_name":"Franke, Beatrice","last_name":"Franke","first_name":"Beatrice"},{"full_name":"Krauth, Julian","last_name":"Krauth","first_name":"Julian"},{"full_name":"Diepold, Marc","last_name":"Diepold","first_name":"Marc"},{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"},{"first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","full_name":"Safari, Laleh"},{"first_name":"Jorge","full_name":"Machado, Jorge","last_name":"Machado"},{"last_name":"Antognini","full_name":"Antognini, Aldo","first_name":"Aldo"},{"first_name":"Franz","full_name":"Kottmann, Franz","last_name":"Kottmann"},{"full_name":"Indelicato, Paul","last_name":"Indelicato","first_name":"Paul"},{"full_name":"Pohl, Randolf","last_name":"Pohl","first_name":"Randolf"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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).","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.","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."},"publisher":"American Physical Society","quality_controlled":"1","oa":1,"doi":"10.1103/PhysRevA.92.022514","date_published":"2015-08-28T00:00:00Z","date_created":"2018-12-11T11:53:30Z","day":"28","publication":"Physical Review A","year":"2015"},{"date_created":"2018-12-11T11:53:29Z","ec_funded":1,"date_published":"2015-04-14T00:00:00Z","doi":"10.1145/2728606.2728630","page":"128 - 133","language":[{"iso":"eng"}],"day":"14","year":"2015","publication_status":"published","month":"04","quality_controlled":"1","publisher":"Springer","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).","oa_version":"None","abstract":[{"lang":"eng","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."}],"department":[{"_id":"ToHe"}],"title":"HYST: A source transformation and translation tool for hybrid automaton models","author":[{"full_name":"Bak, Stanley","last_name":"Bak","first_name":"Stanley"},{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"full_name":"Johnson, Taylor","last_name":"Johnson","first_name":"Taylor"}],"publist_id":"5454","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:33Z","citation":{"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.","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","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","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.","short":"S. Bak, S. Bogomolov, T. Johnson, in:, Springer, 2015, pp. 128–133.","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.","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."},"status":"public","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"conference":{"start_date":"2015-04-14","end_date":"2015-04-16","location":"Seattle, WA, United States","name":"HSCC: Hybrid Systems - Computation and Control"},"type":"conference","_id":"1690"},{"month":"04","publisher":"ACM","scopus_import":1,"oa_version":"None","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"date_created":"2018-12-11T11:53:29Z","doi":"10.1145/2728606.2728617","date_published":"2015-04-14T00:00:00Z","page":"233 - 238","language":[{"iso":"eng"}],"publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","day":"14","publication_status":"published","year":"2015","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"status":"public","conference":{"location":"Seattle, WA, United States","end_date":"2015-04-16","start_date":"2015-04-14","name":"HSCC: Hybrid Systems - Computation and Control"},"type":"conference","_id":"1691","department":[{"_id":"KrCh"}],"title":"Temporal logic motion planning using POMDPs with parity objectives: Case study paper","author":[{"first_name":"Mária","full_name":"Svoreňová, Mária","last_name":"Svoreňová"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Leahy","full_name":"Leahy, Kevin","first_name":"Kevin"},{"first_name":"Hasan","last_name":"Eniser","full_name":"Eniser, Hasan"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Cěrná","full_name":"Cěrná, Ivana","first_name":"Ivana"},{"first_name":"Cǎlin","last_name":"Belta","full_name":"Belta, Cǎlin"}],"publist_id":"5453","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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.","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."},"date_updated":"2021-01-12T06:52:33Z"},{"oa_version":"None","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"}],"month":"02","intvolume":" 60","publisher":"IEEE","scopus_import":1,"quality_controlled":"1","day":"24","publication":"IEEE Transactions on Automatic Control","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","date_published":"2015-02-24T00:00:00Z","volume":60,"doi":"10.1109/TAC.2015.2404612","issue":"9","date_created":"2018-12-11T11:53:30Z","ec_funded":1,"page":"2291 - 2306","_id":"1694","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:34Z","citation":{"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.","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","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","short":"K. Chatterjee, V. Prabhu, IEEE Transactions on Automatic Control 60 (2015) 2291–2306.","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.","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.","ista":"Chatterjee K, Prabhu V. 2015. Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. 60(9), 2291–2306."},"title":"Quantitative temporal simulation and refinement distances for timed systems","department":[{"_id":"KrCh"}],"publist_id":"5450","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}]},{"department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:52:34Z","status":"public","type":"journal_article","_id":"1695","volume":252,"issue":"9","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 252","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1503.03738"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"title":"Evaluation techniques for Gutzwiller wave functions in finite dimensions","publist_id":"5449","author":[{"first_name":"Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","last_name":"Kaczmarczyk"},{"first_name":"Tobias","last_name":"Schickling","full_name":"Schickling, Tobias"},{"last_name":"Bünemann","full_name":"Bünemann, Jörg","first_name":"Jörg"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"J. Kaczmarczyk, T. Schickling, J. Bünemann, Physica Status Solidi (B): Basic Solid State Physics 252 (2015) 2059–2071.","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.","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","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","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."},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"doi":"10.1002/pssb.201552082","date_published":"2015-09-01T00:00:00Z","date_created":"2018-12-11T11:53:31Z","page":"2059 - 2071","day":"01","publication":"Physica Status Solidi (B): Basic Solid State Physics","year":"2015","publisher":"Wiley","quality_controlled":"1","oa":1},{"project":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"article_number":"e1004304","title":"High accuracy decoding of dynamical motion from a large retinal population","author":[{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"full_name":"Botella Soler, Vicente","orcid":"0000-0002-8790-1914","last_name":"Botella Soler","id":"421234E8-F248-11E8-B48F-1D18A9856A87","first_name":"Vicente"},{"last_name":"Simmons","full_name":"Simmons, Kristina","first_name":"Kristina"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"first_name":"Michael","full_name":"Berry, Michael","last_name":"Berry"}],"publist_id":"5447","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015).","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","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","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.","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."},"oa":1,"publisher":"Public Library of Science","quality_controlled":"1","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).","date_created":"2018-12-11T11:53:31Z","doi":"10.1371/journal.pcbi.1004304","date_published":"2015-07-01T00:00:00Z","publication":"PLoS Computational Biology","day":"01","year":"2015","has_accepted_license":"1","pubrep_id":"455","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1697","file_date_updated":"2020-07-14T12:45:12Z","department":[{"_id":"GaTk"}],"ddc":["570"],"date_updated":"2021-01-12T06:52:35Z","intvolume":" 11","month":"07","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"issue":"7","volume":11,"language":[{"iso":"eng"}],"file":[{"checksum":"472b979f3f1cffb37b3e503f085115ca","file_id":"5212","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-455-v1+1_journal.pcbi.1004304.pdf","date_created":"2018-12-12T10:16:25Z","creator":"system","file_size":4673930,"date_updated":"2020-07-14T12:45:12Z"}],"publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","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.","ista":"Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580.","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."},"title":"Adaptive gene introgression after secondary contact","author":[{"orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Setter, Derek","last_name":"Setter","first_name":"Derek"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"}],"publist_id":"5442","project":[{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"L'OREAL Fellowship"}],"day":"01","publication":"Journal of Mathematical Biology","has_accepted_license":"1","year":"2015","doi":"10.1007/s00285-014-0802-y","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:53:32Z","page":"1523 - 1580","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).","quality_controlled":"1","publisher":"Springer","oa":1,"ddc":["576"],"date_updated":"2023-02-23T10:10:36Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:12Z","_id":"1699","status":"public","pubrep_id":"458","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2018-12-12T10:14:27Z","file_name":"IST-2016-458-v1+1_s00285-014-0802-y.pdf","date_updated":"2020-07-14T12:45:12Z","file_size":1321527,"creator":"system","checksum":"00e3a67bda05d4cc165b3a48b41ef9ad","file_id":"5079","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"7","volume":70,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"06","intvolume":" 70","scopus_import":1},{"day":"18","publication":"Physical Review B","year":"2015","doi":"10.1103/PhysRevB.92.125135","date_published":"2015-09-18T00:00:00Z","date_created":"2018-12-11T11:53:31Z","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 ].","publisher":"American Physical Society","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B 92 (2015)."},"title":"Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states","author":[{"full_name":"Wysokiński, Marcin","last_name":"Wysokiński","first_name":"Marcin"},{"orcid":"0000-0002-1629-3675","full_name":"Kaczmarczyk, Jan","last_name":"Kaczmarczyk","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Spałek, Jozef","last_name":"Spałek","first_name":"Jozef"}],"publist_id":"5448","article_number":"125135","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"12","volume":92,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"month":"09","intvolume":" 92","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.07003"}],"date_updated":"2021-01-12T06:52:35Z","department":[{"_id":"MiLe"}],"_id":"1696","status":"public","type":"journal_article"},{"_id":"1701","status":"public","type":"journal_article","date_updated":"2021-01-12T06:52:37Z","department":[{"_id":"GaTk"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"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. ","lang":"eng"}],"month":"09","intvolume":" 112","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577210/"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":112,"issue":"37","project":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 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.","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","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","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."},"title":"Thermodynamics and signatures of criticality in a network of neurons","author":[{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Dario","last_name":"Amodei","full_name":"Amodei, Dario"},{"last_name":"Palmer","full_name":"Palmer, Stephanie","first_name":"Stephanie"},{"full_name":"Berry Ii, Michael","last_name":"Berry Ii","first_name":"Michael"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"}],"publist_id":"5440","external_id":{"pmid":["26330611"]},"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.","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"day":"15","publication":"PNAS","year":"2015","doi":"10.1073/pnas.1514188112","date_published":"2015-09-15T00:00:00Z","date_created":"2018-12-11T11:53:33Z","page":"11508 - 11513"},{"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-01-12T06:52:36Z","type":"journal_article","status":"public","_id":"1698","issue":"4","volume":241,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.3234"}],"month":"04","intvolume":" 241","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","publist_id":"5443","author":[{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Rabinovich, Alexander","last_name":"Rabinovich","first_name":"Alexander"},{"first_name":"Jean","full_name":"Raskin, Jean","last_name":"Raskin"}],"title":"The complexity of multi-mean-payoff and multi-energy games","citation":{"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.","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","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","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.","short":"Y. Velner, K. Chatterjee, L. Doyen, T.A. Henzinger, A. Rabinovich, J. Raskin, Information and Computation 241 (2015) 177–196.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"page":"177 - 196","doi":"10.1016/j.ic.2015.03.001","date_published":"2015-04-01T00:00:00Z","date_created":"2018-12-11T11:53:32Z","year":"2015","day":"01","publication":"Information and Computation","publisher":"Elsevier","quality_controlled":"1","oa":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)."},{"publisher":"American Physical Society","scopus_import":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1506.06007","open_access":"1"}],"month":"08","intvolume":" 92","abstract":[{"text":"We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64×64 square lattice we demonstrate the existence of a novel phase, possessing an "ultralong-range" order. The fingerprint of this phase - the density correlation function - features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms.","lang":"eng"}],"oa_version":"Preprint","acknowledgement":"The work is supported by European Research Council (ERC) Advanced Grant No. 338957 FEMTO/NANO.","volume":92,"issue":"8","doi":"10.1103/PhysRevB.92.081106","date_published":"2015-08-10T00:00:00Z","date_created":"2018-12-11T11:53:32Z","year":"2015","publication_status":"published","day":"10","publication":"Physical Review B","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1700","article_number":"081106","author":[{"last_name":"Van Loon","full_name":"Van Loon, Erik","first_name":"Erik"},{"first_name":"Mikhail","full_name":"Katsnelson, Mikhail","last_name":"Katsnelson"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"publist_id":"5441","department":[{"_id":"MiLe"}],"title":"Ultralong-range order in the Fermi-Hubbard model with long-range interactions","date_updated":"2021-01-12T06:52:37Z","citation":{"mla":"Van Loon, Erik, et al. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” Physical Review B, vol. 92, no. 8, 081106, American Physical Society, 2015, doi:10.1103/PhysRevB.92.081106.","ieee":"E. Van Loon, M. Katsnelson, and M. Lemeshko, “Ultralong-range order in the Fermi-Hubbard model with long-range interactions,” Physical Review B, vol. 92, no. 8. American Physical Society, 2015.","short":"E. Van Loon, M. Katsnelson, M. Lemeshko, Physical Review B 92 (2015).","apa":"Van Loon, E., Katsnelson, M., & Lemeshko, M. (2015). Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.92.081106","ama":"Van Loon E, Katsnelson M, Lemeshko M. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. 2015;92(8). doi:10.1103/PhysRevB.92.081106","chicago":"Van Loon, Erik, Mikhail Katsnelson, and Mikhail Lemeshko. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” Physical Review B. American Physical Society, 2015. https://doi.org/10.1103/PhysRevB.92.081106.","ista":"Van Loon E, Katsnelson M, Lemeshko M. 2015. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. 92(8), 081106."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Deuchert, Andreas, et al. “Note on a Family of Monotone Quantum Relative Entropies.” Letters in Mathematical Physics, vol. 105, no. 10, Springer, 2015, pp. 1449–66, doi:10.1007/s11005-015-0787-5.","short":"A. Deuchert, C. Hainzl, R. Seiringer, Letters in Mathematical Physics 105 (2015) 1449–1466.","ieee":"A. Deuchert, C. Hainzl, and R. Seiringer, “Note on a family of monotone quantum relative entropies,” Letters in Mathematical Physics, vol. 105, no. 10. Springer, pp. 1449–1466, 2015.","apa":"Deuchert, A., Hainzl, C., & Seiringer, R. (2015). Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-015-0787-5","ama":"Deuchert A, Hainzl C, Seiringer R. Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. 2015;105(10):1449-1466. doi:10.1007/s11005-015-0787-5","chicago":"Deuchert, Andreas, Christian Hainzl, and Robert Seiringer. “Note on a Family of Monotone Quantum Relative Entropies.” Letters in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s11005-015-0787-5.","ista":"Deuchert A, Hainzl C, Seiringer R. 2015. Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. 105(10), 1449–1466."},"title":"Note on a family of monotone quantum relative entropies","author":[{"last_name":"Deuchert","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","first_name":"Andreas"},{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5432","day":"05","publication":"Letters in Mathematical Physics","has_accepted_license":"1","year":"2015","doi":"10.1007/s11005-015-0787-5","date_published":"2015-08-05T00:00:00Z","date_created":"2018-12-11T11:53:34Z","page":"1449 - 1466","quality_controlled":"1","publisher":"Springer","oa":1,"ddc":["510"],"date_updated":"2021-01-12T06:52:38Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:45:13Z","_id":"1704","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"file":[{"creator":"dernst","file_size":484967,"date_updated":"2020-07-14T12:45:13Z","file_name":"2015_LettersMathPhys_Deuchert.pdf","date_created":"2019-01-15T14:42:07Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5836","checksum":"fd7307282a314cc1fbbaef77b187516b"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"10","volume":105,"license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Given a convex function (Formula presented.) and two hermitian matrices A and B, Lewin and Sabin study in (Lett Math Phys 104:691–705, 2014) the relative entropy defined by (Formula presented.). Among other things, they prove that the so-defined quantity is monotone if and only if (Formula presented.) is operator monotone. The monotonicity is then used to properly define (Formula presented.) for bounded self-adjoint operators acting on an infinite-dimensional Hilbert space by a limiting procedure. More precisely, for an increasing sequence of finite-dimensional projections (Formula presented.) with (Formula presented.) strongly, the limit (Formula presented.) is shown to exist and to be independent of the sequence of projections (Formula presented.). The question whether this sequence converges to its "obvious" limit, namely (Formula presented.), has been left open. We answer this question in principle affirmatively and show that (Formula presented.). If the operators A and B are regular enough, that is (A − B), (Formula presented.) and (Formula presented.) are trace-class, the identity (Formula presented.) holds."}],"month":"08","intvolume":" 105","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1502.07205","open_access":"1"}]},{"author":[{"first_name":"Linda","full_name":"Broadhurst, Linda","last_name":"Broadhurst"},{"last_name":"Fifield","full_name":"Fifield, Graham","first_name":"Graham"},{"last_name":"Vanzella","full_name":"Vanzella, Bindi","first_name":"Bindi"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"}],"publist_id":"5434","title":"An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas","department":[{"_id":"NiBa"}],"citation":{"ama":"Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023","apa":"Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023","ieee":"L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas,” Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.","short":"L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466.","mla":"Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany, vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023.","ista":"Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 63(5), 455–466.","chicago":"Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023."},"date_updated":"2021-01-12T06:52:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1703","page":"455 - 466","volume":63,"doi":"10.1071/BT15023","date_published":"2015-05-26T00:00:00Z","issue":"5","date_created":"2018-12-11T11:53:34Z","publication_status":"published","year":"2015","day":"26","publication":"Australian Journal of Botany","language":[{"iso":"eng"}],"publisher":"CSIRO","scopus_import":1,"quality_controlled":"1","month":"05","intvolume":" 63","abstract":[{"text":"Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.","lang":"eng"}],"oa_version":"None"},{"language":[{"iso":"eng"}],"publication_status":"published","volume":9355,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider a problem of learning kernels for use in SVM classification in the multi-task and lifelong scenarios and provide generalization bounds on the error of a large margin classifier. Our results show that, under mild conditions on the family of kernels used for learning, solving several related tasks simultaneously is beneficial over single task learning. In particular, as the number of observed tasks grows, assuming that in the considered family of kernels there exists one that yields low approximation error on all tasks, the overhead associated with learning such a kernel vanishes and the complexity converges to that of learning when this good kernel is given to the learner."}],"month":"01","intvolume":" 9355","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1602.06531"}],"date_updated":"2021-01-12T06:52:39Z","department":[{"_id":"ChLa"}],"_id":"1706","status":"public","type":"conference","conference":{"start_date":"2015-10-04","end_date":"2015-10-06","location":"Banff, AB, Canada","name":"ALT: Algorithmic Learning Theory"},"day":"01","year":"2015","date_published":"2015-01-01T00:00:00Z","doi":"10.1007/978-3-319-24486-0_13","date_created":"2018-12-11T11:53:35Z","page":"194 - 208","quality_controlled":"1","publisher":"Springer","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. Pentina and S. Ben David, “Multi-task and lifelong learning of kernels,” presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada, 2015, vol. 9355, pp. 194–208.","short":"A. Pentina, S. Ben David, in:, Springer, 2015, pp. 194–208.","apa":"Pentina, A., & Ben David, S. (2015). Multi-task and lifelong learning of kernels (Vol. 9355, pp. 194–208). Presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada: Springer. https://doi.org/10.1007/978-3-319-24486-0_13","ama":"Pentina A, Ben David S. Multi-task and lifelong learning of kernels. In: Vol 9355. Springer; 2015:194-208. doi:10.1007/978-3-319-24486-0_13","mla":"Pentina, Anastasia, and Shai Ben David. Multi-Task and Lifelong Learning of Kernels. Vol. 9355, Springer, 2015, pp. 194–208, doi:10.1007/978-3-319-24486-0_13.","ista":"Pentina A, Ben David S. 2015. Multi-task and lifelong learning of kernels. ALT: Algorithmic Learning Theory, LNCS, vol. 9355, 194–208.","chicago":"Pentina, Anastasia, and Shai Ben David. “Multi-Task and Lifelong Learning of Kernels,” 9355:194–208. Springer, 2015. https://doi.org/10.1007/978-3-319-24486-0_13."},"title":"Multi-task and lifelong learning of kernels","author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","full_name":"Pentina, Anastasia","last_name":"Pentina"},{"last_name":"Ben David","full_name":"Ben David, Shai","first_name":"Shai"}],"publist_id":"5430","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}]},{"project":[{"_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions"}],"citation":{"mla":"Ratheesh, Aparna, et al. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 71–79, doi:10.1016/j.ceb.2015.07.003.","ieee":"A. Ratheesh, V. Belyaeva, and D. E. Siekhaus, “Drosophila immune cell migration and adhesion during embryonic development and larval immune responses,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 71–79, 2015.","short":"A. Ratheesh, V. Belyaeva, D.E. Siekhaus, Current Opinion in Cell Biology 36 (2015) 71–79.","apa":"Ratheesh, A., Belyaeva, V., & Siekhaus, D. E. (2015). Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.07.003","ama":"Ratheesh A, Belyaeva V, Siekhaus DE. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. 2015;36(10):71-79. doi:10.1016/j.ceb.2015.07.003","chicago":"Ratheesh, Aparna, Vera Belyaeva, and Daria E Siekhaus. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.07.003.","ista":"Ratheesh A, Belyaeva V, Siekhaus DE. 2015. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. 36(10), 71–79."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ratheesh, Aparna","last_name":"Ratheesh","first_name":"Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Belyaeva, Vera","last_name":"Belyaeva","first_name":"Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"publist_id":"5421","title":"Drosophila immune cell migration and adhesion during embryonic development and larval immune responses","oa":1,"quality_controlled":"1","publisher":"Elsevier","year":"2015","has_accepted_license":"1","publication":"Current Opinion in Cell Biology","day":"01","page":"71 - 79","date_created":"2018-12-11T11:53:36Z","doi":"10.1016/j.ceb.2015.07.003","date_published":"2015-10-01T00:00:00Z","_id":"1712","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"346","status":"public","date_updated":"2021-01-12T06:52:41Z","ddc":["573"],"file_date_updated":"2020-07-14T12:45:13Z","department":[{"_id":"DaSi"}],"abstract":[{"text":"The majority of immune cells in Drosophila melanogaster are plasmatocytes; they carry out similar functions to vertebrate macrophages, influencing development as well as protecting against infection and cancer. Plasmatocytes, sometimes referred to with the broader term of hemocytes, migrate widely during embryonic development and cycle in the larvae between sessile and circulating positions. Here we discuss the similarities of plasmatocyte developmental migration and its functions to that of vertebrate macrophages, considering the recent controversy regarding the functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings on the significance of adhesion for plasmatocyte migration in the embryo, as well as proliferation, trans-differentiation, and tumor responses in the larva. We spotlight parallels throughout to vertebrate immune responses.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 36","month":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:13Z","file_size":1023680,"date_created":"2018-12-12T10:14:44Z","file_name":"IST-2015-346-v1+1_Current_Opinion_Review_Ratheesh_et_al_2015.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5098","checksum":"bbb1ee39ca52929aefe4f48752b166ee"}],"ec_funded":1,"issue":"10","volume":36},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics. SIAM, 2015. https://doi.org/10.1137/140993843.","ista":"Akopyan A, Plakhov A. 2015. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 47(4), 2754–2769.","mla":"Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics, vol. 47, no. 4, SIAM, 2015, pp. 2754–69, doi:10.1137/140993843.","apa":"Akopyan, A., & Plakhov, A. (2015). Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. SIAM. https://doi.org/10.1137/140993843","ama":"Akopyan A, Plakhov A. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 2015;47(4):2754-2769. doi:10.1137/140993843","ieee":"A. Akopyan and A. Plakhov, “Minimal resistance of curves under the single impact assumption,” Society for Industrial and Applied Mathematics, vol. 47, no. 4. SIAM, pp. 2754–2769, 2015.","short":"A. Akopyan, A. Plakhov, Society for Industrial and Applied Mathematics 47 (2015) 2754–2769."},"title":"Minimal resistance of curves under the single impact assumption","publist_id":"5423","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"last_name":"Plakhov","full_name":"Plakhov, Alexander","first_name":"Alexander"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"14","publication":"Society for Industrial and Applied Mathematics","year":"2015","doi":"10.1137/140993843","date_published":"2015-07-14T00:00:00Z","date_created":"2018-12-11T11:53:36Z","page":"2754 - 2769","publisher":"SIAM","quality_controlled":"1","oa":1,"date_updated":"2021-01-12T06:52:41Z","department":[{"_id":"HeEd"}],"_id":"1710","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":47,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞."}],"month":"07","intvolume":" 47","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.3736"}]},{"date_updated":"2021-01-12T06:52:49Z","citation":{"chicago":"Colin De Verdière, Éric, Alfredo Hubard, and Arnaud N de Mesmay. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9679-9.","ista":"Colin De Verdière É, Hubard A, de Mesmay AN. 2015. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 53(3), 587–620.","mla":"Colin De Verdière, Éric, et al. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry, vol. 53, no. 3, Springer, 2015, pp. 587–620, doi:10.1007/s00454-015-9679-9.","ieee":"É. Colin De Verdière, A. Hubard, and A. N. de Mesmay, “Discrete systolic inequalities and decompositions of triangulated surfaces,” Discrete & Computational Geometry, vol. 53, no. 3. Springer, pp. 587–620, 2015.","short":"É. Colin De Verdière, A. Hubard, A.N. de Mesmay, Discrete & Computational Geometry 53 (2015) 587–620.","apa":"Colin De Verdière, É., Hubard, A., & de Mesmay, A. N. (2015). Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9679-9","ama":"Colin De Verdière É, Hubard A, de Mesmay AN. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 2015;53(3):587-620. doi:10.1007/s00454-015-9679-9"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5397","author":[{"first_name":"Éric","last_name":"Colin De Verdière","full_name":"Colin De Verdière, Éric"},{"first_name":"Alfredo","last_name":"Hubard","full_name":"Hubard, Alfredo"},{"first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay"}],"title":"Discrete systolic inequalities and decompositions of triangulated surfaces","department":[{"_id":"UlWa"}],"_id":"1730","type":"journal_article","status":"public","year":"2015","publication_status":"published","day":"02","language":[{"iso":"eng"}],"publication":"Discrete & Computational Geometry","page":"587 - 620","issue":"3","date_published":"2015-04-02T00:00:00Z","doi":"10.1007/s00454-015-9679-9","volume":53,"date_created":"2018-12-11T11:53:42Z","abstract":[{"lang":"eng","text":"How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations."}],"oa_version":"Preprint","scopus_import":1,"publisher":"Springer","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1408.4036","open_access":"1"}],"month":"04","intvolume":" 53"},{"_id":"1735","status":"public","pubrep_id":"607","type":"journal_article","ddc":["000"],"date_updated":"2023-02-23T10:12:11Z","file_date_updated":"2020-07-14T12:45:15Z","department":[{"_id":"ChWo"}],"oa_version":"Submitted Version","abstract":[{"text":"This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations.","lang":"eng"}],"month":"05","intvolume":" 34","scopus_import":1,"file":[{"checksum":"590752bf977855b337a80f78a9bc2404","file_id":"5218","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-607-v1+1_coarsegrid.pdf","date_created":"2018-12-12T10:16:30Z","creator":"system","file_size":6312352,"date_updated":"2020-07-14T12:45:15Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":34,"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 473–480.","ieee":"R. Ando, N. Thürey, and C. Wojtan, “A dimension-reduced pressure solver for liquid simulations,” Computer Graphics Forum, vol. 34, no. 2. Wiley, pp. 473–480, 2015.","ama":"Ando R, Thürey N, Wojtan C. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 2015;34(2):473-480. doi:10.1111/cgf.12576","apa":"Ando, R., Thürey, N., & Wojtan, C. (2015). A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12576","mla":"Ando, Ryoichi, et al. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum, vol. 34, no. 2, Wiley, 2015, pp. 473–80, doi:10.1111/cgf.12576.","ista":"Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480.","chicago":"Ando, Ryoichi, Nils Thürey, and Chris Wojtan. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum. Wiley, 2015. https://doi.org/10.1111/cgf.12576."},"title":"A dimension-reduced pressure solver for liquid simulations","author":[{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"},{"first_name":"Nils","last_name":"Thürey","full_name":"Thürey, Nils"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"publist_id":"5389","acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"01","publication":"Computer Graphics Forum","has_accepted_license":"1","year":"2015","doi":"10.1111/cgf.12576","date_published":"2015-05-01T00:00:00Z","date_created":"2018-12-11T11:53:44Z","page":"473 - 480"},{"year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Computer Graphics Forum","day":"01","page":"709 - 733","date_created":"2018-12-11T11:53:43Z","date_published":"2015-05-01T00:00:00Z","doi":"10.1111/cgf.12594","issue":"2","volume":34,"abstract":[{"lang":"eng","text":"Facial appearance capture is now firmly established within academic research and used extensively across various application domains, perhaps most prominently in the entertainment industry through the design of virtual characters in video games and films. While significant progress has occurred over the last two decades, no single survey currently exists that discusses the similarities, differences, and practical considerations of the available appearance capture techniques as applied to human faces. A central difficulty of facial appearance capture is the way light interacts with skin-which has a complex multi-layered structure-and the interactions that occur below the skin surface can, by definition, only be observed indirectly. In this report, we distinguish between two broad strategies for dealing with this complexity. "Image-based methods" try to exhaustively capture the exact face appearance under different lighting and viewing conditions, and then render the face through weighted image combinations. "Parametric methods" instead fit the captured reflectance data to some parametric appearance model used during rendering, allowing for a more lightweight and flexible representation but at the cost of potentially increased rendering complexity or inexact reproduction. The goal of this report is to provide an overview that can guide practitioners and researchers in assessing the tradeoffs between current approaches and identifying directions for future advances in facial appearance capture."}],"oa_version":"None","main_file_link":[{"url":"https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf"}],"quality_controlled":"1","publisher":"Wiley-Blackwell","scopus_import":1,"intvolume":" 34","month":"05","date_updated":"2021-01-12T06:52:52Z","citation":{"ista":"Klehm O, Rousselle F, Papas M, Bradley D, Hery C, Bickel B, Jarosz W, Beeler T. 2015. Recent advances in facial appearance capture. Computer Graphics Forum. 34(2), 709–733.","chicago":"Klehm, Oliver, Fabrice Rousselle, Marios Papas, Derek Bradley, Christophe Hery, Bernd Bickel, Wojciech Jarosz, and Thabo Beeler. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum. Wiley-Blackwell, 2015. https://doi.org/10.1111/cgf.12594.","short":"O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz, T. Beeler, Computer Graphics Forum 34 (2015) 709–733.","ieee":"O. Klehm et al., “Recent advances in facial appearance capture,” Computer Graphics Forum, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015.","ama":"Klehm O, Rousselle F, Papas M, et al. Recent advances in facial appearance capture. Computer Graphics Forum. 2015;34(2):709-733. doi:10.1111/cgf.12594","apa":"Klehm, O., Rousselle, F., Papas, M., Bradley, D., Hery, C., Bickel, B., … Beeler, T. (2015). Recent advances in facial appearance capture. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12594","mla":"Klehm, Oliver, et al. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum, vol. 34, no. 2, Wiley-Blackwell, 2015, pp. 709–33, doi:10.1111/cgf.12594."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5391","author":[{"first_name":"Oliver","last_name":"Klehm","full_name":"Klehm, Oliver"},{"full_name":"Rousselle, Fabrice","last_name":"Rousselle","first_name":"Fabrice"},{"last_name":"Papas","full_name":"Papas, Marios","first_name":"Marios"},{"first_name":"Derek","full_name":"Bradley, Derek","last_name":"Bradley"},{"first_name":"Christophe","last_name":"Hery","full_name":"Hery, Christophe"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"last_name":"Jarosz","full_name":"Jarosz, Wojciech","first_name":"Wojciech"},{"first_name":"Thabo","full_name":"Beeler, Thabo","last_name":"Beeler"}],"department":[{"_id":"BeBi"}],"title":"Recent advances in facial appearance capture","_id":"1734","type":"journal_article","status":"public"},{"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"European Journal of Human Genetics","day":"15","year":"2015","date_created":"2018-12-11T11:54:01Z","date_published":"2015-06-15T00:00:00Z","doi":"10.1038/ejhg.2014.165","page":"753 - 760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 2015;23(6):753-760. doi:10.1038/ejhg.2014.165","apa":"Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. Nature Publishing Group. https://doi.org/10.1038/ejhg.2014.165","ieee":"A. Kuechler et al., “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” European Journal of Human Genetics, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015.","short":"A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760.","mla":"Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:10.1038/ejhg.2014.165.","ista":"Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760.","chicago":"Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics. Nature Publishing Group, 2015. https://doi.org/10.1038/ejhg.2014.165."},"title":"Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome","external_id":{"pmid":["25138099"]},"publist_id":"5324","author":[{"full_name":"Kuechler, Alma","last_name":"Kuechler","first_name":"Alma"},{"full_name":"Zink, Alexander","last_name":"Zink","first_name":"Alexander"},{"last_name":"Wieland","full_name":"Wieland, Thomas","first_name":"Thomas"},{"first_name":"Hermann","last_name":"Lüdecke","full_name":"Lüdecke, Hermann"},{"last_name":"Cremer","full_name":"Cremer, Kirsten","first_name":"Kirsten"},{"first_name":"Leonardo","last_name":"Salviati","full_name":"Salviati, Leonardo"},{"last_name":"Magini","full_name":"Magini, Pamela","first_name":"Pamela"},{"first_name":"Kimia","last_name":"Najafi","full_name":"Najafi, Kimia"},{"first_name":"Christiane","full_name":"Zweier, Christiane","last_name":"Zweier"},{"first_name":"Johanna","full_name":"Czeschik, Johanna","last_name":"Czeschik"},{"first_name":"Stefan","full_name":"Aretz, Stefan","last_name":"Aretz"},{"full_name":"Endele, Sabine","last_name":"Endele","first_name":"Sabine"},{"last_name":"Tamburrino","full_name":"Tamburrino, Federica","first_name":"Federica"},{"full_name":"Pinato, Claudia","last_name":"Pinato","first_name":"Claudia"},{"first_name":"Maurizio","full_name":"Clementi, Maurizio","last_name":"Clementi"},{"first_name":"Jasmin","full_name":"Gundlach, Jasmin","last_name":"Gundlach"},{"first_name":"Carina","last_name":"Maylahn","full_name":"Maylahn, Carina"},{"full_name":"Mazzanti, Laura","last_name":"Mazzanti","first_name":"Laura"},{"first_name":"Eva","last_name":"Wohlleber","full_name":"Wohlleber, Eva"},{"first_name":"Thomas","full_name":"Schwarzmayr, Thomas","last_name":"Schwarzmayr"},{"first_name":"Roxana","full_name":"Kariminejad, Roxana","last_name":"Kariminejad"},{"first_name":"Avner","full_name":"Schlessinger, Avner","last_name":"Schlessinger"},{"first_name":"Dagmar","full_name":"Wieczorek, Dagmar","last_name":"Wieczorek"},{"first_name":"Tim","last_name":"Strom","full_name":"Strom, Tim"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"},{"first_name":"Hartmut","last_name":"Engels","full_name":"Engels, Hartmut"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID.","lang":"eng"}],"intvolume":" 23","month":"06","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"6","volume":23,"_id":"1789","status":"public","type":"journal_article","date_updated":"2021-01-12T06:53:12Z","department":[{"_id":"GaNo"}]},{"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Scientific Reports","day":"12","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:54:06Z","date_published":"2015-06-12T00:00:00Z","doi":"10.1038/srep10781","article_number":"10781","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports, vol. 5, 10781, Nature Publishing Group, 2015, doi:10.1038/srep10781.","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep10781","ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 2015;5. doi:10.1038/srep10781","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep10781.","ista":"Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781."},"title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","publist_id":"5306","author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","last_name":"Altmeyer"},{"first_name":"Younghae","last_name":"Do","full_name":"Do, Younghae"},{"last_name":"Lai","full_name":"Lai, Ying","first_name":"Ying"}],"oa_version":"Published Version","abstract":[{"text":"It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control.","lang":"eng"}],"intvolume":" 5","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_id":"5280","checksum":"7716f582f8c9d82d8f2bf80bf896b440","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:17:26Z","file_name":"IST-2016-450-v1+1_srep10781.pdf","creator":"system","date_updated":"2020-07-14T12:45:16Z","file_size":2449723}],"publication_status":"published","volume":5,"_id":"1804","pubrep_id":"450","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["530"],"date_updated":"2021-01-12T06:53:18Z","file_date_updated":"2020-07-14T12:45:16Z","department":[{"_id":"BjHo"}]},{"publication":"ESAIM - Control, Optimisation and Calculus of Variations","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","date_created":"2018-12-11T11:54:07Z","doi":"10.1051/cocv/2014040","volume":21,"date_published":"2015-05-01T00:00:00Z","issue":"3","page":"603 - 624","oa_version":"Preprint","abstract":[{"text":"We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential.","lang":"eng"}],"intvolume":" 21","month":"05","main_file_link":[{"url":"http://arxiv.org/abs/1401.1727","open_access":"1"}],"oa":1,"publisher":"EDP Sciences","quality_controlled":"1","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and Calculus of Variations. EDP Sciences, 2015. https://doi.org/10.1051/cocv/2014040.","ista":"Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624.","mla":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and Calculus of Variations, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:10.1051/cocv/2014040.","short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624.","ieee":"M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” ESAIM - Control, Optimisation and Calculus of Variations, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.","apa":"Goldman, M., & Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. EDP Sciences. https://doi.org/10.1051/cocv/2014040","ama":"Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 2015;21(3):603-624. doi:10.1051/cocv/2014040"},"date_updated":"2021-01-12T06:53:20Z","title":"Sharp interface limit for two components Bose-Einstein condensates","department":[{"_id":"RoSe"}],"publist_id":"5303","author":[{"first_name":"Michael","last_name":"Goldman","full_name":"Goldman, Michael"},{"id":"4D3BED28-F248-11E8-B48F-1D18A9856A87","first_name":"Jimena","last_name":"Royo-Letelier","full_name":"Royo-Letelier, Jimena"}],"_id":"1807","status":"public","type":"journal_article"},{"abstract":[{"lang":"eng","text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing."}],"oa_version":"Published Version","scopus_import":1,"month":"06","intvolume":" 27","publication_status":"published","file":[{"file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","date_created":"2018-12-12T10:17:23Z","file_size":1047255,"date_updated":"2020-07-14T12:45:17Z","creator":"system","checksum":"1683bb0f42ef892a5b3b71a050d65d25","file_id":"5277","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":27,"ec_funded":1,"_id":"1810","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"493","date_updated":"2021-01-12T06:53:21Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"ToBo"}],"publisher":"Elsevier","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"01","publication":"Current Opinion in Microbiology","page":"1 - 9","date_published":"2015-06-01T00:00:00Z","doi":"10.1016/j.mib.2015.05.008","date_created":"2018-12-11T11:54:08Z","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology, vol. 27, Elsevier, 2015, pp. 1–9, doi:10.1016/j.mib.2015.05.008.","apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. Elsevier. https://doi.org/10.1016/j.mib.2015.05.008","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 2015;27:1-9. doi:10.1016/j.mib.2015.05.008","ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” Current Opinion in Microbiology, vol. 27. Elsevier, pp. 1–9, 2015.","short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9.","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology. Elsevier, 2015. https://doi.org/10.1016/j.mib.2015.05.008.","ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5298","author":[{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution"},{"article_number":"045005","citation":{"mla":"Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” New Journal of Physics, vol. 17, no. 4, 045005, IOP Publishing Ltd., 2015, doi:10.1088/1367-2630/17/4/045005.","apa":"Lahrz, M., Lemeshko, M., & Mathey, L. (2015). Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/4/045005","ama":"Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 2015;17(4). doi:10.1088/1367-2630/17/4/045005","short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","ieee":"M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar Bose–Einstein condensates ,” New Journal of Physics, vol. 17, no. 4. IOP Publishing Ltd., 2015.","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” New Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/4/045005.","ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"5294","author":[{"full_name":"Lahrz, Martin","last_name":"Lahrz","first_name":"Martin"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mathey","full_name":"Mathey, Ludwig","first_name":"Ludwig"}],"title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","oa":1,"quality_controlled":"1","publisher":"IOP Publishing Ltd.","year":"2015","has_accepted_license":"1","publication":"New Journal of Physics","day":"01","date_created":"2018-12-11T11:54:09Z","doi":"10.1088/1367-2630/17/4/045005","date_published":"2015-04-01T00:00:00Z","_id":"1812","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"446","status":"public","date_updated":"2021-01-12T06:53:22Z","ddc":["530"],"department":[{"_id":"MiLe"}],"file_date_updated":"2020-07-14T12:45:17Z","abstract":[{"text":"We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.\r\n","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 17","month":"04","publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5184","checksum":"551f751a75b39b89a1db2f7f498f9a49","creator":"system","file_size":1900925,"date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-446-v1+1_document.pdf","date_created":"2018-12-12T10:15:59Z"}],"issue":"4","volume":17},{"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.0110"}],"month":"05","intvolume":" 56","abstract":[{"lang":"eng","text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms."}],"oa_version":"Preprint","issue":"5","volume":56,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1811","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:53:21Z","publisher":"American Institute of Physics","oa":1,"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]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","date_published":"2015-05-20T00:00:00Z","doi":"10.1063/1.4921227","date_created":"2018-12-11T11:54:08Z","year":"2015","day":"20","publication":"Journal of Mathematical Physics","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_number":"052105","publist_id":"5295","author":[{"last_name":"Safari","full_name":"Safari, Laleh","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"José","full_name":"Santos, José","last_name":"Santos"},{"first_name":"Pedro","full_name":"Amaro, Pedro","last_name":"Amaro"},{"full_name":"Jänkälä, Kari","last_name":"Jänkälä","first_name":"Kari"},{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"}],"title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","citation":{"ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105.","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4921227.","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” Journal of Mathematical Physics, vol. 56, no. 5. American Institute of Physics, 2015.","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., & Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4921227","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 2015;56(5). doi:10.1063/1.4921227","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:10.1063/1.4921227."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Rotation of quantum impurities in the presence of a many-body environment","department":[{"_id":"MiLe"}],"publist_id":"5293","author":[{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001.","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.203001.","short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” Physical Review Letters, vol. 114, no. 20. American Physical Society, 2015.","ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 2015;114(20). doi:10.1103/PhysRevLett.114.203001","apa":"Schmidt, R., & Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.203001","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” Physical Review Letters, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.203001."},"date_updated":"2021-01-12T06:53:22Z","status":"public","type":"journal_article","article_number":"203001","_id":"1813","date_created":"2018-12-11T11:54:09Z","doi":"10.1103/PhysRevLett.114.203001","volume":114,"date_published":"2015-05-18T00:00:00Z","issue":"20","publication":"Physical Review Letters","language":[{"iso":"eng"}],"day":"18","year":"2015","publication_status":"published","intvolume":" 114","month":"05","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.03447"}],"oa":1,"scopus_import":1,"quality_controlled":"1","publisher":"American Physical Society","oa_version":"Preprint","abstract":[{"text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.","lang":"eng"}]},{"_id":"1808","article_number":"7","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:20Z","citation":{"ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2745799","apa":"Gupta, A., & Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2745799","ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.","short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 7, ACM, 2015, doi:10.1145/2745799.","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7.","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2745799."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5302","author":[{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","last_name":"Gupta"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"title":"Guest editors' introduction to special issue on computational methods in systems biology","department":[{"_id":"ToHe"}],"oa_version":"None","quality_controlled":"1","publisher":"ACM","intvolume":" 25","month":"05","publication_status":"published","year":"2015","publication":"ACM Transactions on Modeling and Computer Simulation","language":[{"iso":"eng"}],"day":"01","date_created":"2018-12-11T11:54:07Z","doi":"10.1145/2745799","date_published":"2015-05-01T00:00:00Z","volume":25,"issue":"2"},{"_id":"1817","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:23Z","department":[{"_id":"CaHe"}],"abstract":[{"lang":"eng","text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. "}],"pmid":1,"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/","open_access":"1"}],"month":"03","intvolume":" 521","publication_status":"published","language":[{"iso":"eng"}],"volume":521,"issue":"7551","citation":{"chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature14215.","ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:10.1038/nature14215.","ieee":"S. Porazinski et al., “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” Nature, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221.","ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 2015;521(7551):217-221. doi:10.1038/nature14215","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. Nature Publishing Group. https://doi.org/10.1038/nature14215"},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Sean","last_name":"Porazinski","full_name":"Porazinski, Sean"},{"first_name":"Huijia","full_name":"Wang, Huijia","last_name":"Wang"},{"first_name":"Yoichi","last_name":"Asaoka","full_name":"Asaoka, Yoichi"},{"first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin","last_name":"Behrndt"},{"first_name":"Tatsuo","full_name":"Miyamoto, Tatsuo","last_name":"Miyamoto"},{"last_name":"Morita","full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi"},{"last_name":"Hata","full_name":"Hata, Shoji","first_name":"Shoji"},{"first_name":"Takashi","last_name":"Sasaki","full_name":"Sasaki, Takashi"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"first_name":"Yumi","last_name":"Osada","full_name":"Osada, Yumi"},{"first_name":"Satoshi","last_name":"Asaka","full_name":"Asaka, Satoshi"},{"first_name":"Akihiro","full_name":"Momoi, Akihiro","last_name":"Momoi"},{"first_name":"Sarah","last_name":"Linton","full_name":"Linton, Sarah"},{"full_name":"Miesfeld, Joel","last_name":"Miesfeld","first_name":"Joel"},{"first_name":"Brian","last_name":"Link","full_name":"Link, Brian"},{"first_name":"Takeshi","full_name":"Senga, Takeshi","last_name":"Senga"},{"full_name":"Castillo Morales, Atahualpa","last_name":"Castillo Morales","first_name":"Atahualpa"},{"first_name":"Araxi","last_name":"Urrutia","full_name":"Urrutia, Araxi"},{"first_name":"Nobuyoshi","full_name":"Shimizu, Nobuyoshi","last_name":"Shimizu"},{"first_name":"Hideaki","last_name":"Nagase","full_name":"Nagase, Hideaki"},{"first_name":"Shinya","full_name":"Matsuura, Shinya","last_name":"Matsuura"},{"last_name":"Bagby","full_name":"Bagby, Stefan","first_name":"Stefan"},{"first_name":"Hisato","last_name":"Kondoh","full_name":"Kondoh, Hisato"},{"full_name":"Nishina, Hiroshi","last_name":"Nishina","first_name":"Hiroshi"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Furutani Seiki","full_name":"Furutani Seiki, Makoto","first_name":"Makoto"}],"publist_id":"5289","external_id":{"pmid":["25778702"]},"title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"year":"2015","day":"16","publication":"Nature","page":"217 - 221","doi":"10.1038/nature14215","date_published":"2015-03-16T00:00:00Z","date_created":"2018-12-11T11:54:10Z"},{"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , 5:3496–3502. AAAI Press, 2015.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . Vol 5. AAAI Press; 2015:3496-3502.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , vol. 5, AAAI Press, 2015, pp. 3496–502."},"title":"Optimal cost almost-sure reachability in POMDPs","publist_id":"5286","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Chmelik","full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Raghav","last_name":"Gupta","full_name":"Gupta, Raghav"},{"full_name":"Kanodia, Ayush","last_name":"Kanodia","first_name":"Ayush"}],"external_id":{"arxiv":["1411.3880"]},"acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publisher":"AAAI Press","quality_controlled":"1","oa":1,"day":"01","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","year":"2015","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:54:11Z","page":"3496-3502","_id":"1820","status":"public","type":"conference","conference":{"name":"IAAI: Innovative Applications of Artificial Intelligence","start_date":"2015-01-25","location":"Austin, TX, USA","end_date":"2015-01-30"},"date_updated":"2023-02-23T10:02:57Z","department":[{"_id":"KrCh"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples."}],"month":"06","intvolume":" 5","alternative_title":["Artifical Intelligence"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":5,"related_material":{"record":[{"status":"public","id":"1529","relation":"later_version"}]},"ec_funded":1},{"date_updated":"2023-02-23T10:15:40Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"ChWo"}],"_id":"1814","type":"journal_article","status":"public","pubrep_id":"575","publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:17Z","file_size":23712153,"creator":"system","date_created":"2018-12-12T10:12:15Z","file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4933","checksum":"67c9f4fa370def68cdf31299e48bc91f"}],"language":[{"iso":"eng"}],"issue":"3","volume":34,"ec_funded":1,"abstract":[{"lang":"eng","text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms."}],"oa_version":"Submitted Version","scopus_import":1,"month":"04","intvolume":" 34","citation":{"ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics. ACM, 2015. https://doi.org/10.1145/2714572.","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572","apa":"Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics, vol. 34, no. 3, 27, ACM, 2015, doi:10.1145/2714572."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5292","title":"Water wave animation via wavefront parameter interpolation","article_number":"27","project":[{"grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"has_accepted_license":"1","year":"2015","day":"01","publication":"ACM Transactions on Graphics","date_published":"2015-04-01T00:00:00Z","doi":"10.1145/2714572","date_created":"2018-12-11T11:54:09Z","publisher":"ACM","quality_controlled":"1","oa":1},{"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:53:24Z","status":"public","type":"journal_article","_id":"1818","volume":112,"issue":"20","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"05","intvolume":" 112","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.","lang":"eng"}],"title":"Limits to adaptation along environmental gradients","author":[{"last_name":"Polechova","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"publist_id":"5288","external_id":{"pmid":["25941385"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:10.1073/pnas.1421515112.","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112","apa":"Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112"},"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"doi":"10.1073/pnas.1421515112","date_published":"2015-05-19T00:00:00Z","date_created":"2018-12-11T11:54:11Z","page":"6401 - 6406","day":"19","publication":"PNAS","year":"2015","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1},{"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"author":[{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"5287","title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","citation":{"chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2015.03.007.","ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:10.1016/j.molp.2015.03.007.","apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., & Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2015.03.007","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 2015;8(8):1175-1187. doi:10.1016/j.molp.2015.03.007","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” Molecular Plant, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015.","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","page":"1175 - 1187","doi":"10.1016/j.molp.2015.03.007","date_published":"2015-08-03T00:00:00Z","date_created":"2018-12-11T11:54:11Z","year":"2015","day":"03","publication":"Molecular Plant","type":"journal_article","status":"public","_id":"1819","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:24Z","scopus_import":1,"month":"08","intvolume":" 8","abstract":[{"text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.","lang":"eng"}],"oa_version":"None","volume":8,"issue":"8","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}]},{"ddc":["570"],"date_updated":"2021-01-12T06:53:26Z","department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:45:17Z","_id":"1823","status":"public","pubrep_id":"395","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"5087","checksum":"4289b518fbe2166682fb1a1ef9b405f3","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2015-395-v1+1_807.full.pdf","date_created":"2018-12-12T10:14:34Z","file_size":1273573,"date_updated":"2020-07-14T12:45:17Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":11,"issue":"4","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways."}],"month":"04","intvolume":" 11","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 2015;11(4). doi:10.15252/msb.20156098","apa":"Chevereau, G., & Bollenbach, M. T. (2015). Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.15252/msb.20156098","short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015).","ieee":"G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” Molecular Systems Biology, vol. 11, no. 4. Nature Publishing Group, 2015.","mla":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology, vol. 11, no. 4, 807, Nature Publishing Group, 2015, doi:10.15252/msb.20156098.","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807.","chicago":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology. Nature Publishing Group, 2015. https://doi.org/10.15252/msb.20156098."},"title":"Systematic discovery of drug interaction mechanisms","publist_id":"5283","author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume"},{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"article_number":"807","project":[{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507"}],"day":"01","publication":"Molecular Systems Biology","has_accepted_license":"1","year":"2015","doi":"10.15252/msb.20156098","date_published":"2015-04-01T00:00:00Z","date_created":"2018-12-11T11:54:12Z","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1},{"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"doi":"10.1038/ncomms7977","date_published":"2015-04-24T00:00:00Z","date_created":"2018-12-11T11:54:13Z","has_accepted_license":"1","year":"2015","day":"24","publication":"Nature Communications","article_number":"6977","publist_id":"5282","author":[{"last_name":"Knebel","full_name":"Knebel, Johannes","first_name":"Johannes"},{"first_name":"Markus","last_name":"Weber","full_name":"Weber, Markus"},{"last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Erwin","last_name":"Frey","full_name":"Frey, Erwin"}],"title":"Evolutionary games of condensates in coupled birth-death processes","citation":{"chicago":"Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7977.","ista":"Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977.","mla":"Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications, vol. 6, 6977, Nature Publishing Group, 2015, doi:10.1038/ncomms7977.","short":"J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015).","ieee":"J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates in coupled birth-death processes,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","ama":"Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 2015;6. doi:10.1038/ncomms7977","apa":"Knebel, J., Weber, M., Krüger, T. H., & Frey, E. (2015). Evolutionary games of condensates in coupled birth-death processes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7977"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"04","intvolume":" 6","abstract":[{"text":"Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates.","lang":"eng"}],"oa_version":"Published Version","volume":6,"publication_status":"published","file":[{"file_id":"5245","checksum":"c4cffb5c8b245e658a34eac71a03e7cc","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:54Z","file_name":"IST-2016-451-v1+1_ncomms7977.pdf","creator":"system","date_updated":"2020-07-14T12:45:17Z","file_size":1151501}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"451","_id":"1824","department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:45:17Z","date_updated":"2021-01-12T06:53:26Z","ddc":["530"]},{"date_published":"2015-05-01T00:00:00Z","doi":"10.1098/rstb.2014.0116","date_created":"2018-12-11T11:54:15Z","day":"01","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","year":"2015","quality_controlled":"1","publisher":"Royal Society","oa":1,"acknowledgement":"We thank the German Research Foundation (DFG), the Ministry of Science and Culture of Lower-Saxony (MWK Hannover) and the German Primate Centre (DPZ) for their support of the 9. Göttinger Freilandtage in 2013, a conference at which most contributions to this issue were first presented, the referees of the contributions to this issue for their constructive comments, Meggan Craft for comments, and Helen Eaton for her support in producing this theme issue.","title":"Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies","publist_id":"5272","author":[{"last_name":"Kappeler","full_name":"Kappeler, Peter","first_name":"Peter"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"},{"first_name":"Charles","full_name":"Nunn, Charles","last_name":"Nunn"}],"external_id":{"pmid":["25870402"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kappeler, Peter, Sylvia Cremer, and Charles Nunn. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rstb.2014.0116.","ista":"Kappeler P, Cremer S, Nunn C. 2015. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669), 20140116.","mla":"Kappeler, Peter, et al. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, 20140116, Royal Society, 2015, doi:10.1098/rstb.2014.0116.","apa":"Kappeler, P., Cremer, S., & Nunn, C. (2015). Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2014.0116","ama":"Kappeler P, Cremer S, Nunn C. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0116","short":"P. Kappeler, S. Cremer, C. Nunn, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","ieee":"P. Kappeler, S. Cremer, and C. Nunn, “Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, 2015."},"article_number":"20140116","volume":370,"issue":"1669","language":[{"iso":"eng"}],"publication_status":"published","month":"05","intvolume":" 370","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/","open_access":"1"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"This paper introduces a theme issue presenting the latest developments in research on the impacts of sociality on health and fitness. The articles that follow cover research on societies ranging from insects to humans. Variation in measures of fitness (i.e. survival and reproduction) has been linked to various aspects of sociality in humans and animals alike, and variability in individual health and condition has been recognized as a key mediator of these relationships. Viewed from a broad evolutionary perspective, the evolutionary transitions from a solitary lifestyle to group living have resulted in several new health-related costs and benefits of sociality. Social transmission of parasites within groups represents a major cost of group living, but some behavioural mechanisms, such as grooming, have evolved repeatedly to reduce this cost. Group living also has created novel costs in terms of altered susceptibility to infectious and non-infectious disease as a result of the unavoidable physiological consequences of social competition and integration, which are partly alleviated by social buffering in some vertebrates. Here, we define the relevant aspects of sociality, summarize their health-related costs and benefits, and discuss possible fitness measures in different study systems. Given the pervasive effects of social factors on health and fitness, we propose a synthesis of existing conceptual approaches in disease ecology, ecological immunology and behavioural neurosciences by adding sociality as a key factor, with the goal to generate a broader framework for organismal integration of health-related research.","lang":"eng"}],"department":[{"_id":"SyCr"}],"date_updated":"2021-01-12T06:53:29Z","status":"public","type":"journal_article","_id":"1831"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":160,"issue":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"arxiv.org/abs/1406.5313"}],"month":"07","intvolume":" 160","date_updated":"2021-01-12T06:53:28Z","department":[{"_id":"HeEd"}],"_id":"1828","type":"journal_article","status":"public","year":"2015","day":"01","publication":"Journal of Statistical Physics","page":"163 - 167","doi":"10.1007/s10955-015-1238-5","date_published":"2015-07-01T00:00:00Z","date_created":"2018-12-11T11:54:14Z","quality_controlled":"1","publisher":"Springer","oa":1,"citation":{"chicago":"Akopyan, Arseniy, Sergey Pirogov, and Aleksandr Rybko. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics. Springer, 2015. https://doi.org/10.1007/s10955-015-1238-5.","ista":"Akopyan A, Pirogov S, Rybko A. 2015. Invariant measures of genetic recombination process. Journal of Statistical Physics. 160(1), 163–167.","mla":"Akopyan, Arseniy, et al. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics, vol. 160, no. 1, Springer, 2015, pp. 163–67, doi:10.1007/s10955-015-1238-5.","ama":"Akopyan A, Pirogov S, Rybko A. Invariant measures of genetic recombination process. Journal of Statistical Physics. 2015;160(1):163-167. doi:10.1007/s10955-015-1238-5","apa":"Akopyan, A., Pirogov, S., & Rybko, A. (2015). Invariant measures of genetic recombination process. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-015-1238-5","ieee":"A. Akopyan, S. Pirogov, and A. Rybko, “Invariant measures of genetic recombination process,” Journal of Statistical Physics, vol. 160, no. 1. Springer, pp. 163–167, 2015.","short":"A. Akopyan, S. Pirogov, A. Rybko, Journal of Statistical Physics 160 (2015) 163–167."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5276","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"first_name":"Sergey","full_name":"Pirogov, Sergey","last_name":"Pirogov"},{"first_name":"Aleksandr","last_name":"Rybko","full_name":"Rybko, Aleksandr"}],"article_processing_charge":"No","title":"Invariant measures of genetic recombination process","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}]},{"citation":{"short":"P. Cerny, T.A. Henzinger, L. Kovács, A. Radhakrishna, J. Zwirchmayr, 9032 (2015) 105–131.","ieee":"P. Cerny, T. A. Henzinger, L. Kovács, A. Radhakrishna, and J. Zwirchmayr, “Segment abstraction for worst-case execution time analysis,” vol. 9032. Springer, pp. 105–131, 2015.","apa":"Cerny, P., Henzinger, T. A., Kovács, L., Radhakrishna, A., & Zwirchmayr, J. (2015). Segment abstraction for worst-case execution time analysis. Presented at the ESOP: European Symposium on Programming, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46669-8_5","ama":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. Segment abstraction for worst-case execution time analysis. 2015;9032:105-131. doi:10.1007/978-3-662-46669-8_5","mla":"Cerny, Pavol, et al. Segment Abstraction for Worst-Case Execution Time Analysis. Vol. 9032, Springer, 2015, pp. 105–31, doi:10.1007/978-3-662-46669-8_5.","ista":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. 2015. Segment abstraction for worst-case execution time analysis. 9032, 105–131.","chicago":"Cerny, Pavol, Thomas A Henzinger, Laura Kovács, Arjun Radhakrishna, and Jakob Zwirchmayr. “Segment Abstraction for Worst-Case Execution Time Analysis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46669-8_5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5266","author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Laura","full_name":"Kovács, Laura","last_name":"Kovács"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"},{"first_name":"Jakob","last_name":"Zwirchmayr","full_name":"Zwirchmayr, Jakob"}],"title":"Segment abstraction for worst-case execution time analysis","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"year":"2015","day":"01","page":"105 - 131","date_created":"2018-12-11T11:54:16Z","doi":"10.1007/978-3-662-46669-8_5","date_published":"2015-04-01T00:00:00Z","quality_controlled":"1","publisher":"Springer","date_updated":"2020-08-11T10:09:32Z","department":[{"_id":"ToHe"}],"_id":"1836","series_title":"Lecture Notes in Computer Science","conference":{"name":"ESOP: European Symposium on Programming","start_date":"2015-04-11","end_date":"2015-04-18","location":"London, United Kingdom"},"type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":9032,"abstract":[{"lang":"eng","text":"In the standard framework for worst-case execution time (WCET) analysis of programs, the main data structure is a single instance of integer linear programming (ILP) that represents the whole program. The instance of this NP-hard problem must be solved to find an estimate forWCET, and it must be refined if the estimate is not tight.We propose a new framework for WCET analysis, based on abstract segment trees (ASTs) as the main data structure. The ASTs have two advantages. First, they allow computing WCET by solving a number of independent small ILP instances. Second, ASTs store more expressive constraints, thus enabling a more efficient and precise refinement procedure. In order to realize our framework algorithmically, we develop an algorithm for WCET estimation on ASTs, and we develop an interpolation-based counterexample-guided refinement scheme for ASTs. Furthermore, we extend our framework to obtain parametric estimates of WCET. We experimentally evaluate our approach on a set of examples from WCET benchmark suites and linear-algebra packages. We show that our analysis, with comparable effort, provides WCET estimates that in many cases significantly improve those computed by existing tools."}],"oa_version":"None","alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 9032","month":"04"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"R. Bloem, K. Chatterjee, S. Jacobs, and R. Könighofer, “Assume-guarantee synthesis for concurrent reactive programs with partial information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom, 2015, vol. 9035, pp. 517–532.","short":"R. Bloem, K. Chatterjee, S. Jacobs, R. Könighofer, in:, Springer, 2015, pp. 517–532.","apa":"Bloem, R., Chatterjee, K., Jacobs, S., & Könighofer, R. (2015). Assume-guarantee synthesis for concurrent reactive programs with partial information (Vol. 9035, pp. 517–532). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_50","ama":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. Assume-guarantee synthesis for concurrent reactive programs with partial information. In: Vol 9035. Springer; 2015:517-532. doi:10.1007/978-3-662-46681-0_50","mla":"Bloem, Roderick, et al. Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information. Vol. 9035, Springer, 2015, pp. 517–32, doi:10.1007/978-3-662-46681-0_50.","ista":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. 2015. Assume-guarantee synthesis for concurrent reactive programs with partial information. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9035, 517–532.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Swen Jacobs, and Robert Könighofer. “Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information,” 9035:517–32. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_50."},"title":"Assume-guarantee synthesis for concurrent reactive programs with partial information","author":[{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Jacobs, Swen","last_name":"Jacobs","first_name":"Swen"},{"full_name":"Könighofer, Robert","last_name":"Könighofer","first_name":"Robert"}],"publist_id":"5264","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"day":"01","year":"2015","date_created":"2018-12-11T11:54:17Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1007/978-3-662-46681-0_50","page":"517 - 532","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through the research network RiSE (S11406-N23, S11407-N23) and grant nr. P23499-N23, by the European Commission through an ERC Start grant (279307: Graph Games) and project STANCE (317753), as well as by the German Research Foundation (DFG) through SFB/TR 14 AVACS and project ASDPS(JA 2357/2-1).","oa":1,"publisher":"Springer","date_updated":"2021-01-12T06:53:32Z","department":[{"_id":"KrCh"}],"_id":"1838","status":"public","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2015-04-11","end_date":"2015-04-18","location":"London, United Kingdom"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":9035,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples."}],"intvolume":" 9035","month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.4604"}],"scopus_import":1,"alternative_title":["LNCS"]},{"author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Forejt","full_name":"Forejt, Vojtěch","first_name":"Vojtěch"},{"last_name":"Kučera","full_name":"Kučera, Antonín","first_name":"Antonín"}],"publist_id":"5263","title":"Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_12.","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2015. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 9035, 181–187.","mla":"Brázdil, Tomáš, et al. Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives. Vol. 9035, Springer, 2015, pp. 181–87, doi:10.1007/978-3-662-46681-0_12.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives,” vol. 9035. Springer, pp. 181–187, 2015.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 2015;9035:181-187. doi:10.1007/978-3-662-46681-0_12","apa":"Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2015). Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_12"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"181 - 187","date_created":"2018-12-11T11:54:18Z","doi":"10.1007/978-3-662-46681-0_12","date_published":"2015-01-01T00:00:00Z","year":"2015","day":"01","oa":1,"publisher":"Springer","quality_controlled":"1","department":[{"_id":"KrCh"}],"date_updated":"2020-01-21T13:18:52Z","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2015-04-11","end_date":"2015-04-18","location":"London, United Kingdom"},"type":"conference","status":"public","_id":"1839","series_title":"Lecture Notes in Computer Science","ec_funded":1,"volume":9035,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.03093"}],"alternative_title":["LNCS"],"intvolume":" 9035","month":"01","abstract":[{"lang":"eng","text":"We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies."}],"oa_version":"Preprint"},{"oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","publication":"Journal of Fluid Mechanics","day":"08","year":"2015","date_created":"2018-12-11T11:54:17Z","doi":"10.1017/jfm.2015.184","date_published":"2015-04-08T00:00:00Z","article_number":"R3","project":[{"grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. 2015. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 770(5), R3.","chicago":"Kühnen, Jakob, P Braunshier, M Schwegel, Hendrik Kuhlmann, and Björn Hof. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics. Cambridge University Press, 2015. https://doi.org/10.1017/jfm.2015.184.","short":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, B. Hof, Journal of Fluid Mechanics 770 (2015).","ieee":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, and B. Hof, “Subcritical versus supercritical transition to turbulence in curved pipes,” Journal of Fluid Mechanics, vol. 770, no. 5. Cambridge University Press, 2015.","apa":"Kühnen, J., Braunshier, P., Schwegel, M., Kuhlmann, H., & Hof, B. (2015). Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2015.184","ama":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 2015;770(5). doi:10.1017/jfm.2015.184","mla":"Kühnen, Jakob, et al. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics, vol. 770, no. 5, R3, Cambridge University Press, 2015, doi:10.1017/jfm.2015.184."},"title":"Subcritical versus supercritical transition to turbulence in curved pipes","article_processing_charge":"No","external_id":{"arxiv":["1508.06559"]},"author":[{"full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179","last_name":"Kühnen","first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87"},{"first_name":"P","last_name":"Braunshier","full_name":"Braunshier, P"},{"last_name":"Schwegel","full_name":"Schwegel, M","first_name":"M"},{"first_name":"Hendrik","full_name":"Kuhlmann, Hendrik","last_name":"Kuhlmann"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"publist_id":"5265","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed."}],"intvolume":" 770","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1508.06559","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":770,"issue":"5","_id":"1837","status":"public","type":"journal_article","article_type":"original","date_updated":"2021-01-12T06:53:31Z","department":[{"_id":"BjHo"}]},{"abstract":[{"lang":"eng","text":"The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis."}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497860/"}],"scopus_import":1,"intvolume":" 137","month":"09","publication_status":"published","language":[{"iso":"eng"}],"volume":137,"issue":"6","_id":"1848","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T06:53:36Z","department":[{"_id":"LifeSc"}],"oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2015","publication":"International Journal of Cancer","day":"01","page":"1318 - 1329","date_created":"2018-12-11T11:54:20Z","doi":"10.1002/ijc.29498","date_published":"2015-09-01T00:00:00Z","citation":{"chicago":"Schwamb, Bettina, Robert Pick, Sara Fernández, Kirsten Völp, Jan Heering, Volker Dötsch, Susanne Bösser, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer. Wiley, 2015. https://doi.org/10.1002/ijc.29498.","ista":"Schwamb B, Pick R, Fernández S, Völp K, Heering J, Dötsch V, Bösser S, Jung J, Beinoravičiute Kellner R, Wesely J, Zörnig I, Hammerschmidt M, Nowak M, Penzel R, Zatloukal K, Joos S, Rieker R, Agaimy A, Söder S, Reid Lombardo K, Kendrick M, Bardsley M, Hayashi Y, Asuzu D, Syed S, Ördög T, Zörnig M. 2015. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 137(6), 1318–1329.","mla":"Schwamb, Bettina, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer, vol. 137, no. 6, Wiley, 2015, pp. 1318–29, doi:10.1002/ijc.29498.","ieee":"B. Schwamb et al., “FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors,” International Journal of Cancer, vol. 137, no. 6. Wiley, pp. 1318–1329, 2015.","short":"B. Schwamb, R. Pick, S. Fernández, K. Völp, J. Heering, V. Dötsch, S. Bösser, J. Jung, R. Beinoravičiute Kellner, J. Wesely, I. Zörnig, M. Hammerschmidt, M. Nowak, R. Penzel, K. Zatloukal, S. Joos, R. Rieker, A. Agaimy, S. Söder, K. Reid Lombardo, M. Kendrick, M. Bardsley, Y. Hayashi, D. Asuzu, S. Syed, T. Ördög, M. Zörnig, International Journal of Cancer 137 (2015) 1318–1329.","ama":"Schwamb B, Pick R, Fernández S, et al. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 2015;137(6):1318-1329. doi:10.1002/ijc.29498","apa":"Schwamb, B., Pick, R., Fernández, S., Völp, K., Heering, J., Dötsch, V., … Zörnig, M. (2015). FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. Wiley. https://doi.org/10.1002/ijc.29498"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["25716227"]},"author":[{"full_name":"Schwamb, Bettina","last_name":"Schwamb","first_name":"Bettina"},{"last_name":"Pick","full_name":"Pick, Robert","first_name":"Robert"},{"last_name":"Fernández","full_name":"Fernández, Sara","first_name":"Sara"},{"first_name":"Kirsten","last_name":"Völp","full_name":"Völp, Kirsten"},{"first_name":"Jan","last_name":"Heering","full_name":"Heering, Jan"},{"first_name":"Volker","last_name":"Dötsch","full_name":"Dötsch, Volker"},{"last_name":"Bösser","full_name":"Bösser, Susanne","first_name":"Susanne"},{"full_name":"Jung, Jennifer","last_name":"Jung","first_name":"Jennifer"},{"full_name":"Beinoravičiute Kellner, Rasa","last_name":"Beinoravičiute Kellner","first_name":"Rasa"},{"first_name":"Josephine","last_name":"Wesely","full_name":"Wesely, Josephine"},{"last_name":"Zörnig","full_name":"Zörnig, Inka","first_name":"Inka"},{"first_name":"Matthias","last_name":"Hammerschmidt","full_name":"Hammerschmidt, Matthias"},{"last_name":"Nowak","full_name":"Nowak, Matthias","first_name":"Matthias","id":"30845DAA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Penzel, Roland","last_name":"Penzel","first_name":"Roland"},{"first_name":"Kurt","last_name":"Zatloukal","full_name":"Zatloukal, Kurt"},{"last_name":"Joos","full_name":"Joos, Stefan","first_name":"Stefan"},{"first_name":"Ralf","last_name":"Rieker","full_name":"Rieker, Ralf"},{"first_name":"Abbas","last_name":"Agaimy","full_name":"Agaimy, Abbas"},{"last_name":"Söder","full_name":"Söder, Stephan","first_name":"Stephan"},{"full_name":"Reid Lombardo, Kmarie","last_name":"Reid Lombardo","first_name":"Kmarie"},{"last_name":"Kendrick","full_name":"Kendrick, Michael","first_name":"Michael"},{"first_name":"Michael","full_name":"Bardsley, Michael","last_name":"Bardsley"},{"full_name":"Hayashi, Yujiro","last_name":"Hayashi","first_name":"Yujiro"},{"first_name":"David","full_name":"Asuzu, David","last_name":"Asuzu"},{"last_name":"Syed","full_name":"Syed, Sabriya","first_name":"Sabriya"},{"first_name":"Tamás","full_name":"Ördög, Tamás","last_name":"Ördög"},{"last_name":"Zörnig","full_name":"Zörnig, Martin","first_name":"Martin"}],"publist_id":"5253","title":"FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors"},{"intvolume":" 52","month":"04","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS.","lang":"eng"}],"ec_funded":1,"volume":52,"issue":"2-3","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7854","checksum":"fb4037ddc4fc05f33080dd3547ede350","creator":"dernst","file_size":488482,"date_updated":"2020-07-14T12:45:19Z","file_name":"2015_ActaInfo_Benes.pdf","date_created":"2020-05-15T08:57:44Z"}],"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"1846","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2021-01-12T06:53:35Z","oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T11:54:20Z","date_published":"2015-04-01T00:00:00Z","doi":"10.1007/s00236-015-0215-4","page":"269 - 297","publication":"Acta Informatica","day":"01","year":"2015","has_accepted_license":"1","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"title":"Refinement checking on parametric modal transition systems","article_processing_charge":"No","publist_id":"5255","author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kim","full_name":"Larsen, Kim","last_name":"Larsen"},{"first_name":"Mikael","last_name":"Möller","full_name":"Möller, Mikael"},{"last_name":"Sickert","full_name":"Sickert, Salomon","first_name":"Salomon"},{"last_name":"Srba","full_name":"Srba, Jiří","first_name":"Jiří"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Beneš, Nikola, et al. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica, vol. 52, no. 2–3, Springer, 2015, pp. 269–97, doi:10.1007/s00236-015-0215-4.","ieee":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, and J. Srba, “Refinement checking on parametric modal transition systems,” Acta Informatica, vol. 52, no. 2–3. Springer, pp. 269–297, 2015.","short":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, J. Srba, Acta Informatica 52 (2015) 269–297.","apa":"Beneš, N., Kretinsky, J., Larsen, K., Möller, M., Sickert, S., & Srba, J. (2015). Refinement checking on parametric modal transition systems. Acta Informatica. Springer. https://doi.org/10.1007/s00236-015-0215-4","ama":"Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. Refinement checking on parametric modal transition systems. Acta Informatica. 2015;52(2-3):269-297. doi:10.1007/s00236-015-0215-4","chicago":"Beneš, Nikola, Jan Kretinsky, Kim Larsen, Mikael Möller, Salomon Sickert, and Jiří Srba. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica. Springer, 2015. https://doi.org/10.1007/s00236-015-0215-4.","ista":"Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. 2015. Refinement checking on parametric modal transition systems. Acta Informatica. 52(2–3), 269–297."}},{"article_processing_charge":"No","author":[{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","last_name":"Vandael"},{"first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","last_name":"Espinoza Martinez"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5256","title":"Excitement about inhibitory presynaptic terminals","citation":{"mla":"Vandael, David H., et al. “Excitement about Inhibitory Presynaptic Terminals.” Neuron, vol. 85, no. 6, Elsevier, 2015, pp. 1149–51, doi:10.1016/j.neuron.2015.03.006.","short":"D.H. Vandael, C. Espinoza Martinez, P.M. Jonas, Neuron 85 (2015) 1149–1151.","ieee":"D. H. Vandael, C. Espinoza Martinez, and P. M. Jonas, “Excitement about inhibitory presynaptic terminals,” Neuron, vol. 85, no. 6. Elsevier, pp. 1149–1151, 2015.","apa":"Vandael, D. H., Espinoza Martinez, C., & Jonas, P. M. (2015). Excitement about inhibitory presynaptic terminals. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.03.006","ama":"Vandael DH, Espinoza Martinez C, Jonas PM. Excitement about inhibitory presynaptic terminals. Neuron. 2015;85(6):1149-1151. doi:10.1016/j.neuron.2015.03.006","chicago":"Vandael, David H, Claudia Espinoza Martinez, and Peter M Jonas. “Excitement about Inhibitory Presynaptic Terminals.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.03.006.","ista":"Vandael DH, Espinoza Martinez C, Jonas PM. 2015. Excitement about inhibitory presynaptic terminals. Neuron. 85(6), 1149–1151."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"publisher":"Elsevier","quality_controlled":"1","page":"1149 - 1151","date_created":"2018-12-11T11:54:19Z","date_published":"2015-03-18T00:00:00Z","doi":"10.1016/j.neuron.2015.03.006","year":"2015","has_accepted_license":"1","publication":"Neuron","day":"18","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","pubrep_id":"822","status":"public","_id":"1845","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:19Z","date_updated":"2021-10-08T09:07:34Z","ddc":["570"],"scopus_import":"1","intvolume":" 85","month":"03","abstract":[{"text":"Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression.","lang":"eng"}],"oa_version":"Published Version","issue":"6","volume":85,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5192","checksum":"d1808550e376a0eca2a950fda017cfa6","date_updated":"2020-07-14T12:45:19Z","file_size":411832,"creator":"system","date_created":"2018-12-12T10:16:07Z","file_name":"IST-2017-822-v1+1_Perspective_Fig__Final.pdf"},{"date_updated":"2020-07-14T12:45:19Z","file_size":100769,"creator":"system","date_created":"2018-12-12T10:16:07Z","file_name":"IST-2017-822-v1+2_Perspective_Final2.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5193","checksum":"a279f4ae61e6c8f33d68f69a0d02097d"}]},{"date_updated":"2021-01-12T06:53:33Z","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"_id":"1840","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["0018-9286"]},"language":[{"iso":"eng"}],"volume":60,"issue":"4","abstract":[{"lang":"eng","text":"In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.6603"}],"scopus_import":1,"intvolume":" 60","month":"04","citation":{"mla":"Geiger, Bernhard, et al. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control, vol. 60, no. 4, IEEE, 2015, pp. 1010–22, doi:10.1109/TAC.2014.2364971.","ama":"Geiger B, Petrov T, Kubin G, Koeppl H. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 2015;60(4):1010-1022. doi:10.1109/TAC.2014.2364971","apa":"Geiger, B., Petrov, T., Kubin, G., & Koeppl, H. (2015). Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. IEEE. https://doi.org/10.1109/TAC.2014.2364971","short":"B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022.","ieee":"B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation via information bottleneck,” IEEE Transactions on Automatic Control, vol. 60, no. 4. IEEE, pp. 1010–1022, 2015.","chicago":"Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2014.2364971.","ista":"Geiger B, Petrov T, Kubin G, Koeppl H. 2015. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 60(4), 1010–1022."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5262","author":[{"first_name":"Bernhard","full_name":"Geiger, Bernhard","last_name":"Geiger"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov"},{"first_name":"Gernot","last_name":"Kubin","full_name":"Kubin, Gernot"},{"full_name":"Koeppl, Heinz","last_name":"Koeppl","first_name":"Heinz"}],"title":"Optimal Kullback-Leibler aggregation via information bottleneck","year":"2015","publication":"IEEE Transactions on Automatic Control","day":"01","page":"1010 - 1022","date_created":"2018-12-11T11:54:18Z","date_published":"2015-04-01T00:00:00Z","doi":"10.1109/TAC.2014.2364971","acknowledgement":"This work was supported by the Austrian Research Association under Project 06/12684, by the Swiss National Science Foundation (SNSF) under Grant PP00P2 128503/1, by the SystemsX.ch (the Swiss Inititative for Systems Biology), and by a SNSF Early Postdoc.Mobility Fellowship grant P2EZP2_148797.\r\n","oa":1,"quality_controlled":"1","publisher":"IEEE"},{"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"title":"A new look at reweighted message passing","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"}],"publist_id":"5261","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kolmogorov V. 2015. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 37(5), 919–930.","chicago":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2015. https://doi.org/10.1109/TPAMI.2014.2363465.","apa":"Kolmogorov, V. (2015). A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2014.2363465","ama":"Kolmogorov V. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2015;37(5):919-930. doi:10.1109/TPAMI.2014.2363465","ieee":"V. Kolmogorov, “A new look at reweighted message passing,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5. IEEE, pp. 919–930, 2015.","short":"V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 37 (2015) 919–930.","mla":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5, IEEE, 2015, pp. 919–30, doi:10.1109/TPAMI.2014.2363465."},"publisher":"IEEE","quality_controlled":"1","oa":1,"doi":"10.1109/TPAMI.2014.2363465","date_published":"2015-05-01T00:00:00Z","date_created":"2018-12-11T11:54:18Z","page":"919 - 930","day":"01","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","year":"2015","status":"public","type":"journal_article","_id":"1841","department":[{"_id":"VlKo"}],"date_updated":"2021-01-12T06:53:33Z","month":"05","intvolume":" 37","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1309.5655"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diffusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. The new family of algorithms can be viewed as a generalization of TRW-S from pairwise to higher-order graphical models. We test SRMP on several real-world problems with promising results."}],"issue":"5","volume":37,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"publication_status":"published","year":"2015","day":"01","language":[{"iso":"eng"}],"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","page":"2168 - 2172","doi":"10.1016/j.bbamcr.2015.02.017","volume":1853,"issue":"9","date_published":"2015-09-01T00:00:00Z","date_created":"2018-12-11T11:54:21Z","abstract":[{"lang":"eng","text":"Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium."}],"oa_version":"None","acknowledgement":"The contributing authors were supported by the Ghent University Special Research Fund (to E.H.), the Interuniversity Attraction Poles Programme (IAP VI/33 and IUAP P7/29 ‘MARS’), the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), and the Research Foundation Flanders (to S.V.).","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"month":"09","intvolume":" 1853","date_updated":"2021-01-12T06:53:36Z","citation":{"ista":"Himschoot E, Beeckman T, Friml J, Vanneste S. 2015. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(9), 2168–2172.","chicago":"Himschoot, Ellie, Tom Beeckman, Jiří Friml, and Steffen Vanneste. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2015.02.017.","short":"E. Himschoot, T. Beeckman, J. Friml, S. Vanneste, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 2168–2172.","ieee":"E. Himschoot, T. Beeckman, J. Friml, and S. Vanneste, “Calcium is an organizer of cell polarity in plants,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9. Elsevier, pp. 2168–2172, 2015.","apa":"Himschoot, E., Beeckman, T., Friml, J., & Vanneste, S. (2015). Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2015.02.017","ama":"Himschoot E, Beeckman T, Friml J, Vanneste S. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(9):2168-2172. doi:10.1016/j.bbamcr.2015.02.017","mla":"Himschoot, Ellie, et al. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9, Elsevier, 2015, pp. 2168–72, doi:10.1016/j.bbamcr.2015.02.017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ellie","last_name":"Himschoot","full_name":"Himschoot, Ellie"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"publist_id":"5252","title":"Calcium is an organizer of cell polarity in plants","department":[{"_id":"JiFr"}],"_id":"1849","type":"journal_article","status":"public"},{"intvolume":" 8","month":"03","scopus_import":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637S).","oa_version":"None","date_created":"2018-12-11T11:54:20Z","date_published":"2015-03-02T00:00:00Z","volume":8,"doi":"10.1016/j.molp.2014.12.013","issue":"3","page":"356 - 358","publication":"Molecular Plant","language":[{"iso":"eng"}],"day":"02","publication_status":"published","year":"2015","status":"public","type":"journal_article","_id":"1847","title":"ABP1: Finally docking","department":[{"_id":"JiFr"}],"publist_id":"5254","author":[{"last_name":"Grones","full_name":"Grones, Peter","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358.","chicago":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2014.12.013.","ama":"Grones P, Friml J. ABP1: Finally docking. Molecular Plant. 2015;8(3):356-358. doi:10.1016/j.molp.2014.12.013","apa":"Grones, P., & Friml, J. (2015). ABP1: Finally docking. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2014.12.013","ieee":"P. Grones and J. Friml, “ABP1: Finally docking,” Molecular Plant, vol. 8, no. 3. Elsevier, pp. 356–358, 2015.","short":"P. Grones, J. Friml, Molecular Plant 8 (2015) 356–358.","mla":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant, vol. 8, no. 3, Elsevier, 2015, pp. 356–58, doi:10.1016/j.molp.2014.12.013."},"date_updated":"2021-01-12T06:53:35Z"},{"pubrep_id":"329","status":"public","type":"journal_article","_id":"1850","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"ddc":["576"],"date_updated":"2021-01-12T06:53:37Z","intvolume":" 372","month":"05","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels."}],"ec_funded":1,"issue":"5","volume":372,"language":[{"iso":"eng"}],"file":[{"file_id":"5326","checksum":"3c0dcacc900bc45cc65a453dfda4ca43","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:18:07Z","file_name":"IST-2015-329-v1+1_manuscript.pdf","creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":1546914}],"publication_status":"published","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","publist_id":"5251","author":[{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.02.018.","ista":"Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 372(5), 54–64.","mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:10.1016/j.jtbi.2015.02.018.","short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64.","ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” Journal of Theoretical Biology, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 2015;372(5):54-64. doi:10.1016/j.jtbi.2015.02.018","apa":"Novak, S., & Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.02.018"},"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2018-12-11T11:54:21Z","doi":"10.1016/j.jtbi.2015.02.018","date_published":"2015-05-07T00:00:00Z","page":"54 - 64","publication":"Journal of Theoretical Biology","day":"07","year":"2015","has_accepted_license":"1"},{"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","external_id":{"pmid":["25662095"]},"article_processing_charge":"No","author":[{"first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","full_name":"Priklopil, Tadeas"},{"first_name":"Eva","last_name":"Kisdi","full_name":"Kisdi, Eva"},{"first_name":"Mats","full_name":"Gyllenberg, Mats","last_name":"Gyllenberg"}],"publist_id":"5249","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Priklopil T, Kisdi E, Gyllenberg M. 2015. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 69(4), 1015–1026.","chicago":"Priklopil, Tadeas, Eva Kisdi, and Mats Gyllenberg. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12618.","short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.","ieee":"T. Priklopil, E. Kisdi, and M. Gyllenberg, “Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating,” Evolution, vol. 69, no. 4. Wiley, pp. 1015–1026, 2015.","ama":"Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 2015;69(4):1015-1026. doi:10.1111/evo.12618","apa":"Priklopil, T., Kisdi, E., & Gyllenberg, M. (2015). Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. Wiley. https://doi.org/10.1111/evo.12618","mla":"Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:10.1111/evo.12618."},"oa":1,"quality_controlled":"1","publisher":"Wiley","date_created":"2018-12-11T11:54:21Z","date_published":"2015-02-09T00:00:00Z","doi":"10.1111/evo.12618","page":"1015 - 1026","publication":"Evolution","day":"09","year":"2015","has_accepted_license":"1","status":"public","type":"journal_article","article_type":"original","_id":"1851","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"ddc":["570"],"date_updated":"2022-06-07T10:52:37Z","intvolume":" 69","month":"02","scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them."}],"ec_funded":1,"volume":69,"issue":"4","language":[{"iso":"eng"}],"file":[{"date_created":"2020-05-15T09:05:34Z","file_name":"2015_Evolution_Priklopil.pdf","date_updated":"2020-07-14T12:45:19Z","file_size":967214,"creator":"dernst","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798","file_id":"7855","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]}},{"month":"06","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.6804"}],"publisher":"IEEE","scopus_import":1,"quality_controlled":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Structural support vector machines (SSVMs) are amongst the best performing models for structured computer vision tasks, such as semantic image segmentation or human pose estimation. Training SSVMs, however, is computationally costly, because it requires repeated calls to a structured prediction subroutine (called \\emph{max-oracle}), which has to solve an optimization problem itself, e.g. a graph cut.\r\nIn this work, we introduce a new algorithm for SSVM training that is more efficient than earlier techniques when the max-oracle is computationally expensive, as it is frequently the case in computer vision tasks. The main idea is to (i) combine the recent stochastic Block-Coordinate Frank-Wolfe algorithm with efficient hyperplane caching, and (ii) use an automatic selection rule for deciding whether to call the exact max-oracle or to rely on an approximate one based on the cached hyperplanes.\r\nWe show experimentally that this strategy leads to faster convergence to the optimum with respect to the number of requires oracle calls, and that this translates into faster convergence with respect to the total runtime when the max-oracle is slow compared to the other steps of the algorithm. "}],"date_created":"2018-12-11T11:54:24Z","ec_funded":1,"doi":"10.1109/CVPR.2015.7298890","date_published":"2015-06-01T00:00:00Z","page":"2737 - 2745","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","status":"public","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"},{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"conference":{"start_date":"2015-06-07","location":"Boston, MA, USA","end_date":"2015-06-12","name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","_id":"1859","department":[{"_id":"VlKo"},{"_id":"ChLa"}],"title":"A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle","publist_id":"5240","author":[{"last_name":"Shah","full_name":"Shah, Neel","first_name":"Neel","id":"31ABAF80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:40Z","citation":{"short":"N. Shah, V. Kolmogorov, C. Lampert, in:, IEEE, 2015, pp. 2737–2745.","ieee":"N. Shah, V. Kolmogorov, and C. Lampert, “A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 2737–2745.","apa":"Shah, N., Kolmogorov, V., & Lampert, C. (2015). A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle (pp. 2737–2745). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7298890","ama":"Shah N, Kolmogorov V, Lampert C. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. In: IEEE; 2015:2737-2745. doi:10.1109/CVPR.2015.7298890","mla":"Shah, Neel, et al. A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle. IEEE, 2015, pp. 2737–45, doi:10.1109/CVPR.2015.7298890.","ista":"Shah N, Kolmogorov V, Lampert C. 2015. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. CVPR: Computer Vision and Pattern Recognition, 2737–2745.","chicago":"Shah, Neel, Vladimir Kolmogorov, and Christoph Lampert. “A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle,” 2737–45. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298890."}},{"oa_version":"Submitted Version","abstract":[{"text":"Classifiers for object categorization are usually evaluated by their accuracy on a set of i.i.d. test examples. This provides us with an estimate of the expected error when applying the classifiers to a single new image. In real application, however, classifiers are rarely only used for a single image and then discarded. Instead, they are applied sequentially to many images, and these are typically not i.i.d. samples from a fixed data distribution, but they carry dependencies and their class distribution varies over time. In this work, we argue that the phenomenon of correlated data at prediction time is not a nuisance, but a blessing in disguise. We describe a probabilistic method for adapting classifiers at prediction time without having to retrain them. We also introduce a framework for creating realistically distributed image sequences, which offers a way to benchmark classifier adaptation methods, such as the one we propose. Experiments on the ILSVRC2010 and ILSVRC2012 datasets show that adapting object classification systems at prediction time can significantly reduce their error rate, even with no additional human feedback.","lang":"eng"}],"month":"06","main_file_link":[{"open_access":"1","url":"http://www.cv-foundation.org/openaccess/content_cvpr_2015/papers/Royer_Classifier_Adaptation_at_2015_CVPR_paper.pdf"}],"oa":1,"publisher":"IEEE","quality_controlled":"1","scopus_import":1,"language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","date_created":"2018-12-11T11:54:24Z","ec_funded":1,"date_published":"2015-06-01T00:00:00Z","doi":"10.1109/CVPR.2015.7298746","page":"1401 - 1409","_id":"1860","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"status":"public","conference":{"end_date":"2015-06-12","location":"Boston, MA, United States","start_date":"2015-06-07","name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:41Z","citation":{"chicago":"Royer, Amélie, and Christoph Lampert. “Classifier Adaptation at Prediction Time,” 1401–9. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298746.","ista":"Royer A, Lampert C. 2015. Classifier adaptation at prediction time. CVPR: Computer Vision and Pattern Recognition, 1401–1409.","mla":"Royer, Amélie, and Christoph Lampert. Classifier Adaptation at Prediction Time. IEEE, 2015, pp. 1401–09, doi:10.1109/CVPR.2015.7298746.","ama":"Royer A, Lampert C. Classifier adaptation at prediction time. In: IEEE; 2015:1401-1409. doi:10.1109/CVPR.2015.7298746","apa":"Royer, A., & Lampert, C. (2015). Classifier adaptation at prediction time (pp. 1401–1409). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7298746","ieee":"A. Royer and C. Lampert, “Classifier adaptation at prediction time,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 1401–1409.","short":"A. Royer, C. Lampert, in:, IEEE, 2015, pp. 1401–1409."},"title":"Classifier adaptation at prediction time","department":[{"_id":"ChLa"}],"publist_id":"5239","author":[{"first_name":"Amélie","full_name":"Royer, Amélie","last_name":"Royer"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}]},{"date_published":"2015-10-15T00:00:00Z","doi":"10.1109/CVPR.2015.7298696","date_created":"2018-12-11T11:54:24Z","page":"942 - 950","day":"15","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","month":"10","quality_controlled":"1","publisher":"IEEE","scopus_import":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1406.5362"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study the problem of predicting the future, though only in the probabilistic sense of estimating a future state of a time-varying probability distribution. This is not only an interesting academic problem, but solving this extrapolation problem also has many practical application, e.g. for training classifiers that have to operate under time-varying conditions. Our main contribution is a method for predicting the next step of the time-varying distribution from a given sequence of sample sets from earlier time steps. For this we rely on two recent machine learning techniques: embedding probability distributions into a reproducing kernel Hilbert space, and learning operators by vector-valued regression. We illustrate the working principles and the practical usefulness of our method by experiments on synthetic and real data. We also highlight an exemplary application: training a classifier in a domain adaptation setting without having access to examples from the test time distribution at training time."}],"department":[{"_id":"ChLa"}],"title":"Predicting the future behavior of a time-varying probability distribution","author":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"publist_id":"5241","external_id":{"arxiv":["1406.5362"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lampert, Christoph. Predicting the Future Behavior of a Time-Varying Probability Distribution. IEEE, 2015, pp. 942–50, doi:10.1109/CVPR.2015.7298696.","ieee":"C. Lampert, “Predicting the future behavior of a time-varying probability distribution,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 942–950.","short":"C. Lampert, in:, IEEE, 2015, pp. 942–950.","ama":"Lampert C. Predicting the future behavior of a time-varying probability distribution. In: IEEE; 2015:942-950. doi:10.1109/CVPR.2015.7298696","apa":"Lampert, C. (2015). Predicting the future behavior of a time-varying probability distribution (pp. 942–950). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7298696","chicago":"Lampert, Christoph. “Predicting the Future Behavior of a Time-Varying Probability Distribution,” 942–50. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298696.","ista":"Lampert C. 2015. Predicting the future behavior of a time-varying probability distribution. CVPR: Computer Vision and Pattern Recognition, 942–950."},"date_updated":"2021-01-12T06:53:40Z","status":"public","type":"conference","conference":{"end_date":"2015-06-12","location":"Boston, MA, United States","start_date":"2015-06-07","name":"CVPR: Computer Vision and Pattern Recognition"},"_id":"1858"},{"_id":"1857","status":"public","type":"conference","conference":{"location":"Boston, MA, United States","end_date":"2015-06-12","start_date":"2015-06-07","name":"CVPR: Computer Vision and Pattern Recognition"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Pentina A, Sharmanska V, Lampert C. 2015. Curriculum learning of multiple tasks. CVPR: Computer Vision and Pattern Recognition, 5492–5500.","chicago":"Pentina, Anastasia, Viktoriia Sharmanska, and Christoph Lampert. “Curriculum Learning of Multiple Tasks,” 5492–5500. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299188.","ama":"Pentina A, Sharmanska V, Lampert C. Curriculum learning of multiple tasks. In: IEEE; 2015:5492-5500. doi:10.1109/CVPR.2015.7299188","apa":"Pentina, A., Sharmanska, V., & Lampert, C. (2015). Curriculum learning of multiple tasks (pp. 5492–5500). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7299188","ieee":"A. Pentina, V. Sharmanska, and C. Lampert, “Curriculum learning of multiple tasks,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 5492–5500.","short":"A. Pentina, V. Sharmanska, C. Lampert, in:, IEEE, 2015, pp. 5492–5500.","mla":"Pentina, Anastasia, et al. Curriculum Learning of Multiple Tasks. IEEE, 2015, pp. 5492–500, doi:10.1109/CVPR.2015.7299188."},"date_updated":"2023-02-23T10:17:31Z","title":"Curriculum learning of multiple tasks","department":[{"_id":"ChLa"}],"publist_id":"5243","author":[{"first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","last_name":"Pentina","full_name":"Pentina, Anastasia"},{"first_name":"Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","last_name":"Sharmanska"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Sharing information between multiple tasks enables algorithms to achieve good generalization performance even from small amounts of training data. However, in a realistic scenario of multi-task learning not all tasks are equally related to each other, hence it could be advantageous to transfer information only between the most related tasks. In this work we propose an approach that processes multiple tasks in a sequence with sharing between subsequent tasks instead of solving all tasks jointly. Subsequently, we address the question of curriculum learning of tasks, i.e. finding the best order of tasks to be learned. Our approach is based on a generalization bound criterion for choosing the task order that optimizes the average expected classification performance over all tasks. Our experimental results show that learning multiple related tasks sequentially can be more effective than learning them jointly, the order in which tasks are being solved affects the overall performance, and that our model is able to automatically discover the favourable order of tasks. "}],"month":"06","publisher":"IEEE","quality_controlled":"1","scopus_import":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1412.1353","open_access":"1"}],"day":"01","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","doi":"10.1109/CVPR.2015.7299188","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:54:23Z","page":"5492 - 5500"},{"project":[{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"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"}],"title":"Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection","author":[{"first_name":"Jens","full_name":"Hühner, Jens","last_name":"Hühner"},{"orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro"},{"last_name":"Neusüß","full_name":"Neusüß, Christian","first_name":"Christian"},{"full_name":"Lämmerhofer, Michael","last_name":"Lämmerhofer","first_name":"Michael"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"}],"publist_id":"5230","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hühner, Jens, Álvaro Inglés Prieto, Christian Neusüß, Michael Lämmerhofer, and Harald L Janovjak. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” Electrophoresis. Wiley, 2015. https://doi.org/10.1002/elps.201400451.","ista":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. 2015. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. 36(4), 518–525.","mla":"Hühner, Jens, et al. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” Electrophoresis, vol. 36, no. 4, Wiley, 2015, pp. 518–25, doi:10.1002/elps.201400451.","ama":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. 2015;36(4):518-525. doi:10.1002/elps.201400451","apa":"Hühner, J., Inglés Prieto, Á., Neusüß, C., Lämmerhofer, M., & Janovjak, H. L. (2015). Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. Wiley. https://doi.org/10.1002/elps.201400451","short":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, H.L. Janovjak, Electrophoresis 36 (2015) 518–525.","ieee":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, and H. L. Janovjak, “Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection,” Electrophoresis, vol. 36, no. 4. Wiley, pp. 518–525, 2015."},"quality_controlled":"1","publisher":"Wiley","date_published":"2015-02-01T00:00:00Z","doi":"10.1002/elps.201400451","date_created":"2018-12-11T11:54:26Z","page":"518 - 525","day":"01","publication":"Electrophoresis","year":"2015","status":"public","pubrep_id":"836","type":"journal_article","_id":"1867","department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T06:53:43Z","month":"02","intvolume":" 36","scopus_import":1,"oa_version":"None","abstract":[{"text":"Cultured mammalian cells essential are model systems in basic biology research, production platforms of proteins for medical use, and testbeds in synthetic biology. Flavin cofactors, in particular flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), are critical for cellular redox reactions and sense light in naturally occurring photoreceptors and optogenetic tools. Here, we quantified flavin contents of commonly used mammalian cell lines. We first compared three procedures for extraction of free and noncovalently protein-bound flavins and verified extraction using fluorescence spectroscopy. For separation, two CE methods with different BGEs were established, and detection was performed by LED-induced fluorescence with limit of detections (LODs 0.5-3.8 nM). We found that riboflavin (RF), FMN, and FAD contents varied significantly between cell lines. RF (3.1-14 amol/cell) and FAD (2.2-17.0 amol/cell) were the predominant flavins, while FMN (0.46-3.4 amol/cell) was found at markedly lower levels. Observed flavin contents agree with those previously extracted from mammalian tissues, yet reduced forms of RF were detected that were not described previously. Quantification of flavins in mammalian cell lines will allow a better understanding of cellular redox reactions and optogenetic tools.","lang":"eng"}],"issue":"4","volume":36,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"chicago":"Robert, Hélène, Wim Grunewald, Michael Sauer, Bernard Cannoot, Mercedes Soriano, Ranjan Swarup, Dolf Weijers, Malcolm Bennett, Kim Boutilier, and Jiří Friml. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.115832.","ista":"Robert H, Grunewald W, Sauer M, Cannoot B, Soriano M, Swarup R, Weijers D, Bennett M, Boutilier K, Friml J. 2015. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 142(4), 702–711.","mla":"Robert, Hélène, et al. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 702–11, doi:10.1242/dev.115832.","ieee":"H. Robert et al., “Plant embryogenesis requires AUX/LAX-mediated auxin influx,” Development, vol. 142, no. 4. Company of Biologists, pp. 702–711, 2015.","short":"H. Robert, W. Grunewald, M. Sauer, B. Cannoot, M. Soriano, R. Swarup, D. Weijers, M. Bennett, K. Boutilier, J. Friml, Development 142 (2015) 702–711.","ama":"Robert H, Grunewald W, Sauer M, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 2015;142(4):702-711. doi:10.1242/dev.115832","apa":"Robert, H., Grunewald, W., Sauer, M., Cannoot, B., Soriano, M., Swarup, R., … Friml, J. (2015). Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. Company of Biologists. https://doi.org/10.1242/dev.115832"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Robert","full_name":"Robert, Hélène","first_name":"Hélène"},{"full_name":"Grunewald, Wim","last_name":"Grunewald","first_name":"Wim"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"full_name":"Cannoot, Bernard","last_name":"Cannoot","first_name":"Bernard"},{"first_name":"Mercedes","full_name":"Soriano, Mercedes","last_name":"Soriano"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"last_name":"Bennett","full_name":"Bennett, Malcolm","first_name":"Malcolm"},{"full_name":"Boutilier, Kim","last_name":"Boutilier","first_name":"Kim"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"5231","title":"Plant embryogenesis requires AUX/LAX-mediated auxin influx","acknowledgement":"W.G. is a post-doctoral fellow of the Research Foundation Flanders. H.S.R. is supported by Employment of Best Young Scientists for International Cooperation Empowerment [CZ.1.07/2.3.00/30.0037], co-financed by the European Social Fund and the state budget of the Czech Republic. Mi.S. was funded by the Ramón y Cajal program. This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], project ‘CEITEC – Central European Institute of Technology’ [CZ.1.05/1.1.00/02.0068], the European Social Fund [CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GACR [GA13-40637S] to J.F. We acknowledge funding from the Biological and Biotechnological Science Research Council (BBSRC) and Engineering Physics Science Research Council (EPSRC) to R.S. and M.B","publisher":"Company of Biologists","quality_controlled":"1","year":"2015","day":"15","publication":"Development","page":"702 - 711","date_published":"2015-02-15T00:00:00Z","doi":"10.1242/dev.115832","date_created":"2018-12-11T11:54:26Z","_id":"1865","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:43Z","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop betweenMONOPTEROS(ARF5)-dependent auxin signalling and auxin transport. ThisMONOPTEROSdependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling."}],"oa_version":"None","scopus_import":1,"month":"02","intvolume":" 142","publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":142,"ec_funded":1},{"quality_controlled":"1","publisher":"American Physical Society","scopus_import":1,"month":"02","intvolume":" 91","abstract":[{"text":"We investigate high-dimensional nonlinear dynamical systems exhibiting multiple resonances under adiabatic parameter variations. Our motivations come from experimental considerations where time-dependent sweeping of parameters is a practical approach to probing and characterizing the bifurcations of the system. The question is whether bifurcations so detected are faithful representations of the bifurcations intrinsic to the original stationary system. Utilizing a harmonically forced, closed fluid flow system that possesses multiple resonances and solving the Navier-Stokes equation under proper boundary conditions, we uncover the phenomenon of the early effect. Specifically, as a control parameter, e.g., the driving frequency, is adiabatically increased from an initial value, resonances emerge at frequency values that are lower than those in the corresponding stationary system. The phenomenon is established by numerical characterization of physical quantities through the resonances, which include the kinetic energy and the vorticity field, and a heuristic analysis based on the concept of instantaneous frequency. A simple formula is obtained which relates the resonance points in the time-dependent and time-independent systems. Our findings suggest that, in general, any true bifurcation of a nonlinear dynamical system can be unequivocally uncovered through adiabatic parameter sweeping, in spite of a shift in the bifurcation point, which is of value to experimental studies of nonlinear dynamical systems.","lang":"eng"}],"oa_version":"None","doi":"10.1103/PhysRevE.91.022906","date_published":"2015-02-09T00:00:00Z","volume":91,"issue":"2","date_created":"2018-12-11T11:54:27Z","publication_identifier":{"issn":["1539-3755"]},"year":"2015","publication_status":"published","day":"09","language":[{"iso":"eng"}],"publication":"Physical Review E","type":"journal_article","status":"public","_id":"1868","article_number":"022906","author":[{"first_name":"Youngyong","last_name":"Park","full_name":"Park, Youngyong"},{"full_name":"Do, Younghae","last_name":"Do","first_name":"Younghae"},{"last_name":"Altmeyer","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yingcheng","last_name":"Lai","full_name":"Lai, Yingcheng"},{"first_name":"Gyuwon","full_name":"Lee, Gyuwon","last_name":"Lee"}],"publist_id":"5229","title":"Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances","department":[{"_id":"BjHo"}],"date_updated":"2021-01-12T06:53:44Z","citation":{"ieee":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, and G. Lee, “Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances,” Physical Review E, vol. 91, no. 2. American Physical Society, 2015.","short":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, G. Lee, Physical Review E 91 (2015).","ama":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. 2015;91(2). doi:10.1103/PhysRevE.91.022906","apa":"Park, Y., Do, Y., Altmeyer, S., Lai, Y., & Lee, G. (2015). Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.91.022906","mla":"Park, Youngyong, et al. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” Physical Review E, vol. 91, no. 2, 022906, American Physical Society, 2015, doi:10.1103/PhysRevE.91.022906.","ista":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. 2015. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. 91(2), 022906.","chicago":"Park, Youngyong, Younghae Do, Sebastian Altmeyer, Yingcheng Lai, and Gyuwon Lee. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.91.022906."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"The Altshuler–Shklovskii formulas (Altshuler and Shklovskii, BZh Eksp Teor Fiz 91:200, 1986) predict, for any disordered quantum system in the diffusive regime, a universal power law behaviour for the correlation functions of the mesoscopic eigenvalue density. In this paper and its companion (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013), we prove these formulas for random band matrices. In (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013) we introduced a diagrammatic approach and presented robust estimates on general diagrams under certain simplifying assumptions. In this paper, we remove these assumptions by giving a general estimate of the subleading diagrams. We also give a precise analysis of the leading diagrams which give rise to the Altschuler–Shklovskii power laws. Moreover, we introduce a family of general random band matrices which interpolates between real symmetric (β = 1) and complex Hermitian (β = 2) models, and track the transition for the mesoscopic density–density correlation. Finally, we address the higher-order correlation functions by proving that they behave asymptotically according to a Gaussian process whose covariance is given by the Altshuler–Shklovskii formulas.\r\n"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1309.5107"}],"month":"03","intvolume":" 16","publication_status":"published","language":[{"iso":"eng"}],"volume":16,"issue":"3","ec_funded":1,"_id":"1864","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:42Z","department":[{"_id":"LaEr"}],"publisher":"Springer","oa":1,"year":"2015","day":"01","publication":"Annales Henri Poincare","page":"709 - 799","date_published":"2015-03-01T00:00:00Z","doi":"10.1007/s00023-014-0333-5","date_created":"2018-12-11T11:54:26Z","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"citation":{"apa":"Erdös, L., & Knowles, A. (2015). The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-014-0333-5","ama":"Erdös L, Knowles A. The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. 2015;16(3):709-799. doi:10.1007/s00023-014-0333-5","short":"L. Erdös, A. Knowles, Annales Henri Poincare 16 (2015) 709–799.","ieee":"L. Erdös and A. Knowles, “The Altshuler–Shklovskii formulas for random band matrices II: The general case,” Annales Henri Poincare, vol. 16, no. 3. Springer, pp. 709–799, 2015.","mla":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” Annales Henri Poincare, vol. 16, no. 3, Springer, 2015, pp. 709–99, doi:10.1007/s00023-014-0333-5.","ista":"Erdös L, Knowles A. 2015. The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. 16(3), 709–799.","chicago":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” Annales Henri Poincare. Springer, 2015. https://doi.org/10.1007/s00023-014-0333-5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5233","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Antti","full_name":"Knowles, Antti","last_name":"Knowles"}],"title":"The Altshuler–Shklovskii formulas for random band matrices II: The general case"},{"date_published":"2015-02-01T00:00:00Z","doi":"10.1145/2688906","volume":25,"issue":"2","date_created":"2018-12-11T11:54:25Z","day":"01","publication":"ACM Transactions on Modeling and Computer Simulation","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","month":"02","intvolume":" 25","publisher":"ACM","scopus_import":1,"quality_controlled":"1","oa_version":"None","acknowledgement":"HYCON2; EC; European Commission\r\n","abstract":[{"text":"Continuous-time Markov chains are commonly used in practice for modeling biochemical reaction networks in which the inherent randomness of themolecular interactions cannot be ignored. This has motivated recent research effort into methods for parameter inference and experiment design for such models. The major difficulty is that such methods usually require one to iteratively solve the chemical master equation that governs the time evolution of the probability distribution of the system. This, however, is rarely possible, and even approximation techniques remain limited to relatively small and simple systems. An alternative explored in this article is to base methods on only some low-order moments of the entire probability distribution. We summarize the theory behind such moment-based methods for parameter inference and experiment design and provide new case studies where we investigate their performance.","lang":"eng"}],"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"title":"Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks","publist_id":"5238","author":[{"last_name":"Ruess","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob"},{"first_name":"John","last_name":"Lygeros","full_name":"Lygeros, John"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015).","ieee":"J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.","apa":"Ruess, J., & Lygeros, J. (2015). Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2688906","ama":"Ruess J, Lygeros J. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2688906","mla":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 8, ACM, 2015, doi:10.1145/2688906.","ista":"Ruess J, Lygeros J. 2015. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 25(2), 8.","chicago":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2688906."},"date_updated":"2021-01-12T06:53:41Z","status":"public","type":"journal_article","article_number":"8","_id":"1861"},{"status":"public","type":"journal_article","_id":"1866","department":[{"_id":"ToHe"}],"title":"The equivalence problem for finite automata: Technical perspective","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"last_name":"Raskin","full_name":"Raskin, Jean","first_name":"Jean"}],"publist_id":"5232","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Henzinger, Thomas A., and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” Communications of the ACM, vol. 58, no. 2, ACM, 2015, pp. 86–86, doi:10.1145/2701001.","ieee":"T. A. Henzinger and J. Raskin, “The equivalence problem for finite automata: Technical perspective,” Communications of the ACM, vol. 58, no. 2. ACM, pp. 86–86, 2015.","short":"T.A. Henzinger, J. Raskin, Communications of the ACM 58 (2015) 86–86.","apa":"Henzinger, T. A., & Raskin, J. (2015). The equivalence problem for finite automata: Technical perspective. Communications of the ACM. ACM. https://doi.org/10.1145/2701001","ama":"Henzinger TA, Raskin J. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 2015;58(2):86-86. doi:10.1145/2701001","chicago":"Henzinger, Thomas A, and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” Communications of the ACM. ACM, 2015. https://doi.org/10.1145/2701001.","ista":"Henzinger TA, Raskin J. 2015. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 58(2), 86–86."},"date_updated":"2021-01-12T06:53:43Z","intvolume":" 58","month":"01","publisher":"ACM","scopus_import":1,"oa_version":"None","date_created":"2018-12-11T11:54:26Z","date_published":"2015-01-28T00:00:00Z","issue":"2","doi":"10.1145/2701001","volume":58,"page":"86-86","language":[{"iso":"eng"}],"publication":"Communications of the ACM","day":"28","year":"2015","publication_status":"published"},{"pubrep_id":"563","status":"public","type":"journal_article","_id":"1871","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"JiFr"}],"ddc":["570"],"date_updated":"2021-01-12T06:53:45Z","intvolume":" 128","month":"01","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.","lang":"eng"}],"volume":128,"issue":"1","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":1688844,"date_created":"2018-12-12T10:11:00Z","file_name":"IST-2016-563-v1+1_1.full.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"24c779f4cd9d549ca6833e26f486be27","file_id":"4852"}],"publication_status":"published","title":"Auxin transporters and binding proteins at a glance","author":[{"last_name":"Grones","full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"publist_id":"5225","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 1–7.","chicago":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.159418.","ama":"Grones P, Friml J. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 2015;128(1):1-7. doi:10.1242/jcs.159418","apa":"Grones, P., & Friml, J. (2015). Auxin transporters and binding proteins at a glance. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.159418","ieee":"P. Grones and J. Friml, “Auxin transporters and binding proteins at a glance,” Journal of Cell Science, vol. 128, no. 1. Company of Biologists, pp. 1–7, 2015.","short":"P. Grones, J. Friml, Journal of Cell Science 128 (2015) 1–7.","mla":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science, vol. 128, no. 1, Company of Biologists, 2015, pp. 1–7, doi:10.1242/jcs.159418."},"oa":1,"quality_controlled":"1","publisher":"Company of Biologists","acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP]; European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GAČR [grant number GA13-40637S]","date_created":"2018-12-11T11:54:28Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1242/jcs.159418","page":"1 - 7","publication":"Journal of Cell Science","day":"01","year":"2015","has_accepted_license":"1"},{"intvolume":" 25","month":"07","scopus_import":1,"publisher":"Wiley","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource."}],"date_created":"2018-12-11T11:54:29Z","date_published":"2015-07-01T00:00:00Z","doi":"10.1002/hipo.22407","issue":"7","volume":25,"page":"838 - 857","language":[{"iso":"eng"}],"publication":"Hippocampus","day":"01","year":"2015","publication_status":"published","status":"public","type":"journal_article","_id":"1874","title":"A three-plane architectonic atlas of the rat hippocampal region","department":[{"_id":"JoCs"}],"author":[{"last_name":"Boccara","full_name":"Boccara, Charlotte","orcid":"0000-0001-7237-5109","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","first_name":"Charlotte"},{"first_name":"Lisa","last_name":"Kjønigsen","full_name":"Kjønigsen, Lisa"},{"full_name":"Hammer, Ingvild","last_name":"Hammer","first_name":"Ingvild"},{"last_name":"Bjaalie","full_name":"Bjaalie, Jan","first_name":"Jan"},{"first_name":"Trygve","full_name":"Leergaard, Trygve","last_name":"Leergaard"},{"first_name":"Menno","last_name":"Witter","full_name":"Witter, Menno"}],"publist_id":"5222","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:46Z","citation":{"chicago":"Boccara, Charlotte N., Lisa Kjønigsen, Ingvild Hammer, Jan Bjaalie, Trygve Leergaard, and Menno Witter. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus. Wiley, 2015. https://doi.org/10.1002/hipo.22407.","ista":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. 2015. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 25(7), 838–857.","mla":"Boccara, Charlotte N., et al. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus, vol. 25, no. 7, Wiley, 2015, pp. 838–57, doi:10.1002/hipo.22407.","ama":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 2015;25(7):838-857. doi:10.1002/hipo.22407","apa":"Boccara, C. N., Kjønigsen, L., Hammer, I., Bjaalie, J., Leergaard, T., & Witter, M. (2015). A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22407","ieee":"C. N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, and M. Witter, “A three-plane architectonic atlas of the rat hippocampal region,” Hippocampus, vol. 25, no. 7. Wiley, pp. 838–857, 2015.","short":"C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter, Hippocampus 25 (2015) 838–857."}},{"type":"journal_article","status":"public","_id":"1873","publist_id":"5224","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik"}],"external_id":{"arxiv":["1408.2058"]},"department":[{"_id":"KrCh"}],"title":"POMDPs under probabilistic semantics","date_updated":"2021-01-12T06:53:46Z","citation":{"mla":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence, vol. 221, Elsevier, 2015, pp. 46–72, doi:10.1016/j.artint.2014.12.009.","apa":"Chatterjee, K., & Chmelik, M. (2015). POMDPs under probabilistic semantics. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2014.12.009","ama":"Chatterjee K, Chmelik M. POMDPs under probabilistic semantics. Artificial Intelligence. 2015;221:46-72. doi:10.1016/j.artint.2014.12.009","ieee":"K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” Artificial Intelligence, vol. 221. Elsevier, pp. 46–72, 2015.","short":"K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72.","chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence. Elsevier, 2015. https://doi.org/10.1016/j.artint.2014.12.009.","ista":"Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial Intelligence. 221, 46–72."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","scopus_import":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1408.2058","open_access":"1"}],"month":"04","intvolume":" 221","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with limit-average payoff, where a reward value in the interval [0,1] is associated with every transition, and the payoff of an infinite path is the long-run average of the rewards. We consider two types of path constraints: (i) a quantitative constraint defines the set of paths where the payoff is at least a given threshold λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative constraint with λ1=1. We consider the computation of the almost-sure winning set, where the controller needs to ensure that the path constraint is satisfied with probability 1. Our main results for qualitative path constraints are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative path constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We also present a prototype implementation of our EXPTIME algorithm and experimental results on several examples.","lang":"eng"}],"oa_version":"Preprint","page":"46 - 72","date_published":"2015-04-01T00:00:00Z","doi":"10.1016/j.artint.2014.12.009","volume":221,"date_created":"2018-12-11T11:54:28Z","publication_status":"published","year":"2015","day":"01","language":[{"iso":"eng"}],"publication":"Artificial Intelligence"},{"volume":259,"issue":"2","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf","date_created":"2018-12-12T10:11:19Z","creator":"system","file_size":2899898,"date_updated":"2020-07-14T12:45:19Z","file_id":"4872","checksum":"3649c5372d1644062d728ea9287e367f","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","intvolume":" 259","month":"08","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions."}],"file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"JiFr"}],"ddc":["570"],"date_updated":"2021-01-12T06:53:48Z","pubrep_id":"459","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1879","date_created":"2018-12-11T11:54:30Z","date_published":"2015-08-01T00:00:00Z","doi":"10.1111/jmi.12211","page":"80 - 96","publication":"Journal of Microscopy","day":"01","year":"2015","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","acknowledgement":"The Zeiss Merlin with Gatan 3View2XP and Zeiss Auriga were acquired through a CLEM grant from Minister Ingrid Lieten to the VIB Bio-Imaging-Core. Michiel Krols and Saskia Lippens are the recipients of a fellowship from the FWO (Fonds Wetenschappelijk Onderzoek) of Flanders.","title":"Developing 3D SEM in a broad biological context","publist_id":"5218","author":[{"first_name":"A","full_name":"Kremer, A","last_name":"Kremer"},{"first_name":"Stefaan","last_name":"Lippens","full_name":"Lippens, Stefaan"},{"first_name":"Sonia","full_name":"Bartunkova, Sonia","last_name":"Bartunkova"},{"first_name":"Bob","last_name":"Asselbergh","full_name":"Asselbergh, Bob"},{"first_name":"Cendric","full_name":"Blanpain, Cendric","last_name":"Blanpain"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699"},{"last_name":"Goossens","full_name":"Goossens, A","first_name":"A"},{"last_name":"Holt","full_name":"Holt, Matthew","first_name":"Matthew"},{"last_name":"Janssens","full_name":"Janssens, Sophie","first_name":"Sophie"},{"last_name":"Krols","full_name":"Krols, Michiel","first_name":"Michiel"},{"last_name":"Larsimont","full_name":"Larsimont, Jean","first_name":"Jean"},{"first_name":"Conor","full_name":"Mc Guire, Conor","last_name":"Mc Guire"},{"first_name":"Moritz","full_name":"Nowack, Moritz","last_name":"Nowack"},{"first_name":"Xavier","full_name":"Saelens, Xavier","last_name":"Saelens"},{"first_name":"Andreas","last_name":"Schertel","full_name":"Schertel, Andreas"},{"full_name":"Schepens, B","last_name":"Schepens","first_name":"B"},{"full_name":"Slezak, M","last_name":"Slezak","first_name":"M"},{"first_name":"Vincent","full_name":"Timmerman, Vincent","last_name":"Timmerman"},{"full_name":"Theunis, Clara","last_name":"Theunis","first_name":"Clara"},{"full_name":"Van Brempt, Ronald","last_name":"Van Brempt","first_name":"Ronald"},{"full_name":"Visser, Y","last_name":"Visser","first_name":"Y"},{"first_name":"Christophe","last_name":"Guérin","full_name":"Guérin, Christophe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kremer, A., et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy, vol. 259, no. 2, Wiley-Blackwell, 2015, pp. 80–96, doi:10.1111/jmi.12211.","short":"A. Kremer, S. Lippens, S. Bartunkova, B. Asselbergh, C. Blanpain, M. Fendrych, A. Goossens, M. Holt, S. Janssens, M. Krols, J. Larsimont, C. Mc Guire, M. Nowack, X. Saelens, A. Schertel, B. Schepens, M. Slezak, V. Timmerman, C. Theunis, R. Van Brempt, Y. Visser, C. Guérin, Journal of Microscopy 259 (2015) 80–96.","ieee":"A. Kremer et al., “Developing 3D SEM in a broad biological context,” Journal of Microscopy, vol. 259, no. 2. Wiley-Blackwell, pp. 80–96, 2015.","apa":"Kremer, A., Lippens, S., Bartunkova, S., Asselbergh, B., Blanpain, C., Fendrych, M., … Guérin, C. (2015). Developing 3D SEM in a broad biological context. Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/jmi.12211","ama":"Kremer A, Lippens S, Bartunkova S, et al. Developing 3D SEM in a broad biological context. Journal of Microscopy. 2015;259(2):80-96. doi:10.1111/jmi.12211","chicago":"Kremer, A, Stefaan Lippens, Sonia Bartunkova, Bob Asselbergh, Cendric Blanpain, Matyas Fendrych, A Goossens, et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy. Wiley-Blackwell, 2015. https://doi.org/10.1111/jmi.12211.","ista":"Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont J, Mc Guire C, Nowack M, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, Van Brempt R, Visser Y, Guérin C. 2015. Developing 3D SEM in a broad biological context. Journal of Microscopy. 259(2), 80–96."}},{"author":[{"first_name":"Martin","full_name":"Könenberg, Martin","last_name":"Könenberg"},{"last_name":"Moser","full_name":"Moser, Thomas","first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yngvason, Jakob","last_name":"Yngvason","first_name":"Jakob"}],"publist_id":"5214","title":"Superfluid behavior of a Bose-Einstein condensate in a random potential","citation":{"mla":"Könenberg, Martin, et al. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics, vol. 17, 013022, IOP Publishing Ltd., 2015, doi:10.1088/1367-2630/17/1/013022.","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics 17 (2015).","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluid behavior of a Bose-Einstein condensate in a random potential,” New Journal of Physics, vol. 17. IOP Publishing Ltd., 2015.","apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2015). Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/1/013022","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 2015;17. doi:10.1088/1367-2630/17/1/013022","chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/1/013022.","ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2015. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 17, 013022."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"article_number":"013022","date_published":"2015-01-15T00:00:00Z","doi":"10.1088/1367-2630/17/1/013022","date_created":"2018-12-11T11:54:30Z","has_accepted_license":"1","year":"2015","day":"15","publication":"New Journal of Physics","quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1,"acknowledgement":"Support from the Natural Sciences and Engineering Research Council of Canada NSERC (MK and RS) and from the Austrian Science Fund FWF (JY, under project P 22929-N16) is gratefully acknowledged","file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:53:48Z","ddc":["530"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"447","_id":"1880","volume":17,"publication_status":"published","file":[{"creator":"system","file_size":768108,"date_updated":"2020-07-14T12:45:20Z","file_name":"IST-2016-447-v1+1_document_1_.pdf","date_created":"2018-12-12T10:12:44Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4963","checksum":"38fdf2b5ac30445e26a5d613abd84b16"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"01","intvolume":" 17","abstract":[{"text":"We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity in the ground state of a one-dimensional model of interacting bosons in a strong random potential. We prove rigorously that in a certain parameter regime the superfluid fraction can be arbitrarily small while complete BEC prevails. In another regime there is both complete BEC and complete superfluidity, despite the strong disorder","lang":"eng"}],"oa_version":"Published Version"},{"scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"http://arxiv.org/abs/1408.1256","open_access":"1"}],"month":"01","intvolume":" 8997","abstract":[{"lang":"eng","text":"We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations."}],"oa_version":"Preprint","volume":8997,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"location":"Bertinoro, Italy","end_date":"2014-09-12","start_date":"2014-09-10","name":"FACS: Formal Aspects of Component Software"},"status":"public","_id":"1882","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2021-01-12T06:53:49Z","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) project S11402-N23 (RiSE), and by the Czech Science Foundation, grant No. P202/12/G061.","page":"306 - 324","doi":"10.1007/978-3-319-15317-9_19","date_published":"2015-01-30T00:00:00Z","date_created":"2018-12-11T11:54:31Z","year":"2015","day":"30","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"publist_id":"5216","author":[{"first_name":"Uli","last_name":"Fahrenberg","full_name":"Fahrenberg, Uli"},{"last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Axel","last_name":"Legay","full_name":"Legay, Axel"},{"first_name":"Louis","last_name":"Traonouez","full_name":"Traonouez, Louis"}],"title":"Compositionality for quantitative specifications","citation":{"ista":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. 2015. Compositionality for quantitative specifications. FACS: Formal Aspects of Component Software, LNCS, vol. 8997, 306–324.","chicago":"Fahrenberg, Uli, Jan Kretinsky, Axel Legay, and Louis Traonouez. “Compositionality for Quantitative Specifications,” 8997:306–24. Springer, 2015. https://doi.org/10.1007/978-3-319-15317-9_19.","apa":"Fahrenberg, U., Kretinsky, J., Legay, A., & Traonouez, L. (2015). Compositionality for quantitative specifications (Vol. 8997, pp. 306–324). Presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy: Springer. https://doi.org/10.1007/978-3-319-15317-9_19","ama":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. Compositionality for quantitative specifications. In: Vol 8997. Springer; 2015:306-324. doi:10.1007/978-3-319-15317-9_19","short":"U. Fahrenberg, J. Kretinsky, A. Legay, L. Traonouez, in:, Springer, 2015, pp. 306–324.","ieee":"U. Fahrenberg, J. Kretinsky, A. Legay, and L. Traonouez, “Compositionality for quantitative specifications,” presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy, 2015, vol. 8997, pp. 306–324.","mla":"Fahrenberg, Uli, et al. Compositionality for Quantitative Specifications. Vol. 8997, Springer, 2015, pp. 306–24, doi:10.1007/978-3-319-15317-9_19."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"issue":"2","volume":91,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 91","month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1012.3298","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n","lang":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:53:49Z","status":"public","article_type":"original","type":"journal_article","_id":"1883","date_created":"2018-12-11T11:54:31Z","date_published":"2015-02-02T00:00:00Z","doi":"10.1103/PhysRevE.91.022803","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","day":"02","year":"2015","oa":1,"quality_controlled":"1","publisher":"American Institute of Physics","title":"Anomalous scaling in an age-dependent branching model","article_processing_charge":"No","external_id":{"arxiv":["1012.3298"]},"author":[{"first_name":"Stephanie","full_name":"Keller-Schmidt, Stephanie","last_name":"Keller-Schmidt"},{"orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat"},{"last_name":"Eguíluz","full_name":"Eguíluz, Víctor","first_name":"Víctor"},{"last_name":"Hernandez Garcia","full_name":"Hernandez Garcia, Emilio","first_name":"Emilio"},{"full_name":"Klemm, Konstantin","last_name":"Klemm","first_name":"Konstantin"}],"publist_id":"5213","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(2), 022803.","chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803.","ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute of Physics, 2015.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.022803","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803","mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803."},"article_number":"022803"},{"oa_version":"None","abstract":[{"text":"Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian Peninsula, with some localized populations in the French Pyrenees. Within the genus, a dozen species have been recognized based on morphological diversity, most of them with limited distribution area, in small populations and frequently with potential threats to their survival. To date, however, a molecular evaluation of the current systematic treatments has not been carried out. The aim of the present study is to infer phylogenetic relationships among its subordinate taxa by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS) DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by both ITS and rps16 intron sequence analyses. Furthermore, time estimates using BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26 Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD, for rps16 intron).","lang":"eng"}],"month":"01","intvolume":" 128","quality_controlled":"1","publisher":"Springer","scopus_import":1,"day":"24","language":[{"iso":"eng"}],"publication":"Journal of Plant Research","publication_status":"published","year":"2015","doi":"10.1007/s10265-014-0691-6","volume":128,"issue":"2","date_published":"2015-01-24T00:00:00Z","date_created":"2018-12-11T11:54:30Z","page":"223 - 238","_id":"1878","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research. Springer, 2015. https://doi.org/10.1007/s10265-014-0691-6.","ista":"Cires Rodriguez E, Prieto J. 2015. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 128(2), 223–238.","mla":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research, vol. 128, no. 2, Springer, 2015, pp. 223–38, doi:10.1007/s10265-014-0691-6.","short":"E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.","ieee":"E. Cires Rodriguez and J. Prieto, “Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula,” Journal of Plant Research, vol. 128, no. 2. Springer, pp. 223–238, 2015.","apa":"Cires Rodriguez, E., & Prieto, J. (2015). Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. Springer. https://doi.org/10.1007/s10265-014-0691-6","ama":"Cires Rodriguez E, Prieto J. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 2015;128(2):223-238. doi:10.1007/s10265-014-0691-6"},"date_updated":"2021-01-12T06:53:47Z","title":"Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula","department":[{"_id":"JiFr"}],"publist_id":"5217","author":[{"full_name":"Cires Rodriguez, Eduardo","last_name":"Cires Rodriguez","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Eduardo"},{"full_name":"Prieto, José","last_name":"Prieto","first_name":"José"}]},{"quality_controlled":"1","publisher":"Genetics Society of America","scopus_import":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1404.5599","open_access":"1"}],"month":"01","intvolume":" 199","abstract":[{"text":"The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail. ","lang":"eng"}],"oa_version":"Preprint","page":"39 - 59","date_published":"2015-01-01T00:00:00Z","doi":"10.1534/genetics.114.171850","volume":199,"issue":"1","date_created":"2018-12-11T11:54:32Z","publication_status":"published","year":"2015","day":"01","publication":"Genetics","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1885","author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"first_name":"Julien","full_name":"Dubuis, Julien","last_name":"Dubuis"},{"first_name":"Mariela","last_name":"Petkova","full_name":"Petkova, Mariela"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"}],"publist_id":"5210","department":[{"_id":"GaTk"}],"title":"Positional information, positional error, and readout precision in morphogenesis: A mathematical framework","citation":{"mla":"Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.","ama":"Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 2015;199(1):39-59. doi:10.1534/genetics.114.171850","apa":"Tkačik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.114.171850","ieee":"G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.","short":"G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.","chicago":"Tkačik, Gašper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/10.1534/genetics.114.171850.","ista":"Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 199(1), 39–59."},"date_updated":"2021-01-12T06:53:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:13Z","citation":{"chicago":"Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710.","ista":"Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710.","mla":"Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.062710.","ama":"Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710","apa":"Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710","short":"T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","ieee":"T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015."},"title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","department":[{"_id":"GaTk"}],"publist_id":"5145","author":[{"full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"article_number":"062710","_id":"1940","status":"public","type":"journal_article","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","language":[{"iso":"eng"}],"day":"15","year":"2015","publication_status":"published","date_created":"2018-12-11T11:54:49Z","volume":91,"issue":"6","doi":"10.1103/PhysRevE.91.062710","date_published":"2015-06-15T00:00:00Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models."}],"intvolume":" 91","month":"06","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1501.04015","open_access":"1"}],"publisher":"American Institute of Physics","quality_controlled":"1","scopus_import":1},{"author":[{"last_name":"Pausinger","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"full_name":"Steinerberger, Stefan","last_name":"Steinerberger","first_name":"Stefan"}],"publist_id":"5152","title":"On the distribution of local extrema in quantum chaos","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:54:12Z","citation":{"chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” Physics Letters, Section A. Elsevier, 2015. https://doi.org/10.1016/j.physleta.2014.12.010.","ista":"Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 379(6), 535–541.","mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” Physics Letters, Section A, vol. 379, no. 6, Elsevier, 2015, pp. 535–41, doi:10.1016/j.physleta.2014.12.010.","ieee":"F. Pausinger and S. Steinerberger, “On the distribution of local extrema in quantum chaos,” Physics Letters, Section A, vol. 379, no. 6. Elsevier, pp. 535–541, 2015.","short":"F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.","ama":"Pausinger F, Steinerberger S. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 2015;379(6):535-541. doi:10.1016/j.physleta.2014.12.010","apa":"Pausinger, F., & Steinerberger, S. (2015). On the distribution of local extrema in quantum chaos. Physics Letters, Section A. Elsevier. https://doi.org/10.1016/j.physleta.2014.12.010"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1938","page":"535 - 541","date_published":"2015-03-06T00:00:00Z","issue":"6","volume":379,"doi":"10.1016/j.physleta.2014.12.010","date_created":"2018-12-11T11:54:49Z","publication_status":"published","year":"2015","day":"06","publication":"Physics Letters, Section A","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","month":"03","intvolume":" 379","abstract":[{"text":"We numerically investigate the distribution of extrema of 'chaotic' Laplacian eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a) we count extrema on grid graphs with a small number of randomly added edges and show the behavior to coincide with the 1957 prediction of Longuet-Higgins for the continuous case and (b) we compute the regularity of their spatial distribution using discrepancy, which is a classical measure from the theory of Monte Carlo integration. The first part suggests that grid graphs with randomly added edges should behave like two-dimensional surfaces with ergodic geodesic flow; in the second part we show that the extrema are more regularly distributed in space than the grid Z2.","lang":"eng"}],"oa_version":"None","acknowledgement":"F.P. was supported by the Graduate School of IST Austria. S.S. was partially supported by CRC1060 of the DFG\r\nThe authors thank Olga Symonova and Michael Kerber for sharing their implementation of the persistence algorithm. "},{"department":[{"_id":"JiFr"}],"title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants","publist_id":"5140","author":[{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:15Z","citation":{"ista":"Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 23(2), 116–123.","chicago":"Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology. Elsevier, 2015. https://doi.org/10.1016/j.pbi.2014.12.002.","ieee":"H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants,” Current Opinion in Plant Biology, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.","short":"H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 116–123.","ama":"Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 2015;23(2):116-123. doi:10.1016/j.pbi.2014.12.002","apa":"Rakusová, H., Fendrych, M., & Friml, J. (2015). Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2014.12.002","mla":"Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology, vol. 23, no. 2, Elsevier, 2015, pp. 116–23, doi:10.1016/j.pbi.2014.12.002."},"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"status":"public","type":"journal_article","_id":"1944","date_created":"2018-12-11T11:54:51Z","ec_funded":1,"doi":"10.1016/j.pbi.2014.12.002","volume":23,"date_published":"2015-02-01T00:00:00Z","issue":"2","page":"116 - 123","language":[{"iso":"eng"}],"publication":"Current Opinion in Plant Biology","day":"01","year":"2015","publication_status":"published","intvolume":" 23","month":"02","quality_controlled":"1","publisher":"Elsevier","scopus_import":1,"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology (IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions) of the European Union","oa_version":"None"},{"citation":{"apa":"Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach, T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008","ama":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008","ieee":"A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct representation of concurrent trace sets,” presented at the POPL: Principles of Programming Languages, Mumbai, India, 2015, pp. 433–444.","short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","mla":"Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets. ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.","ista":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct representation of concurrent trace sets. POPL: Principles of Programming Languages, 433–444.","chicago":"Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta, and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44. ACM, 2015. https://doi.org/10.1145/2676726.2677008."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"},{"last_name":"Samanta","full_name":"Samanta, Roopsha","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten","full_name":"Tarrach, Thorsten","orcid":"0000-0003-4409-8487","last_name":"Tarrach"}],"publist_id":"5091","title":"Succinct representation of concurrent trace sets","publisher":"ACM","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"15","page":"433 - 444","doi":"10.1145/2676726.2677008","date_published":"2015-01-15T00:00:00Z","date_created":"2018-12-11T11:55:05Z","_id":"1992","type":"conference","conference":{"end_date":"2015-01-17","location":"Mumbai, India","start_date":"2015-01-15","name":"POPL: Principles of Programming Languages"},"status":"public","pubrep_id":"317","date_updated":"2021-01-12T06:54:33Z","ddc":["005"],"file_date_updated":"2020-07-14T12:45:22Z","department":[{"_id":"ToHe"}],"abstract":[{"text":"We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings.\r\n\r\nWe claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"01","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"publication_status":"published","file":[{"file_name":"IST-2015-317-v1+1_author_version.pdf","date_created":"2018-12-12T10:17:56Z","creator":"system","file_size":399462,"date_updated":"2020-07-14T12:45:22Z","checksum":"f0d4395b600f410a191256ac0b73af32","file_id":"5314","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}]},{"oa_version":"Preprint","abstract":[{"text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials.","lang":"eng"}],"month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.0077"}],"scopus_import":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Journal of Symbolic Computation","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015","date_created":"2018-12-11T11:55:07Z","issue":"May-June","doi":"10.1016/j.jsc.2014.09.014","volume":"68/Part 2","date_published":"2015-05-01T00:00:00Z","page":"285 - 296","_id":"1997","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:35Z","citation":{"mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:10.1016/j.jsc.2014.09.014.","apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2014.09.014","ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 2015;68/Part 2(May-June):285-296. doi:10.1016/j.jsc.2014.09.014","ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” Journal of Symbolic Computation. Elsevier, 2015. https://doi.org/10.1016/j.jsc.2014.09.014.","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296."},"department":[{"_id":"CaUh"}],"title":"The three-state toric homogeneous Markov chain model has Markov degree two","author":[{"first_name":"Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87","last_name":"Noren","full_name":"Noren, Patrik"}],"publist_id":"5082"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139.","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139","apa":"Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:10.1111/sjos.12139."},"title":"Iterative scaling in curved exponential families","author":[{"full_name":"Klimova, Anna","last_name":"Klimova","first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tamás","full_name":"Rudas, Tamás","last_name":"Rudas"}],"publist_id":"5068","day":"01","publication":"Scandinavian Journal of Statistics","year":"2015","date_published":"2015-09-01T00:00:00Z","doi":"10.1111/sjos.12139","date_created":"2018-12-11T11:55:11Z","page":"832 - 847","acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","publisher":"Wiley","quality_controlled":"1","oa":1,"date_updated":"2021-01-12T06:54:41Z","department":[{"_id":"CaUh"}],"_id":"2008","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":42,"issue":"3","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package."}],"month":"09","intvolume":" 42","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3282"}]},{"department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:40Z","type":"journal_article","status":"public","_id":"2006","issue":"3","volume":24,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1109.3436","open_access":"1"}],"scopus_import":1,"intvolume":" 24","month":"06","abstract":[{"lang":"eng","text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. "}],"oa_version":"Preprint","article_processing_charge":"No","publist_id":"5070","author":[{"last_name":"Hein","full_name":"Hein, Nicolas","first_name":"Nicolas"},{"last_name":"Hillar","full_name":"Hillar, Christopher","first_name":"Christopher"},{"full_name":"Martin Del Campo Sanchez, Abraham","last_name":"Martin Del Campo Sanchez","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","first_name":"Abraham"},{"full_name":"Sottile, Frank","last_name":"Sottile","first_name":"Frank"},{"first_name":"Zach","full_name":"Teitler, Zach","last_name":"Teitler"}],"title":"The monotone secant conjecture in the real Schubert calculus","citation":{"ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.","ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 2015;24(3):261-269. doi:10.1080/10586458.2014.980044","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044","ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” Experimental Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis, 2015, pp. 261–69, doi:10.1080/10586458.2014.980044."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"261 - 269","date_created":"2018-12-11T11:55:10Z","date_published":"2015-06-23T00:00:00Z","doi":"10.1080/10586458.2014.980044","year":"2015","publication":"Experimental Mathematics","day":"23","oa":1,"publisher":"Taylor & Francis","quality_controlled":"1"},{"month":"07","intvolume":" 87","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.6617"}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association."}],"issue":"7","doi":"10.1016/j.csda.2015.01.017","volume":87,"date_published":"2015-07-01T00:00:00Z","date_created":"2018-12-11T11:55:13Z","page":"57 - 72","day":"01","language":[{"iso":"eng"}],"publication":"Computational Statistics & Data Analysis","publication_status":"published","year":"2015","status":"public","type":"journal_article","_id":"2014","title":"Faithfulness and learning hypergraphs from discrete distributions","department":[{"_id":"CaUh"}],"author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova","full_name":"Klimova, Anna"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"publist_id":"5062","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis 87 (2015) 57–72.","ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” Computational Statistics & Data Analysis, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 2015;87(7):57-72. doi:10.1016/j.csda.2015.01.017","apa":"Klimova, A., Uhler, C., & Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. Elsevier. https://doi.org/10.1016/j.csda.2015.01.017","mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:10.1016/j.csda.2015.01.017.","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72.","chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis. Elsevier, 2015. https://doi.org/10.1016/j.csda.2015.01.017."},"date_updated":"2021-01-12T06:54:43Z"},{"ddc":["570"],"date_updated":"2021-01-12T06:54:48Z","file_date_updated":"2020-07-14T12:45:25Z","department":[{"_id":"DaSi"}],"_id":"2025","pubrep_id":"615","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4936","checksum":"5bb328edebb6a91337cadd7d63f961b7","file_size":926685,"date_updated":"2020-07-14T12:45:25Z","creator":"system","file_name":"IST-2016-615-v1+1_BBAMCR.pdf","date_created":"2018-12-12T10:12:18Z"}],"publication_status":"published","issue":"1","volume":1853,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins."}],"intvolume":" 1853","month":"01","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2014.10.009.","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156.","mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:10.1016/j.bbamcr.2014.10.009.","ieee":"D. Kawada et al., “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.","short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156.","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2014.10.009","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(1):144-156. doi:10.1016/j.bbamcr.2014.10.009"},"title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","publist_id":"5047","author":[{"last_name":"Kawada","full_name":"Kawada, Daiki","first_name":"Daiki"},{"first_name":"Hiromu","full_name":"Kobayashi, Hiromu","last_name":"Kobayashi"},{"full_name":"Tomita, Tsuyoshi","last_name":"Tomita","first_name":"Tsuyoshi"},{"last_name":"Nakata","full_name":"Nakata, Eisuke","first_name":"Eisuke"},{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"first_name":"Jiro","last_name":"Toshimaa","full_name":"Toshimaa, Jiro"}],"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:55:17Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1016/j.bbamcr.2014.10.009","page":"144 - 156","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"year":"2015","publication_status":"published","publication":"Computers and Fluids","language":[{"iso":"eng"}],"day":"01","page":"1 - 11","date_created":"2018-12-11T11:55:18Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1016/j.compfluid.2014.09.021","volume":106,"issue":"1","abstract":[{"lang":"eng","text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes."}],"oa_version":"Preprint","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1311.2481","open_access":"1"}],"scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","intvolume":" 106","month":"01","citation":{"chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids. Elsevier, 2015. https://doi.org/10.1016/j.compfluid.2014.09.021.","ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11.","mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:10.1016/j.compfluid.2014.09.021.","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.","ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” Computers and Fluids, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","apa":"Shi, L., Rampp, M., Hof, B., & Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. Elsevier. https://doi.org/10.1016/j.compfluid.2014.09.021","ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 2015;106(1):1-11. doi:10.1016/j.compfluid.2014.09.021"},"date_updated":"2021-01-12T06:54:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Shi, Liang","last_name":"Shi","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang"},{"first_name":"Markus","last_name":"Rampp","full_name":"Rampp, Markus"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"}],"publist_id":"5042","title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","department":[{"_id":"BjHo"}],"_id":"2030","type":"journal_article","status":"public"}]