[{"title":"Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model","volume":28,"type":"journal_article","status":"public","publisher":"IOP Publishing Ltd.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","quality_controlled":"1","publication_status":"published","issue":"17","citation":{"apa":"Tomski, A., & Kaczmarczyk, J. (2016). Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/0953-8984/28/17/175701","short":"A. Tomski, J. Kaczmarczyk, Journal of Physics: Condensed Matter 28 (2016).","ieee":"A. Tomski and J. Kaczmarczyk, “Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model,” Journal of Physics: Condensed Matter, vol. 28, no. 17. IOP Publishing Ltd., 2016.","mla":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter, vol. 28, no. 17, 175701, IOP Publishing Ltd., 2016, doi:10.1088/0953-8984/28/17/175701.","chicago":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter. IOP Publishing Ltd., 2016. https://doi.org/10.1088/0953-8984/28/17/175701.","ista":"Tomski A, Kaczmarczyk J. 2016. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 28(17), 175701.","ama":"Tomski A, Kaczmarczyk J. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 2016;28(17). doi:10.1088/0953-8984/28/17/175701"},"date_created":"2018-12-11T11:51:55Z","publist_id":"5788","ec_funded":1,"author":[{"full_name":"Tomski, Andrzej","first_name":"Andrzej","last_name":"Tomski"},{"full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kaczmarczyk"}],"publication":"Journal of Physics: Condensed Matter","doi":"10.1088/0953-8984/28/17/175701","language":[{"iso":"eng"}],"intvolume":" 28","day":"29","scopus_import":1,"year":"2016","date_updated":"2021-01-12T06:50:36Z","date_published":"2016-03-29T00:00:00Z","month":"03","article_number":"175701","abstract":[{"lang":"eng","text":"We study the superconducting phase of the Hubbard model using the Gutzwiller variational wave function (GWF) and the recently proposed diagrammatic expansion technique (DE-GWF). The DE-GWF method works on the level of the full GWF and in the thermodynamic limit. Here, we consider a finite-size system to study the accuracy of the results as a function of the system size (which is practically unrestricted). We show that the finite-size scaling used, e.g. in the variational Monte Carlo method can lead to significant, uncontrolled errors. The presented research is the first step towards applying the DE-GWF method in studies of inhomogeneous situations, including systems with impurities, defects, inhomogeneous phases, or disorder."}],"department":[{"_id":"MiLe"}],"_id":"1419","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"date_updated":"2021-01-12T06:50:39Z","year":"2016","day":"01","_id":"1427","department":[{"_id":"CaGu"},{"_id":"JoBo"}],"month":"03","date_published":"2016-03-01T00:00:00Z","citation":{"mla":"Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269.","chicago":"Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msv269.","ista":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. 2016. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 33(3), 761–769.","ama":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269","short":"M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769.","apa":"Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv269","ieee":"M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016."},"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)"},"publication_status":"published","pubrep_id":"588","status":"public","type":"journal_article","volume":33,"language":[{"iso":"eng"}],"intvolume":" 33","doi":"10.1093/molbev/msv269","publication":"Molecular Biology and Evolution","author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato"},{"last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","full_name":"Igler, Claudia"},{"full_name":"Moreno, Anaisa","first_name":"Anaisa","last_name":"Moreno"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"}],"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5772","scopus_import":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"file":[{"file_id":"4751","content_type":"application/pdf","file_name":"IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf","date_created":"2018-12-12T10:09:27Z","creator":"system","checksum":"1f456ce1d2aa2f67176a1709f9702ecf","date_updated":"2020-07-14T12:44:53Z","relation":"main_file","access_level":"open_access","file_size":648115}],"page":"761 - 769","abstract":[{"text":"Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner.","lang":"eng"}],"has_accepted_license":"1","issue":"3","quality_controlled":"1","oa_version":"Published Version","publisher":"Oxford University Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Epistatic interactions in the arabinose cis-regulatory element","oa":1,"ddc":["570","576"],"ec_funded":1,"date_created":"2018-12-11T11:51:57Z"},{"file_date_updated":"2020-07-14T12:44:53Z","author":[{"full_name":"Könenberg, Martin","last_name":"Könenberg","first_name":"Martin"},{"last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Moser, Thomas"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"},{"full_name":"Yngvason, Jakob","last_name":"Yngvason","first_name":"Jakob"}],"publist_id":"5770","intvolume":" 691","language":[{"iso":"eng"}],"publication":"Journal of Physics: Conference Series","doi":"10.1088/1742-6596/691/1/012016","conference":{"name":"24th International Laser Physics Workshop (LPHYS'15)","location":"Shanghai, China","start_date":"2015-08-21","end_date":"2015-08-25"},"publication_status":"published","pubrep_id":"585","volume":691,"type":"conference","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)"},"citation":{"ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential,” in Journal of Physics: Conference Series, Shanghai, China, 2016, vol. 691, no. 1.","apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2016). Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In Journal of Physics: Conference Series (Vol. 691). Shanghai, China: IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/691/1/012016","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, in:, Journal of Physics: Conference Series, IOP Publishing Ltd., 2016.","ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2016. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. Journal of Physics: Conference Series. 24th International Laser Physics Workshop (LPHYS’15) vol. 691, 012016.","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In: Journal of Physics: Conference Series. Vol 691. IOP Publishing Ltd.; 2016. doi:10.1088/1742-6596/691/1/012016","mla":"Könenberg, Martin, et al. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” Journal of Physics: Conference Series, vol. 691, no. 1, 012016, IOP Publishing Ltd., 2016, doi:10.1088/1742-6596/691/1/012016.","chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” In Journal of Physics: Conference Series, Vol. 691. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1742-6596/691/1/012016."},"article_number":"012016","date_published":"2016-03-07T00:00:00Z","month":"03","department":[{"_id":"RoSe"}],"_id":"1428","day":"07","date_updated":"2021-01-12T06:50:40Z","year":"2016","date_created":"2018-12-11T11:51:58Z","ddc":["510","530"],"oa":1,"oa_version":"Published Version","quality_controlled":"1","title":"Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential","publisher":"IOP Publishing Ltd.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"1","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"file":[{"file_name":"IST-2016-585-v1+1_JPCS_691_1_012016.pdf","date_created":"2018-12-12T10:10:55Z","content_type":"application/pdf","file_id":"4847","access_level":"open_access","relation":"main_file","file_size":1434688,"creator":"system","checksum":"109db801749072c3f6c8f1a1848700fa","date_updated":"2020-07-14T12:44:53Z"}],"abstract":[{"text":"We report on a mathematically rigorous analysis of the superfluid properties of a Bose- Einstein condensate in the many-body ground state of a one-dimensional model of interacting bosons in a random potential.","lang":"eng"}],"has_accepted_license":"1","scopus_import":1},{"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)"},"citation":{"ieee":"M. Chakra, C. Hilbe, and A. Traulsen, “Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites,” Royal Society Open Science, vol. 3, no. 5. Royal Society, The, 2016.","short":"M. Chakra, C. Hilbe, A. Traulsen, Royal Society Open Science 3 (2016).","apa":"Chakra, M., Hilbe, C., & Traulsen, A. (2016). Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.160036","ista":"Chakra M, Hilbe C, Traulsen A. 2016. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 3(5), 160036.","ama":"Chakra M, Hilbe C, Traulsen A. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 2016;3(5). doi:10.1098/rsos.160036","mla":"Chakra, Maria, et al. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science, vol. 3, no. 5, 160036, Royal Society, The, 2016, doi:10.1098/rsos.160036.","chicago":"Chakra, Maria, Christian Hilbe, and Arne Traulsen. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science. Royal Society, The, 2016. https://doi.org/10.1098/rsos.160036."},"volume":3,"type":"journal_article","status":"public","publication_status":"published","pubrep_id":"589","publication":"Royal Society Open Science","acknowledgement":"C.H. gratefully acknowledges funding by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","doi":"10.1098/rsos.160036","intvolume":" 3","language":[{"iso":"eng"}],"publist_id":"5776","file_date_updated":"2020-07-14T12:44:53Z","author":[{"full_name":"Chakra, Maria","last_name":"Chakra","first_name":"Maria"},{"last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"last_name":"Traulsen","first_name":"Arne","full_name":"Traulsen, Arne"}],"year":"2016","date_updated":"2021-01-12T06:50:39Z","day":"01","department":[{"_id":"KrCh"}],"_id":"1426","date_published":"2016-05-01T00:00:00Z","month":"05","article_number":"160036","issue":"5","title":"Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society, The","quality_controlled":"1","oa_version":"Published Version","ddc":["000"],"oa":1,"date_created":"2018-12-11T11:51:57Z","scopus_import":1,"abstract":[{"text":"Brood parasites exploit their host in order to increase their own fitness. Typically, this results in an arms race between parasite trickery and host defence. Thus, it is puzzling to observe hosts that accept parasitism without any resistance. The ‘mafia’ hypothesis suggests that these hosts accept parasitism to avoid retaliation. Retaliation has been shown to evolve when the hosts condition their response to mafia parasites, who use depredation as a targeted response to rejection. However, it is unclear if acceptance would also emerge when ‘farming’ parasites are present in the population. Farming parasites use depredation to synchronize the timing with the host, destroying mature clutches to force the host to re-nest. Herein, we develop an evolutionary model to analyse the interaction between depredatory parasites and their hosts. We show that coevolutionary cycles between farmers and mafia can still induce host acceptance of brood parasites. However, this equilibrium is unstable and in the long-run the dynamics of this host–parasite interaction exhibits strong oscillations: when farmers are the majority, accepters conditional to mafia (the host will reject first and only accept after retaliation by the parasite) have a higher fitness than unconditional accepters (the host always accepts parasitism). This leads to an increase in mafia parasites’ fitness and in turn induce an optimal environment for accepter hosts.","lang":"eng"}],"file":[{"file_name":"IST-2016-589-v1+1_160036.full.pdf","date_created":"2018-12-12T10:14:49Z","file_id":"5104","content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","checksum":"bf84211b31fe87451e738ba301d729c3","creator":"system","file_size":937002,"relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1"},{"intvolume":" 6","language":[{"iso":"eng"}],"publication":"Scientific Reports","doi":"10.1038/srep25676","acknowledgement":"C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475.","file_date_updated":"2020-07-14T12:44:53Z","author":[{"first_name":"Seung","last_name":"Baek","full_name":"Baek, Seung"},{"full_name":"Jeong, Hyeongchai","first_name":"Hyeongchai","last_name":"Jeong"},{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"publist_id":"5784","citation":{"mla":"Baek, Seung, et al. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports, vol. 6, 25676, Nature Publishing Group, 2016, doi:10.1038/srep25676.","chicago":"Baek, Seung, Hyeongchai Jeong, Christian Hilbe, and Martin Nowak. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep25676.","ama":"Baek S, Jeong H, Hilbe C, Nowak M. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 2016;6. doi:10.1038/srep25676","ista":"Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 6, 25676.","apa":"Baek, S., Jeong, H., Hilbe, C., & Nowak, M. (2016). Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep25676","short":"S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).","ieee":"S. Baek, H. Jeong, C. Hilbe, and M. Nowak, “Comparing reactive and memory-one strategies of direct reciprocity,” Scientific Reports, vol. 6. Nature Publishing Group, 2016."},"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)"},"pubrep_id":"590","publication_status":"published","type":"journal_article","volume":6,"status":"public","department":[{"_id":"KrCh"}],"_id":"1423","article_number":"25676","date_published":"2016-05-10T00:00:00Z","month":"05","date_updated":"2021-01-12T06:50:38Z","year":"2016","day":"10","ddc":["000"],"oa":1,"date_created":"2018-12-11T11:51:56Z","quality_controlled":"1","oa_version":"Published Version","title":"Comparing reactive and memory-one strategies of direct reciprocity","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","abstract":[{"text":"Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player's previous move, and memory-one strategies, which take into account the own and the co-player's previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation.","lang":"eng"}],"file":[{"date_created":"2018-12-12T10:18:08Z","file_name":"IST-2016-590-v1+1_srep25676.pdf","file_id":"5327","content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","creator":"system","checksum":"ee17c482370d2e1b3add393710d3c696","file_size":1349915,"relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1","scopus_import":1},{"year":"2016","date_updated":"2021-01-12T06:50:38Z","day":"01","department":[{"_id":"RoSe"}],"_id":"1422","date_published":"2016-07-01T00:00:00Z","month":"07","citation":{"apa":"Frank, R., Hainzl, C., Schlein, B., & Seiringer, R. (2016). Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0847-5","short":"R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923.","ieee":"R. Frank, C. Hainzl, B. Schlein, and R. Seiringer, “Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations,” Letters in Mathematical Physics, vol. 106, no. 7. Springer, pp. 913–923, 2016.","mla":"Frank, Rupert, et al. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics, vol. 106, no. 7, Springer, 2016, pp. 913–23, doi:10.1007/s11005-016-0847-5.","chicago":"Frank, Rupert, Christian Hainzl, Benjamin Schlein, and Robert Seiringer. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0847-5.","ama":"Frank R, Hainzl C, Schlein B, Seiringer R. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 2016;106(7):913-923. doi:10.1007/s11005-016-0847-5","ista":"Frank R, Hainzl C, Schlein B, Seiringer R. 2016. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 106(7), 913–923."},"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","volume":106,"status":"public","publication_status":"published","pubrep_id":"591","publication":"Letters in Mathematical Physics","doi":"10.1007/s11005-016-0847-5","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","language":[{"iso":"eng"}],"intvolume":" 106","publist_id":"5785","file_date_updated":"2020-07-14T12:44:53Z","author":[{"last_name":"Frank","first_name":"Rupert","full_name":"Frank, Rupert"},{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"last_name":"Schlein","first_name":"Benjamin","full_name":"Schlein, Benjamin"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"scopus_import":1,"abstract":[{"lang":"eng","text":"We study the time-dependent Bogoliubov–de-Gennes equations for generic translation-invariant fermionic many-body systems. For initial states that are close to thermal equilibrium states at temperatures near the critical temperature, we show that the magnitude of the order parameter stays approximately constant in time and, in particular, does not follow a time-dependent Ginzburg–Landau equation, which is often employed as a phenomenological description and predicts a decay of the order parameter in time. The full non-linear structure of the equations is necessary to understand this behavior."}],"has_accepted_license":"1","page":"913 - 923","file":[{"file_id":"5181","content_type":"application/pdf","date_created":"2018-12-12T10:15:57Z","file_name":"IST-2016-591-v1+1_s11005-016-0847-5.pdf","checksum":"fb404923d8ca9a1faeb949561f26cbea","creator":"system","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","relation":"main_file","file_size":458968}],"article_processing_charge":"Yes (via OA deal)","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"issue":"7","title":"Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","oa_version":"Published Version","ddc":["510","530"],"oa":1,"date_created":"2018-12-11T11:51:56Z"},{"language":[{"iso":"eng"}],"doi":"10.1145/2883817.2883837","author":[{"full_name":"Bak, Stanley","first_name":"Stanley","last_name":"Bak"},{"last_name":"Bogomolov","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Johnson","first_name":"Taylor","full_name":"Johnson, Taylor"},{"first_name":"Pradyot","last_name":"Prakash","full_name":"Prakash, Pradyot"}],"date_created":"2018-12-11T11:51:55Z","ec_funded":1,"publist_id":"5786","citation":{"ista":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. 2016. Scalable static hybridization methods for analysis of nonlinear systems. HSCC 2016: International Conference on Hybrid Systems: Computation and Control, 155–164.","ama":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. Scalable static hybridization methods for analysis of nonlinear systems. In: Springer; 2016:155-164. doi:10.1145/2883817.2883837","mla":"Bak, Stanley, et al. Scalable Static Hybridization Methods for Analysis of Nonlinear Systems. Springer, 2016, pp. 155–64, doi:10.1145/2883817.2883837.","chicago":"Bak, Stanley, Sergiy Bogomolov, Thomas A Henzinger, Taylor Johnson, and Pradyot Prakash. “Scalable Static Hybridization Methods for Analysis of Nonlinear Systems,” 155–64. Springer, 2016. https://doi.org/10.1145/2883817.2883837.","ieee":"S. Bak, S. Bogomolov, T. A. Henzinger, T. Johnson, and P. Prakash, “Scalable static hybridization methods for analysis of nonlinear systems,” presented at the HSCC 2016: International Conference on Hybrid Systems: Computation and Control, Vienna, Austria, 2016, pp. 155–164.","short":"S. Bak, S. Bogomolov, T.A. Henzinger, T. Johnson, P. Prakash, in:, Springer, 2016, pp. 155–164.","apa":"Bak, S., Bogomolov, S., Henzinger, T. A., Johnson, T., & Prakash, P. (2016). Scalable static hybridization methods for analysis of nonlinear systems (pp. 155–164). Presented at the HSCC 2016: International Conference on Hybrid Systems: Computation and Control, Vienna, Austria: Springer. https://doi.org/10.1145/2883817.2883837"},"quality_controlled":"1","oa_version":"None","publication_status":"published","conference":{"end_date":"2016-04-14","location":"Vienna, Austria","start_date":"2016-04-12","name":"HSCC 2016: International Conference on Hybrid Systems: Computation and Control"},"type":"conference","title":"Scalable static hybridization methods for analysis of nonlinear systems","publisher":"Springer","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"_id":"1421","page":"155 - 164","abstract":[{"lang":"eng","text":"Hybridization methods enable the analysis of hybrid automata with complex, nonlinear dynamics through a sound abstraction process. Complex dynamics are converted to simpler ones with added noise, and then analysis is done using a reachability method for the simpler dynamics. Several such recent approaches advocate that only "dynamic" hybridization techniquesi.e., those where the dynamics are abstracted on-The-fly during a reachability computation are effective. In this paper, we demonstrate this is not the case, and create static hybridization methods that are more scalable than earlier approaches. The main insight in our approach is that quick, numeric simulations can be used to guide the process, eliminating the need for an exponential number of hybridization domains. Transitions between domains are generally timetriggered, avoiding accumulated error from geometric intersections. We enhance our static technique by combining time-Triggered transitions with occasional space-Triggered transitions, and demonstrate the benefits of the combined approach in what we call mixed-Triggered hybridization. Finally, error modes are inserted to confirm that the reachable states stay within the hybridized regions. The developed techniques can scale to higher dimensions than previous static approaches, while enabling the parallelization of the main performance bottleneck for many dynamic hybridization approaches: The nonlinear optimization required for sound dynamics abstraction. We implement our method as a model transformation pass in the HYST tool, and perform reachability analysis and evaluation using an unmodified version of SpaceEx on nonlinear models with up to six dimensions."}],"date_published":"2016-04-11T00:00:00Z","month":"04","date_updated":"2021-01-12T06:50:37Z","year":"2016","scopus_import":1,"day":"11"},{"abstract":[{"lang":"eng","text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. "}],"page":"1523 - 1548","article_processing_charge":"No","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"scopus_import":"1","external_id":{"arxiv":["1510.08344"]},"date_created":"2018-12-11T11:51:55Z","ec_funded":1,"oa":1,"title":"A general approximation for the dynamics of quantitative traits","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Genetics Society of America","quality_controlled":"1","oa_version":"Preprint","issue":"4","main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"date_published":"2016-04-06T00:00:00Z","month":"04","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"_id":"1420","day":"06","year":"2016","date_updated":"2022-08-01T10:49:55Z","publist_id":"5787","author":[{"orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","last_name":"Bod'ová","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publication":"Genetics","doi":"10.1534/genetics.115.184127","language":[{"iso":"eng"}],"intvolume":" 202","type":"journal_article","volume":202,"status":"public","publication_status":"published","citation":{"ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.","apa":"Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.","mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127."}},{"has_accepted_license":"1","file":[{"file_id":"5177","content_type":"application/pdf","date_created":"2018-12-12T10:15:53Z","file_name":"IST-2016-583-v1+1_ncomms11332.pdf","file_size":965176,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:53Z","creator":"system","checksum":"6484fa81a2e52e4fdd7935e1ae6091d4"}],"abstract":[{"text":"Solitons are localized waves formed by a balance of focusing and defocusing effects. These nonlinear waves exist in diverse forms of matter yet exhibit similar properties including stability, periodic recurrence and particle-like trajectories. One important property is soliton fission, a process by which an energetic higher-order soliton breaks apart due to dispersive or nonlinear perturbations. Here we demonstrate through both experiment and theory that nonlinear photocarrier generation can induce soliton fission. Using near-field measurements, we directly observe the nonlinear spatial and temporal evolution of optical pulses in situ in a nanophotonic semiconductor waveguide. We develop an analytic formalism describing the free-carrier dispersion (FCD) perturbation and show the experiment exceeds the minimum threshold by an order of magnitude. We confirm these observations with a numerical nonlinear Schrödinger equation model. These results provide a fundamental explanation and physical scaling of optical pulse evolution in free-carrier media and could enable improved supercontinuum sources in gas based and integrated semiconductor waveguides.","lang":"eng"}],"scopus_import":1,"ddc":["530"],"oa":1,"date_created":"2018-12-11T11:51:58Z","oa_version":"Published Version","quality_controlled":"1","title":"Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides","publisher":"Nature Publishing Group","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoFi"}],"_id":"1429","article_number":"11332 (2016)","date_published":"2016-04-15T00:00:00Z","month":"04","date_updated":"2021-01-12T06:50:40Z","year":"2016","day":"15","language":[{"iso":"eng"}],"intvolume":" 7","publication":"Nature Communications","doi":"10.1038/ncomms11332","acknowledgement":"This research was supported by the Australian Research Council (ARC) Center of Excellence CUDOS (CE110001018), ARC Laureate Fellowship (FL120100029), ARC Discovery Early Career Researcher Award (DECRA DE120102069), the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO). L.K. acknowledges funding from ERC Advanced Investigator Grant (no. 240438-CONSTANS). A.D.R, S.C., and G.L. acknowledge financial support from the ERC-Pharos programme lead by A. P. Mosk.","file_date_updated":"2020-07-14T12:44:53Z","author":[{"full_name":"Husko, Chad","last_name":"Husko","first_name":"Chad"},{"id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Wulf","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378"},{"last_name":"Lefrançois","first_name":"Simon","full_name":"Lefrançois, Simon"},{"full_name":"Combrié, Sylvain","last_name":"Combrié","first_name":"Sylvain"},{"first_name":"Gaëlle","last_name":"Lehoucq","full_name":"Lehoucq, Gaëlle"},{"first_name":"Alfredo","last_name":"De Rossi","full_name":"De Rossi, Alfredo"},{"last_name":"Eggleton","first_name":"Benjamin","full_name":"Eggleton, Benjamin"},{"first_name":"Laurens","last_name":"Kuipers","full_name":"Kuipers, Laurens"}],"publist_id":"5769","citation":{"ieee":"C. Husko et al., “Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","apa":"Husko, C., Wulf, M., Lefrançois, S., Combrié, S., Lehoucq, G., De Rossi, A., … Kuipers, L. (2016). Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11332","short":"C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B. Eggleton, L. Kuipers, Nature Communications 7 (2016).","ista":"Husko C, Wulf M, Lefrançois S, Combrié S, Lehoucq G, De Rossi A, Eggleton B, Kuipers L. 2016. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 7, 11332 (2016).","ama":"Husko C, Wulf M, Lefrançois S, et al. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 2016;7. doi:10.1038/ncomms11332","mla":"Husko, Chad, et al. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications, vol. 7, 11332 (2016), Nature Publishing Group, 2016, doi:10.1038/ncomms11332.","chicago":"Husko, Chad, Matthias Wulf, Simon Lefrançois, Sylvain Combrié, Gaëlle Lehoucq, Alfredo De Rossi, Benjamin Eggleton, and Laurens Kuipers. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11332."},"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)"},"publication_status":"published","pubrep_id":"583","type":"journal_article","volume":7,"status":"public"},{"scopus_import":1,"abstract":[{"lang":"eng","text":"The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow."}],"has_accepted_license":"1","file":[{"file_id":"5272","content_type":"application/pdf","date_created":"2018-12-12T10:17:19Z","file_name":"IST-2016-584-v1+1_peerj-1865.pdf","checksum":"c27d898598a1e3d7f629607a309254e1","creator":"system","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","relation":"main_file","file_size":1216360}],"quality_controlled":"1","oa_version":"Published Version","publisher":"PeerJ","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon","issue":"3","date_created":"2018-12-11T11:51:59Z","oa":1,"ddc":["570"],"day":"01","date_updated":"2021-01-12T06:50:41Z","year":"2016","article_number":"1865","month":"01","date_published":"2016-01-01T00:00:00Z","_id":"1431","department":[{"_id":"SyCr"}],"pubrep_id":"584","publication_status":"published","status":"public","type":"journal_article","volume":2016,"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)"},"citation":{"ama":"Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016;2016(3). doi:10.7717/peerj.1865","ista":"Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865.","chicago":"Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ. PeerJ, 2016. https://doi.org/10.7717/peerj.1865.","mla":"Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ, vol. 2016, no. 3, 1865, PeerJ, 2016, doi:10.7717/peerj.1865.","ieee":"A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon,” PeerJ, vol. 2016, no. 3. PeerJ, 2016.","short":"A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).","apa":"Tartally, A., Kelager, A., Fürst, M., & Nash, D. (2016). Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. PeerJ. https://doi.org/10.7717/peerj.1865"},"author":[{"first_name":"András","last_name":"Tartally","full_name":"Tartally, András"},{"full_name":"Kelager, Andreas","first_name":"Andreas","last_name":"Kelager"},{"id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Fürst","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X"},{"full_name":"Nash, David","last_name":"Nash","first_name":"David"}],"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5767","language":[{"iso":"eng"}],"intvolume":" 2016","doi":"10.7717/peerj.1865","publication":"PeerJ"},{"date_published":"2016-08-01T00:00:00Z","month":"08","department":[{"_id":"LaEr"}],"_id":"1434","day":"01","year":"2016","date_updated":"2021-01-12T06:50:42Z","publist_id":"5764","author":[{"orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang"},{"last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","last_name":"Schnelli","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"publication":"Journal of Functional Analysis","doi":"10.1016/j.jfa.2016.04.006","intvolume":" 271","language":[{"iso":"eng"}],"volume":271,"type":"journal_article","status":"public","publication_status":"published","citation":{"ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,” Journal of Functional Analysis, vol. 271, no. 3. Academic Press, pp. 672–719, 2016.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016) 672–719.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2016). Local stability of the free additive convolution. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2016.04.006","ama":"Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution. Journal of Functional Analysis. 2016;271(3):672-719. doi:10.1016/j.jfa.2016.04.006","ista":"Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution. Journal of Functional Analysis. 271(3), 672–719.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2016.04.006.","mla":"Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis, vol. 271, no. 3, Academic Press, 2016, pp. 672–719, doi:10.1016/j.jfa.2016.04.006."},"page":"672 - 719","abstract":[{"text":"We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B on scales down to N−2/3N−2/3.","lang":"eng"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"scopus_import":1,"date_created":"2018-12-11T11:52:00Z","ec_funded":1,"oa":1,"title":"Local stability of the free additive convolution","publisher":"Academic Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","quality_controlled":"1","issue":"3","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1508.05905"}]},{"date_published":"2016-01-01T00:00:00Z","month":"01","department":[{"_id":"RoSe"}],"_id":"1436","day":"01","date_updated":"2021-01-12T06:50:43Z","year":"2016","file_date_updated":"2020-07-14T12:44:54Z","author":[{"full_name":"Bach, Volker","last_name":"Bach","first_name":"Volker"},{"full_name":"Breteaux, Sébastien","first_name":"Sébastien","last_name":"Breteaux"},{"full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P","last_name":"Petrat"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"},{"last_name":"Tzaneteas","first_name":"Tim","full_name":"Tzaneteas, Tim"}],"publist_id":"5763","intvolume":" 105","language":[{"iso":"eng"}],"publication":"Journal de Mathématiques Pures et Appliquées","doi":"10.1016/j.matpur.2015.09.003","pubrep_id":"581","publication_status":"published","volume":105,"type":"journal_article","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"ista":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.","ama":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 2016;105(1):1-30. doi:10.1016/j.matpur.2015.09.003","chicago":"Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées. Elsevier, 2016. https://doi.org/10.1016/j.matpur.2015.09.003.","mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:10.1016/j.matpur.2015.09.003.","ieee":"V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction,” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1. Elsevier, pp. 1–30, 2016.","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30.","apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., & Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. Elsevier. https://doi.org/10.1016/j.matpur.2015.09.003"},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"abstract":[{"lang":"eng","text":"We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system."}],"page":"1 - 30","file":[{"creator":"system","checksum":"c5afe1f6935bc7f2b546adbde1d31a35","date_updated":"2020-07-14T12:44:54Z","relation":"main_file","access_level":"open_access","file_size":658491,"file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf","date_created":"2018-12-12T10:10:36Z","content_type":"application/pdf","file_id":"4825"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":1,"date_created":"2018-12-11T11:52:00Z","ec_funded":1,"ddc":["510","530"],"oa":1,"oa_version":"Published Version","quality_controlled":"1","title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","issue":"1"},{"file":[{"date_updated":"2020-07-14T12:44:54Z","checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da","creator":"system","file_size":1395180,"access_level":"open_access","relation":"main_file","file_name":"IST-2016-580-v1+1_1207393.pdf","date_created":"2018-12-12T10:09:17Z","content_type":"application/pdf","file_id":"4740"}],"has_accepted_license":"1","abstract":[{"text":"ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states.","lang":"eng"}],"scopus_import":1,"date_created":"2018-12-11T11:52:00Z","oa":1,"ddc":["570"],"oa_version":"Published Version","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Hindawi Publishing Corporation","title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction","article_number":"1207393","month":"01","date_published":"2016-01-01T00:00:00Z","_id":"1435","department":[{"_id":"PeJo"}],"day":"01","date_updated":"2021-01-12T06:50:43Z","year":"2016","author":[{"full_name":"Guzmán, José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","last_name":"Guzmán"},{"first_name":"Zoltan","last_name":"Gerevich","full_name":"Gerevich, Zoltan"}],"file_date_updated":"2020-07-14T12:44:54Z","publist_id":"5762","intvolume":" 2016","language":[{"iso":"eng"}],"doi":"10.1155/2016/1207393","publication":"Neural Plasticity","pubrep_id":"580","publication_status":"published","status":"public","type":"journal_article","volume":2016,"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)"},"citation":{"chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity. Hindawi Publishing Corporation, 2016. https://doi.org/10.1155/2016/1207393.","mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:10.1155/2016/1207393.","ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016;2016. doi:10.1155/2016/1207393","ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.","apa":"Guzmán, J., & Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. Hindawi Publishing Corporation. https://doi.org/10.1155/2016/1207393","short":"J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016).","ieee":"J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction,” Neural Plasticity, vol. 2016. Hindawi Publishing Corporation, 2016."}},{"day":"11","year":"2016","date_updated":"2021-01-12T06:50:45Z","date_published":"2016-01-11T00:00:00Z","month":"01","alternative_title":["ACM SIGPLAN Notices"],"department":[{"_id":"ToHe"}],"_id":"1439","type":"conference","volume":"20-22","status":"public","conference":{"end_date":"2016-01-22","name":"POPL: Principles of Programming Languages","location":"St. Petersburg, FL, USA","start_date":"2016-01-20"},"publication_status":"published","citation":{"chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415. ACM, 2016. https://doi.org/10.1145/2837614.2837650.","mla":"Dragoi, Cezara, et al. PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms. Vol. 20–22, ACM, 2016, pp. 400–15, doi:10.1145/2837614.2837650.","ama":"Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:10.1145/2837614.2837650","ista":"Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2016). PSYNC: A partially synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp. 400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837650","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous language for fault-tolerant distributed algorithms,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415."},"publist_id":"5759","author":[{"last_name":"Dragoi","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","full_name":"Dragoi, Cezara"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien"}],"doi":"10.1145/2837614.2837650","acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","language":[{"iso":"eng"}],"scopus_import":1,"abstract":[{"lang":"eng","text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification."}],"page":"400 - 415","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","publisher":"ACM","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://hal.inria.fr/hal-01251199/","open_access":"1"}],"date_created":"2018-12-11T11:52:01Z","ec_funded":1,"oa":1},{"language":[{"iso":"eng"}],"intvolume":" 24","doi":"10.1016/j.str.2016.01.002","acknowledgement":"The author thanks Banerjee et al. (2016) for providing coordinates prior to public release and apologizes to colleagues whose work was not cited or discussed due to the limited space available. The author is supported by grants from EU FP7 (CIG-303564), HFSP (RGY0084_2012), and FWF (W1232).","publication":"Structure","author":[{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak"}],"publist_id":"5756","ec_funded":1,"date_created":"2018-12-11T11:52:02Z","citation":{"apa":"Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. Cell Press. https://doi.org/10.1016/j.str.2016.01.002","short":"H.L. Janovjak, Structure 24 (2016) 213–215.","ieee":"H. L. Janovjak, “Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain,” Structure, vol. 24, no. 2. Cell Press, pp. 213–215, 2016.","mla":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” Structure, vol. 24, no. 2, Cell Press, 2016, pp. 213–15, doi:10.1016/j.str.2016.01.002.","chicago":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” Structure. Cell Press, 2016. https://doi.org/10.1016/j.str.2016.01.002.","ama":"Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 2016;24(2):213-215. doi:10.1016/j.str.2016.01.002","ista":"Janovjak HL. 2016. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 24(2), 213–215."},"issue":"2","publication_status":"published","oa_version":"None","quality_controlled":"1","publisher":"Cell Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","volume":24,"title":"Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain","_id":"1440","project":[{"grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets"}],"department":[{"_id":"HaJa"}],"page":"213 - 215","month":"02","date_published":"2016-02-02T00:00:00Z","date_updated":"2021-01-12T06:50:46Z","year":"2016","scopus_import":1,"day":"02"},{"doi":"10.1007/s11192-016-1842-4","publication":"Scientometrics","intvolume":" 107","language":[{"iso":"eng"}],"publist_id":"5750","author":[{"full_name":"Calatrava Moreno, Maria","last_name":"Calatrava Moreno","first_name":"Maria"},{"last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas"},{"full_name":"Werthner, Hannes","first_name":"Hannes","last_name":"Werthner"}],"file_date_updated":"2020-07-14T12:44:55Z","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)"},"citation":{"chicago":"Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” Scientometrics. Springer, 2016. https://doi.org/10.1007/s11192-016-1842-4.","mla":"Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” Scientometrics, vol. 107, no. 1, Springer, 2016, pp. 213–32, doi:10.1007/s11192-016-1842-4.","ista":"Calatrava Moreno M, Auzinger T, Werthner H. 2016. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. 107(1), 213–232.","ama":"Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. 2016;107(1):213-232. doi:10.1007/s11192-016-1842-4","apa":"Calatrava Moreno, M., Auzinger, T., & Werthner, H. (2016). On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. Springer. https://doi.org/10.1007/s11192-016-1842-4","short":"M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016) 213–232.","ieee":"M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data,” Scientometrics, vol. 107, no. 1. Springer, pp. 213–232, 2016."},"status":"public","volume":107,"type":"journal_article","pubrep_id":"530","publication_status":"published","_id":"1446","department":[{"_id":"BeBi"}],"month":"04","date_published":"2016-04-01T00:00:00Z","year":"2016","date_updated":"2021-11-16T08:29:11Z","day":"01","related_material":{"link":[{"url":"https://doi.org/10.1007/s11192-016-1902-9","relation":"erratum"}]},"oa":1,"ddc":["000"],"date_created":"2018-12-11T11:52:04Z","issue":"1","publisher":"Springer","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data","quality_controlled":"1","oa_version":"Published Version","file":[{"file_size":806035,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:55Z","creator":"system","checksum":"32d46268588b87d9b686492018e6a2b2","file_name":"IST-2016-530-v1+1_s11192-016-1842-4.pdf","date_created":"2018-12-12T10:10:56Z","content_type":"application/pdf","file_id":"4848"}],"has_accepted_license":"1","page":"213 - 232","abstract":[{"text":"The accuracy of interdisciplinarity measurements is directly related to the quality of the underlying bibliographic data. Existing indicators of interdisciplinarity are not capable of reflecting the inaccuracies introduced by incorrect and incomplete records because correct and complete bibliographic data can rarely be obtained. This is the case for the Rao–Stirling index, which cannot handle references that are not categorized into disciplinary fields. We introduce a method that addresses this problem. It extends the Rao–Stirling index to acknowledge missing data by calculating its interval of uncertainty using computational optimization. The evaluation of our method indicates that the uncertainty interval is not only useful for estimating the inaccuracy of interdisciplinarity measurements, but it also delivers slightly more accurate aggregated interdisciplinarity measurements than the Rao–Stirling index.","lang":"eng"}],"article_processing_charge":"No","scopus_import":"1"},{"department":[{"_id":"JaMa"}],"_id":"1448","date_published":"2016-06-01T00:00:00Z","month":"06","date_updated":"2021-01-12T06:50:49Z","year":"2016","day":"01","language":[{"iso":"eng"}],"intvolume":" 26","publication":"The Annals of Applied Probability","acknowledgement":"Supported by the German Research Foundation through the Collaborative Research Center 1060\r\nThe Mathematics of Emergent Effects and the Hausdorff Center for Mathematics. Part of this work has been done while M. Fathi visited J. Maas at the University of Bonn in July 2014.We would like to thank the referees for their careful reading of the manuscript. ","doi":"10.1214/15-AAP1133","author":[{"full_name":"Fathi, Max","first_name":"Max","last_name":"Fathi"},{"last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"}],"publist_id":"5748","citation":{"ama":"Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 2016;26(3):1774-1806. doi:10.1214/15-AAP1133","ista":"Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 26(3), 1774–1806.","chicago":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/15-AAP1133.","mla":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” The Annals of Applied Probability, vol. 26, no. 3, Institute of Mathematical Statistics, 2016, pp. 1774–806, doi:10.1214/15-AAP1133.","ieee":"M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting systems,” The Annals of Applied Probability, vol. 26, no. 3. Institute of Mathematical Statistics, pp. 1774–1806, 2016.","short":"M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.","apa":"Fathi, M., & Maas, J. (2016). Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AAP1133"},"publication_status":"published","volume":26,"type":"journal_article","status":"public","abstract":[{"text":"We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli–Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities.","lang":"eng"}],"page":"1774 - 1806","scopus_import":1,"oa":1,"date_created":"2018-12-11T11:52:05Z","issue":"3","main_file_link":[{"url":"http://arxiv.org/abs/1501.00562","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","title":"Entropic Ricci curvature bounds for discrete interacting systems","publisher":"Institute of Mathematical Statistics","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"day":"15","year":"2016","date_updated":"2021-01-12T06:51:00Z","month":"01","date_published":"2016-01-15T00:00:00Z","_id":"1476","department":[{"_id":"DaSi"}],"status":"public","type":"journal_article","volume":129,"publication_status":"published","pubrep_id":"767","citation":{"ista":"Toshima J, Horikomi C, Okada A, Hatori M, Nagano M, Masuda A, Yamamoto W, Siekhaus DE, Toshima J. 2016. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 129(2), 367–379.","ama":"Toshima J, Horikomi C, Okada A, et al. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 2016;129(2):367-379. doi:10.1242/jcs.176651","chicago":"Toshima, Junko, Chika Horikomi, Asuka Okada, Makiko Hatori, Makoto Nagano, Atsushi Masuda, Wataru Yamamoto, Daria E Siekhaus, and Jiro Toshima. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2016. https://doi.org/10.1242/jcs.176651.","mla":"Toshima, Junko, et al. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” Journal of Cell Science, vol. 129, no. 2, Company of Biologists, 2016, pp. 367–79, doi:10.1242/jcs.176651.","ieee":"J. Toshima et al., “Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis,” Journal of Cell Science, vol. 129, no. 2. Company of Biologists, pp. 367–379, 2016.","apa":"Toshima, J., Horikomi, C., Okada, A., Hatori, M., Nagano, M., Masuda, A., … Toshima, J. (2016). Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.176651","short":"J. Toshima, C. Horikomi, A. Okada, M. Hatori, M. Nagano, A. Masuda, W. Yamamoto, D.E. Siekhaus, J. Toshima, Journal of Cell Science 129 (2016) 367–379."},"publist_id":"5720","author":[{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"full_name":"Horikomi, Chika","first_name":"Chika","last_name":"Horikomi"},{"last_name":"Okada","first_name":"Asuka","full_name":"Okada, Asuka"},{"full_name":"Hatori, Makiko","first_name":"Makiko","last_name":"Hatori"},{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"first_name":"Atsushi","last_name":"Masuda","full_name":"Masuda, Atsushi"},{"full_name":"Yamamoto, Wataru","last_name":"Yamamoto","first_name":"Wataru"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"last_name":"Toshima","first_name":"Jiro","full_name":"Toshima, Jiro"}],"file_date_updated":"2020-07-14T12:44:56Z","acknowledgement":"We are grateful to Anthony Bretscher (Cornell University, NY) for providing the bni1-12 bnr1Δ (Y4135) strain. J.Y.T. was supported by a Japan Society for the Promotion of Science (JSPS) KAKENHI grant [grant number 26440067]; the Takeda Science Foundation; and the Novartis Foundation (Japan). J.T. was supported by a JSPS KAKENHI grant [grant number 25440054]; the Takeda Science Foundation; and the Kurata Memorial Hitachi Science and Technology Foundation. D.E.S. was supported by the European Union [grant number PCIG12-GA-2012-334077].","doi":"10.1242/jcs.176651","publication":"Journal of Cell Science","language":[{"iso":"eng"}],"intvolume":" 129","scopus_import":1,"file":[{"access_level":"open_access","relation":"main_file","file_size":7176912,"creator":"system","checksum":"2da0a09149a9ed956cdf79a95c17f08a","date_updated":"2020-07-14T12:44:56Z","date_created":"2018-12-12T10:11:08Z","file_name":"IST-2017-767-v1+1_367.full.pdf","content_type":"application/pdf","file_id":"4861"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis"}],"page":"367 - 379","project":[{"_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions"}],"publisher":"Company of Biologists","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis","oa_version":"Published Version","quality_controlled":"1","issue":"2","ec_funded":1,"date_created":"2018-12-11T11:52:14Z","oa":1,"ddc":["570","576"]},{"ec_funded":1,"date_created":"2018-12-11T11:52:14Z","oa":1,"ddc":["570"],"oa_version":"Published Version","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"eLife Sciences Publications","title":"Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton","issue":"February 2016","project":[{"grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7"}],"abstract":[{"text":"The actin cytoskeleton plays important roles in the formation and internalization of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes along actin cables, however, the molecular machinery regulating interaction between endocytic vesicles and actin cables is poorly understood. The Eps15-like protein Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several endocytic compartments. Early endosomes were highly localized in the actin concentrations and displayed movement along actin cables. The dephosphorylated form of Pan1p also caused stable associations between endocytic vesicles and actin cables, and between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of a novel mechanism that regulates endocytic compartment interactions with each other and with actin cables.","lang":"eng"}],"has_accepted_license":"1","file":[{"file_name":"IST-2016-529-v1+1_elife-10276-v1.pdf","date_created":"2018-12-12T10:10:08Z","file_id":"4793","content_type":"application/pdf","checksum":"d1cc44870580756ba8badd8e41adfdb5","creator":"system","date_updated":"2020-07-14T12:44:56Z","relation":"main_file","access_level":"open_access","file_size":5198001}],"scopus_import":1,"author":[{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"first_name":"Eri","last_name":"Furuya","full_name":"Furuya, Eri"},{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"first_name":"Chisa","last_name":"Kanno","full_name":"Kanno, Chisa"},{"first_name":"Yuta","last_name":"Sakamoto","full_name":"Sakamoto, Yuta"},{"full_name":"Ebihara, Masashi","first_name":"Masashi","last_name":"Ebihara"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"file_date_updated":"2020-07-14T12:44:56Z","publist_id":"5721","language":[{"iso":"eng"}],"intvolume":" 5","doi":"10.7554/eLife.10276","publication":"eLife","pubrep_id":"529","publication_status":"published","status":"public","volume":5,"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)"},"citation":{"ieee":"J. Toshima et al., “Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton,” eLife, vol. 5, no. February 2016. eLife Sciences Publications, 2016.","short":"J. Toshima, E. Furuya, M. Nagano, C. Kanno, Y. Sakamoto, M. Ebihara, D.E. Siekhaus, J. Toshima, ELife 5 (2016).","apa":"Toshima, J., Furuya, E., Nagano, M., Kanno, C., Sakamoto, Y., Ebihara, M., … Toshima, J. (2016). Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.10276","ama":"Toshima J, Furuya E, Nagano M, et al. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 2016;5(February 2016). doi:10.7554/eLife.10276","ista":"Toshima J, Furuya E, Nagano M, Kanno C, Sakamoto Y, Ebihara M, Siekhaus DE, Toshima J. 2016. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 5(February 2016), e10276.","chicago":"Toshima, Junko, Eri Furuya, Makoto Nagano, Chisa Kanno, Yuta Sakamoto, Masashi Ebihara, Daria E Siekhaus, and Jiro Toshima. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.10276.","mla":"Toshima, Junko, et al. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” ELife, vol. 5, no. February 2016, e10276, eLife Sciences Publications, 2016, doi:10.7554/eLife.10276."},"article_number":"e10276","month":"02","date_published":"2016-02-25T00:00:00Z","_id":"1475","department":[{"_id":"DaSi"}],"day":"25","date_updated":"2021-01-12T06:50:59Z","year":"2016"},{"file_date_updated":"2020-07-14T12:44:56Z","author":[{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"},{"full_name":"Warzel, Simone","last_name":"Warzel","first_name":"Simone"}],"publist_id":"5716","language":[{"iso":"eng"}],"intvolume":" 18","publication":"New Journal of Physics","doi":"10.1088/1367-2630/18/3/035002","publication_status":"published","pubrep_id":"579","volume":18,"type":"journal_article","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)"},"citation":{"ieee":"R. Seiringer and S. Warzel, “Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas,” New Journal of Physics, vol. 18, no. 3. IOP Publishing Ltd., 2016.","apa":"Seiringer, R., & Warzel, S. (2016). Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/3/035002","short":"R. Seiringer, S. Warzel, New Journal of Physics 18 (2016).","ama":"Seiringer R, Warzel S. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 2016;18(3). doi:10.1088/1367-2630/18/3/035002","ista":"Seiringer R, Warzel S. 2016. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 18(3), 035002.","mla":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” New Journal of Physics, vol. 18, no. 3, 035002, IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/3/035002.","chicago":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” New Journal of Physics. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/3/035002."},"article_number":"035002","date_published":"2016-02-29T00:00:00Z","month":"02","department":[{"_id":"RoSe"}],"_id":"1478","day":"29","date_updated":"2021-01-12T06:51:01Z","year":"2016","date_created":"2018-12-11T11:52:15Z","ddc":["510","530"],"oa":1,"quality_controlled":"1","oa_version":"Published Version","title":"Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IOP Publishing Ltd.","issue":"3","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"}],"file":[{"checksum":"4f959eabc19d2a2f518318a450a4d424","creator":"system","date_updated":"2020-07-14T12:44:56Z","relation":"main_file","access_level":"open_access","file_size":965607,"file_name":"IST-2016-579-v1+1_njp_18_3_035002.pdf","date_created":"2018-12-12T10:17:22Z","content_type":"application/pdf","file_id":"5276"}],"has_accepted_license":"1","abstract":[{"text":"We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature.","lang":"eng"}],"scopus_import":1},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Oxford University Press","volume":112,"type":"journal_article","title":"Exponential varieties","publication_status":"published","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1412.6185","open_access":"1"}],"issue":"1","citation":{"ieee":"M. Michałek, B. Sturmfels, C. Uhler, and P. Zwiernik, “Exponential varieties,” Proceedings of the London Mathematical Society, vol. 112, no. 1. Oxford University Press, pp. 27–56, 2016.","short":"M. Michałek, B. Sturmfels, C. Uhler, P. Zwiernik, Proceedings of the London Mathematical Society 112 (2016) 27–56.","apa":"Michałek, M., Sturmfels, B., Uhler, C., & Zwiernik, P. (2016). Exponential varieties. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms/pdv066","ista":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. 2016. Exponential varieties. Proceedings of the London Mathematical Society. 112(1), 27–56.","ama":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. Exponential varieties. Proceedings of the London Mathematical Society. 2016;112(1):27-56. doi:10.1112/plms/pdv066","mla":"Michałek, Mateusz, et al. “Exponential Varieties.” Proceedings of the London Mathematical Society, vol. 112, no. 1, Oxford University Press, 2016, pp. 27–56, doi:10.1112/plms/pdv066.","chicago":"Michałek, Mateusz, Bernd Sturmfels, Caroline Uhler, and Piotr Zwiernik. “Exponential Varieties.” Proceedings of the London Mathematical Society. Oxford University Press, 2016. https://doi.org/10.1112/plms/pdv066."},"publist_id":"5714","date_created":"2018-12-11T11:52:16Z","author":[{"first_name":"Mateusz","last_name":"Michałek","full_name":"Michałek, Mateusz"},{"full_name":"Sturmfels, Bernd","first_name":"Bernd","last_name":"Sturmfels"},{"last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"},{"full_name":"Zwiernik, Piotr","last_name":"Zwiernik","first_name":"Piotr"}],"doi":"10.1112/plms/pdv066","publication":"Proceedings of the London Mathematical Society","oa":1,"language":[{"iso":"eng"}],"intvolume":" 112","day":"07","scopus_import":1,"year":"2016","date_updated":"2021-01-12T06:51:02Z","month":"01","date_published":"2016-01-07T00:00:00Z","abstract":[{"lang":"eng","text":"Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. "}],"page":"27 - 56","_id":"1480","department":[{"_id":"CaUh"}]},{"scopus_import":1,"abstract":[{"text":"Rhythms with time scales of multiple cycles per second permeate the mammalian brain, yet neuroscientists are not certain of their functional roles. One leading idea is that coherent oscillation between two brain regions facilitates the exchange of information between them. In rats, the hippocampus and the vibrissal sensorimotor system both are characterized by rhythmic oscillation in the theta range, 5–12 Hz. Previous work has been divided as to whether the two rhythms are independent or coherent. To resolve this question, we acquired three measures from rats—whisker motion, hippocampal local field potential (LFP), and barrel cortex unit firing—during a whisker-mediated texture discrimination task and during control conditions (not engaged in a whisker-mediated memory task). Compared to control conditions, the theta band of hippocampal LFP showed a marked increase in power as the rats approached and then palpated the texture. Phase synchronization between whisking and hippocampal LFP increased by almost 50% during approach and texture palpation. In addition, a greater proportion of barrel cortex neurons showed firing that was phase-locked to hippocampal theta while rats were engaged in the discrimination task. Consistent with a behavioral consequence of phase synchronization, the rats identified the texture more rapidly and with lower error likelihood on trials in which there was an increase in theta-whisking coherence at the moment of texture palpation. These results suggest that coherence between the whisking rhythm, barrel cortex firing, and hippocampal LFP is augmented selectively during epochs in which the rat collects sensory information and that such coherence enhances the efficiency of integration of stimulus information into memory and decision-making centers.","lang":"eng"}],"has_accepted_license":"1","file":[{"checksum":"3a5ce0d4e4e36bd6ceb4be761f85644a","creator":"system","date_updated":"2020-07-14T12:44:57Z","access_level":"open_access","relation":"main_file","file_size":2879899,"file_name":"IST-2016-518-v1+1_journal.pbio.1002384.PDF","date_created":"2018-12-12T10:15:11Z","content_type":"application/pdf","file_id":"5129"}],"publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination","quality_controlled":"1","oa_version":"Published Version","issue":"2","date_created":"2018-12-11T11:52:18Z","oa":1,"ddc":["570"],"day":"18","year":"2016","date_updated":"2021-01-12T06:51:05Z","month":"02","date_published":"2016-02-18T00:00:00Z","article_number":"e1002384","_id":"1487","department":[{"_id":"JoCs"}],"status":"public","volume":14,"type":"journal_article","publication_status":"published","pubrep_id":"518","citation":{"apa":"Grion, N., Akrami, A., Zuo, Y., Stella, F., & Diamond, M. (2016). Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002384","short":"N. Grion, A. Akrami, Y. Zuo, F. Stella, M. Diamond, PLoS Biology 14 (2016).","ieee":"N. Grion, A. Akrami, Y. Zuo, F. Stella, and M. Diamond, “Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination,” PLoS Biology, vol. 14, no. 2. Public Library of Science, 2016.","chicago":"Grion, Natalia, Athena Akrami, Yangfang Zuo, Federico Stella, and Mathew Diamond. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.1002384.","mla":"Grion, Natalia, et al. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” PLoS Biology, vol. 14, no. 2, e1002384, Public Library of Science, 2016, doi:10.1371/journal.pbio.1002384.","ama":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. 2016;14(2). doi:10.1371/journal.pbio.1002384","ista":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. 2016. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. 14(2), e1002384."},"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)"},"publist_id":"5700","author":[{"first_name":"Natalia","last_name":"Grion","full_name":"Grion, Natalia"},{"first_name":"Athena","last_name":"Akrami","full_name":"Akrami, Athena"},{"full_name":"Zuo, Yangfang","last_name":"Zuo","first_name":"Yangfang"},{"last_name":"Stella","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","full_name":"Stella, Federico"},{"last_name":"Diamond","first_name":"Mathew","full_name":"Diamond, Mathew"}],"file_date_updated":"2020-07-14T12:44:57Z","doi":"10.1371/journal.pbio.1002384","acknowledgement":"We thank Eric Maris, Demian Battaglia, and Rodrigo Quian Quiroga for useful discussions. We are grateful to Fabrizio Manzino and Marco Gigante for construction of the behavioral apparatus, Igor Perkon for developing custom whisker tracking software and to Francesca Pulecchi for animal care and histological processing.","publication":"PLoS Biology","language":[{"iso":"eng"}],"intvolume":" 14"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization","oa_version":"Published Version","quality_controlled":"1","issue":"2","date_created":"2018-12-11T11:52:17Z","oa":1,"ddc":["570"],"scopus_import":1,"file":[{"file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF","date_created":"2018-12-12T10:14:16Z","content_type":"application/pdf","file_id":"5066","file_size":4297148,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:57Z","checksum":"6066146e527335030f83aa5924ab72a6","creator":"system"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation."}],"status":"public","volume":11,"type":"journal_article","pubrep_id":"521","publication_status":"published","citation":{"ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 2016;11(2). doi:10.1371/journal.pone.0147830","ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830.","mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:10.1371/journal.pone.0147830.","chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0147830.","ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” PLoS One, vol. 11, no. 2. Public Library of Science, 2016.","apa":"Adibi, M., Yoshida, S., Weijers, D., & Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0147830","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016)."},"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)"},"publist_id":"5711","author":[{"full_name":"Adibi, Milad","last_name":"Adibi","first_name":"Milad"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"last_name":"Fleck","first_name":"Christian","full_name":"Fleck, Christian"}],"file_date_updated":"2020-07-14T12:44:57Z","doi":"10.1371/journal.pone.0147830","acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","publication":"PLoS One","intvolume":" 11","language":[{"iso":"eng"}],"day":"01","year":"2016","date_updated":"2021-01-12T06:51:03Z","month":"02","date_published":"2016-02-01T00:00:00Z","article_number":"e0147830","_id":"1482","department":[{"_id":"JiFr"}]},{"language":[{"iso":"eng"}],"intvolume":" 26","doi":"10.1016/j.tcb.2016.02.003","acknowledgement":"We thank Maciek Adamowski for helpful discussions and Qiang Zhu and Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues whose work we could not include owing to space limitations.","publication":"Trends in Cell Biology","author":[{"full_name":"Chen, Xu","last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wu, Shuang","last_name":"Wu","first_name":"Shuang"},{"first_name":"Zengyu","last_name":"Liu","full_name":"Liu, Zengyu"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ","last_name":"Friml","first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:44:57Z","publist_id":"5704","citation":{"chicago":"Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology. Cell Press, 2016. https://doi.org/10.1016/j.tcb.2016.02.003.","mla":"Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology, vol. 26, no. 6, Cell Press, 2016, pp. 409–19, doi:10.1016/j.tcb.2016.02.003.","ista":"Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.","ama":"Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 2016;26(6):409-419. doi:10.1016/j.tcb.2016.02.003","apa":"Chen, X., Wu, S., Liu, Z., & Friml, J. (2016). Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2016.02.003","short":"X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.","ieee":"X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control of cortical microtubule orientation,” Trends in Cell Biology, vol. 26, no. 6. Cell Press, pp. 409–419, 2016."},"publication_status":"published","pubrep_id":"1002","status":"public","volume":26,"type":"journal_article","_id":"1484","department":[{"_id":"JiFr"}],"month":"06","date_published":"2016-06-01T00:00:00Z","date_updated":"2021-01-12T06:51:04Z","year":"2016","day":"01","oa":1,"ddc":["581"],"article_type":"review","date_created":"2018-12-11T11:52:17Z","issue":"6","quality_controlled":"1","oa_version":"Submitted Version","publisher":"Cell Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Environmental and endogenous control of cortical microtubule orientation","page":"409 - 419","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","file_size":2329117,"checksum":"b229e5bb4676ec3e27b7b9ea603b3a63","creator":"system","date_updated":"2020-07-14T12:44:57Z","content_type":"application/pdf","file_id":"5155","date_created":"2018-12-12T10:15:34Z","file_name":"IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf"}],"scopus_import":1},{"citation":{"ama":"De Martino D. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 2016;13(1). doi:10.1088/1478-3975/13/1/016003","ista":"De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.","chicago":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/1/016003.","mla":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology, vol. 13, no. 1, 016003, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/1/016003.","ieee":"D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” Physical Biology, vol. 13, no. 1. IOP Publishing Ltd., 2016.","short":"D. De Martino, Physical Biology 13 (2016).","apa":"De Martino, D. (2016). Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/1/016003"},"status":"public","volume":13,"type":"journal_article","publication_status":"published","doi":"10.1088/1478-3975/13/1/016003","publication":"Physical Biology","language":[{"iso":"eng"}],"intvolume":" 13","publist_id":"5702","author":[{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino"}],"year":"2016","date_updated":"2021-01-12T06:51:04Z","day":"29","_id":"1485","department":[{"_id":"GaTk"}],"month":"01","date_published":"2016-01-29T00:00:00Z","article_number":"016003","main_file_link":[{"url":"http://arxiv.org/abs/1505.04613","open_access":"1"}],"issue":"1","publisher":"IOP Publishing Ltd.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis","oa_version":"Preprint","quality_controlled":"1","oa":1,"ec_funded":1,"date_created":"2018-12-11T11:52:18Z","scopus_import":1,"abstract":[{"text":"In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism.","lang":"eng"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}]},{"date_updated":"2021-01-12T06:51:04Z","year":"2016","scopus_import":1,"day":"24","department":[{"_id":"RoSe"}],"_id":"1486","abstract":[{"text":"We review recent results concerning the mathematical properties of the Bardeen-Cooper-Schrieffer (BCS) functional of superconductivity, which were obtained in a series of papers, partly in collaboration with R. Frank, E. Hamza, S. Naboko, and J. P. Solovej. Our discussion includes, in particular, an investigation of the critical temperature for a general class of interaction potentials, as well as a study of its dependence on external fields. We shall explain how the Ginzburg-Landau model can be derived from the BCS theory in a suitable parameter regime.","lang":"eng"}],"article_number":"021101","date_published":"2016-02-24T00:00:00Z","month":"02","citation":{"short":"C. Hainzl, R. Seiringer, Journal of Mathematical Physics 57 (2016).","apa":"Hainzl, C., & Seiringer, R. (2016). The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4941723","ieee":"C. Hainzl and R. Seiringer, “The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties,” Journal of Mathematical Physics, vol. 57, no. 2. American Institute of Physics, 2016.","mla":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” Journal of Mathematical Physics, vol. 57, no. 2, 021101, American Institute of Physics, 2016, doi:10.1063/1.4941723.","chicago":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” Journal of Mathematical Physics. American Institute of Physics, 2016. https://doi.org/10.1063/1.4941723.","ama":"Hainzl C, Seiringer R. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. 2016;57(2). doi:10.1063/1.4941723","ista":"Hainzl C, Seiringer R. 2016. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. 57(2), 021101."},"issue":"2","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1511.01995"}],"oa_version":"Preprint","publication_status":"published","quality_controlled":"1","type":"journal_article","volume":57,"title":"The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties","status":"public","publisher":"American Institute of Physics","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"intvolume":" 57","oa":1,"publication":"Journal of Mathematical Physics","doi":"10.1063/1.4941723","author":[{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"date_created":"2018-12-11T11:52:18Z","publist_id":"5701"},{"oa":1,"ddc":["570"],"date_created":"2018-12-11T11:52:19Z","issue":"2","publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis."}],"file":[{"creator":"system","checksum":"7f8fa1b3a29f94c0a14dd4465278cdbc","date_updated":"2020-07-14T12:44:57Z","relation":"main_file","access_level":"open_access","file_size":5904773,"date_created":"2018-12-12T10:13:42Z","file_name":"IST-2016-517-v1+1_journal.pbio.1002382_1_.PDF","file_id":"5027","content_type":"application/pdf"}],"has_accepted_license":"1","scopus_import":1,"doi":"10.1371/journal.pbio.1002382","acknowledgement":"We thank Silvia Arber, Thomas Jessell, Kenneth M. Murphy, Carlton Bates, Hideki Enomoto, Liqun Luo and Andrew McMahon for mouse strains; Thomas Jessell for antibodies; and Laura Martinez Prat for experimental assistance.","publication":"PLoS Biology","language":[{"iso":"eng"}],"intvolume":" 14","publist_id":"5699","author":[{"full_name":"Riccio, Paul","last_name":"Riccio","first_name":"Paul"},{"full_name":"Cebrián, Cristina","first_name":"Cristina","last_name":"Cebrián"},{"first_name":"Hui","last_name":"Zong","full_name":"Zong, Hui"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Costantini, Frank","last_name":"Costantini","first_name":"Frank"}],"file_date_updated":"2020-07-14T12:44:57Z","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)"},"citation":{"ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis,” PLoS Biology, vol. 14, no. 2. Public Library of Science, 2016.","short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, PLoS Biology 14 (2016).","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2016). Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002382","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. 2016;14(2). doi:10.1371/journal.pbio.1002382","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2016. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. 14(2), e1002382.","chicago":"Riccio, Paul, Cristina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.1002382.","mla":"Riccio, Paul, et al. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” PLoS Biology, vol. 14, no. 2, e1002382, Public Library of Science, 2016, doi:10.1371/journal.pbio.1002382."},"status":"public","volume":14,"type":"journal_article","pubrep_id":"517","publication_status":"published","_id":"1488","department":[{"_id":"SiHi"}],"month":"02","date_published":"2016-02-19T00:00:00Z","article_number":"e1002382","year":"2016","date_updated":"2023-02-23T10:01:08Z","day":"19","related_material":{"record":[{"relation":"research_data","id":"9703","status":"deleted"}]}},{"year":"2016","date_updated":"2021-01-12T06:51:05Z","day":"01","_id":"1489","department":[{"_id":"LaEr"}],"month":"04","date_published":"2016-04-01T00:00:00Z","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)"},"citation":{"apa":"Ajanki, O. H., Erdös, L., & Krüger, T. H. (2016). Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1479-y","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Journal of Statistical Physics 163 (2016) 280–302.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Local spectral statistics of Gaussian matrices with correlated entries,” Journal of Statistical Physics, vol. 163, no. 2. Springer, pp. 280–302, 2016.","mla":"Ajanki, Oskari H., et al. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” Journal of Statistical Physics, vol. 163, no. 2, Springer, 2016, pp. 280–302, doi:10.1007/s10955-016-1479-y.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” Journal of Statistical Physics. Springer, 2016. https://doi.org/10.1007/s10955-016-1479-y.","ama":"Ajanki OH, Erdös L, Krüger TH. Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. 2016;163(2):280-302. doi:10.1007/s10955-016-1479-y","ista":"Ajanki OH, Erdös L, Krüger TH. 2016. Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. 163(2), 280–302."},"status":"public","type":"journal_article","volume":163,"publication_status":"published","pubrep_id":"516","doi":"10.1007/s10955-016-1479-y","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). Oskari H. Ajanki was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council. László Erdős was Partially supported by ERC Advanced Grant RANMAT No. 338804. Torben Krüger was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council.","publication":"Journal of Statistical Physics","language":[{"iso":"eng"}],"intvolume":" 163","publist_id":"5698","author":[{"first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","last_name":"Ajanki","full_name":"Ajanki, Oskari H"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krüger","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"file_date_updated":"2020-07-14T12:44:57Z","scopus_import":1,"page":"280 - 302","file":[{"date_created":"2018-12-12T10:11:16Z","file_name":"IST-2016-516-v1+1_s10955-016-1479-y.pdf","file_id":"4869","content_type":"application/pdf","checksum":"7139598dcb1cafbe6866bd2bfd732b33","creator":"system","date_updated":"2020-07-14T12:44:57Z","relation":"main_file","access_level":"open_access","file_size":660602}],"abstract":[{"lang":"eng","text":"We prove optimal local law, bulk universality and non-trivial decay for the off-diagonal elements of the resolvent for a class of translation invariant Gaussian random matrix ensembles with correlated entries. "}],"has_accepted_license":"1","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"article_processing_charge":"Yes (via OA deal)","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"Local spectral statistics of Gaussian matrices with correlated entries","quality_controlled":"1","oa_version":"Published Version","oa":1,"ddc":["510"],"ec_funded":1,"date_created":"2018-12-11T11:52:19Z"},{"department":[{"_id":"MiSi"}],"_id":"1490","date_published":"2016-02-23T00:00:00Z","month":"02","year":"2016","date_updated":"2021-01-12T06:51:07Z","day":"23","publication":"Cell Reports","doi":"10.1016/j.celrep.2016.01.048","language":[{"iso":"eng"}],"intvolume":" 14","publist_id":"5697","file_date_updated":"2020-07-14T12:44:58Z","author":[{"last_name":"Russo","first_name":"Erica","full_name":"Russo, Erica"},{"first_name":"Alvaro","last_name":"Teijeira","full_name":"Teijeira, Alvaro"},{"orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ann","last_name":"Willrodt","full_name":"Willrodt, Ann"},{"first_name":"Joël","last_name":"Bloch","full_name":"Bloch, Joël"},{"full_name":"Nitschké, Maximilian","first_name":"Maximilian","last_name":"Nitschké"},{"full_name":"Santambrogio, Laura","first_name":"Laura","last_name":"Santambrogio"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Halin","first_name":"Cornelia","full_name":"Halin, Cornelia"}],"citation":{"apa":"Russo, E., Teijeira, A., Vaahtomeri, K., Willrodt, A., Bloch, J., Nitschké, M., … Halin, C. (2016). Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.01.048","short":"E. Russo, A. Teijeira, K. Vaahtomeri, A. Willrodt, J. Bloch, M. Nitschké, L. Santambrogio, D. Kerjaschki, M.K. Sixt, C. Halin, Cell Reports 14 (2016) 1723–1734.","ieee":"E. Russo et al., “Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels,” Cell Reports, vol. 14, no. 7. Cell Press, pp. 1723–1734, 2016.","mla":"Russo, Erica, et al. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” Cell Reports, vol. 14, no. 7, Cell Press, 2016, pp. 1723–34, doi:10.1016/j.celrep.2016.01.048.","chicago":"Russo, Erica, Alvaro Teijeira, Kari Vaahtomeri, Ann Willrodt, Joël Bloch, Maximilian Nitschké, Laura Santambrogio, Dontscho Kerjaschki, Michael K Sixt, and Cornelia Halin. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” Cell Reports. Cell Press, 2016. https://doi.org/10.1016/j.celrep.2016.01.048.","ista":"Russo E, Teijeira A, Vaahtomeri K, Willrodt A, Bloch J, Nitschké M, Santambrogio L, Kerjaschki D, Sixt MK, Halin C. 2016. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 14(7), 1723–1734.","ama":"Russo E, Teijeira A, Vaahtomeri K, et al. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 2016;14(7):1723-1734. doi:10.1016/j.celrep.2016.01.048"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"volume":14,"type":"journal_article","status":"public","pubrep_id":"515","publication_status":"published","file":[{"date_created":"2018-12-12T10:12:30Z","file_name":"IST-2016-515-v1+1_1-s2.0-S2211124716300262-main.pdf","file_id":"4948","content_type":"application/pdf","creator":"system","checksum":"c98c1151d5f1e5ce1643a83d8d7f3c29","date_updated":"2020-07-14T12:44:58Z","access_level":"open_access","relation":"main_file","file_size":5489897}],"page":"1723 - 1734","has_accepted_license":"1","abstract":[{"text":"To induce adaptive immunity, dendritic cells (DCs) migrate through afferent lymphatic vessels (LVs) to draining lymph nodes (dLNs). This process occurs in several consecutive steps. Upon entry into lymphatic capillaries, DCs first actively crawl into downstream collecting vessels. From there, they are next passively and rapidly transported to the dLN by lymph flow. Here, we describe a role for the chemokine CCL21 in intralymphatic DC crawling. Performing time-lapse imaging in murine skin, we found that blockade of CCL21-but not the absence of lymph flow-completely abolished DC migration from capillaries toward collecting vessels and reduced the ability of intralymphatic DCs to emigrate from skin. Moreover, we found that in vitro low laminar flow established a CCL21 gradient along lymphatic endothelial monolayers, thereby inducing downstream-directed DC migration. These findings reveal a role for intralymphatic CCL21 in promoting DC trafficking to dLNs, through the formation of a flow-induced gradient.","lang":"eng"}],"scopus_import":1,"ddc":["570"],"oa":1,"date_created":"2018-12-11T11:52:19Z","issue":"7","title":"Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","oa_version":"Published Version","quality_controlled":"1"},{"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A new method and a new scaling for deriving fermionic mean-field dynamics","quality_controlled":"1","oa_version":"Published Version","issue":"1","ec_funded":1,"date_created":"2018-12-11T11:52:20Z","oa":1,"ddc":["510","530"],"scopus_import":1,"file":[{"content_type":"application/pdf","file_id":"5246","file_name":"IST-2016-514-v1+1_s11040-016-9204-2.pdf","date_created":"2018-12-12T10:16:55Z","date_updated":"2020-07-14T12:44:58Z","checksum":"eb5d2145ef0d377c4f78bf06e18f4529","creator":"system","file_size":911310,"access_level":"open_access","relation":"main_file"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"We introduce a new method for deriving the time-dependent Hartree or Hartree-Fock equations as an effective mean-field dynamics from the microscopic Schrödinger equation for fermionic many-particle systems in quantum mechanics. The method is an adaption of the method used in Pickl (Lett. Math. Phys. 97 (2) 151–164 2011) for bosonic systems to fermionic systems. It is based on a Gronwall type estimate for a suitable measure of distance between the microscopic solution and an antisymmetrized product state. We use this method to treat a new mean-field limit for fermions with long-range interactions in a large volume. Some of our results hold for singular attractive or repulsive interactions. We can also treat Coulomb interaction assuming either a mild singularity cutoff or certain regularity conditions on the solutions to the Hartree(-Fock) equations. In the considered limit, the kinetic and interaction energy are of the same order, while the average force is subleading. For some interactions, we prove that the Hartree(-Fock) dynamics is a more accurate approximation than a simpler dynamics that one would expect from the subleading force. With our method we also treat the mean-field limit coupled to a semiclassical limit, which was discussed in the literature before, and we recover some of the previous results. All results hold for initial data close (but not necessarily equal) to antisymmetrized product states and we always provide explicit rates of convergence."}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"article_processing_charge":"Yes (via OA deal)","status":"public","volume":19,"type":"journal_article","pubrep_id":"514","publication_status":"published","citation":{"chicago":"Petrat, Sören P, and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry. Springer, 2016. https://doi.org/10.1007/s11040-016-9204-2.","mla":"Petrat, Sören P., and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry, vol. 19, no. 1, 3, Springer, 2016, doi:10.1007/s11040-016-9204-2.","ama":"Petrat SP, Pickl P. A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. 2016;19(1). doi:10.1007/s11040-016-9204-2","ista":"Petrat SP, Pickl P. 2016. A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. 19(1), 3.","short":"S.P. Petrat, P. Pickl, Mathematical Physics, Analysis and Geometry 19 (2016).","apa":"Petrat, S. P., & Pickl, P. (2016). A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-016-9204-2","ieee":"S. P. Petrat and P. Pickl, “A new method and a new scaling for deriving fermionic mean-field dynamics,” Mathematical Physics, Analysis and Geometry, vol. 19, no. 1. Springer, 2016."},"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)"},"publist_id":"5690","author":[{"orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P","last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P"},{"last_name":"Pickl","first_name":"Peter","full_name":"Pickl, Peter"}],"file_date_updated":"2020-07-14T12:44:58Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","doi":"10.1007/s11040-016-9204-2","publication":"Mathematical Physics, Analysis and Geometry","language":[{"iso":"eng"}],"intvolume":" 19","day":"01","year":"2016","date_updated":"2021-01-12T06:51:08Z","month":"03","date_published":"2016-03-01T00:00:00Z","article_number":"3","_id":"1493","department":[{"_id":"RoSe"}]},{"publication_status":"published","status":"public","type":"journal_article","volume":30,"citation":{"ieee":"P. Marhavý et al., “Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation,” Genes and Development, vol. 30, no. 4. Cold Spring Harbor Laboratory Press, pp. 471–483, 2016.","short":"P. Marhavý, J.C. Montesinos López, A. Abuzeineh, D. Van Damme, J. Vermeer, J. Duclercq, H. Rakusova, P. Marhavá, J. Friml, N. Geldner, E. Benková, Genes and Development 30 (2016) 471–483.","apa":"Marhavý, P., Montesinos López, J. C., Abuzeineh, A., Van Damme, D., Vermeer, J., Duclercq, J., … Benková, E. (2016). Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.276964.115","ama":"Marhavý P, Montesinos López JC, Abuzeineh A, et al. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 2016;30(4):471-483. doi:10.1101/gad.276964.115","ista":"Marhavý P, Montesinos López JC, Abuzeineh A, Van Damme D, Vermeer J, Duclercq J, Rakusova H, Marhavá P, Friml J, Geldner N, Benková E. 2016. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 30(4), 471–483.","mla":"Marhavý, Peter, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and Development, vol. 30, no. 4, Cold Spring Harbor Laboratory Press, 2016, pp. 471–83, doi:10.1101/gad.276964.115.","chicago":"Marhavý, Peter, Juan C Montesinos López, Anas Abuzeineh, Daniël Van Damme, Joop Vermeer, Jérôme Duclercq, Hana Rakusova, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.276964.115."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"author":[{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741"},{"full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C","last_name":"Montesinos López"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"full_name":"Van Damme, Daniël","last_name":"Van Damme","first_name":"Daniël"},{"full_name":"Vermeer, Joop","first_name":"Joop","last_name":"Vermeer"},{"full_name":"Duclercq, Jérôme","last_name":"Duclercq","first_name":"Jérôme"},{"last_name":"Rakusova","first_name":"Hana","full_name":"Rakusova, Hana"},{"last_name":"Marhavá","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavá, Petra"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Geldner, Niko","last_name":"Geldner","first_name":"Niko"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková"}],"file_date_updated":"2020-07-14T12:44:58Z","publist_id":"5691","intvolume":" 30","language":[{"iso":"eng"}],"doi":"10.1101/gad.276964.115","acknowledgement":"This work was supported by a European Research Council Starting Inde-pendent Research grant (ERC-2007-Stg-207362-HCPO to J.D.), Research Foundation-Flanders (G033711N to A.A.), and the Austrian Science Fund (FWF01_I1774S to E.B.). P.M. is indebted to the Federation of European Biochemical Sciences for a Long-Term Fellowship. ","publication":"Genes and Development","day":"01","date_updated":"2021-01-12T06:51:08Z","year":"2016","month":"03","date_published":"2016-03-01T00:00:00Z","_id":"1492","department":[{"_id":"EvBe"}],"oa_version":"Published Version","quality_controlled":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cold Spring Harbor Laboratory Press","title":"Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation","issue":"4","date_created":"2018-12-11T11:52:20Z","oa":1,"ddc":["570"],"license":"https://creativecommons.org/licenses/by-nc/4.0/","scopus_import":1,"external_id":{"pmid":[" 26883363"]},"pmid":1,"file":[{"date_created":"2019-01-25T09:56:11Z","file_name":"2016_GeneDev_Marhavy.pdf","content_type":"application/pdf","file_id":"5883","access_level":"open_access","relation":"main_file","file_size":2757636,"checksum":"ea394498ee56270e021d1028a29358a0","creator":"kschuh","date_updated":"2020-07-14T12:44:58Z"}],"has_accepted_license":"1","page":"471 - 483","abstract":[{"text":"To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated cells with a preserved prolif eration capacity. The root pericycle represents a unique tissue with conditional meristematic activity, and its tight control determines initiation of lateral organs. Here we show that the meristematic activity of the pericycle is constrained by the interaction with the adjacent endodermis. Release of these restraints by elimination of endo dermal cells by single-cell ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis removal substitutes for the phytohormone auxin-dependent initiation of the pericycle meristematic activity. However, auxin is indispensable to steer the cell division plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally distinct role for auxin during lateral root initiation. In the endodermis, auxin releases constraints arising from cell-to-cell interactions that compromise the pericycle meristematic activity, whereas, in the pericycle, auxin defines the orientation of the cell division plane to initiate lateral roots.","lang":"eng"}]},{"day":"07","date_updated":"2021-01-12T06:51:09Z","year":"2016","article_number":"032502","date_published":"2016-03-07T00:00:00Z","month":"03","department":[{"_id":"MiLe"}],"_id":"1496","publication_status":"published","volume":93,"type":"journal_article","status":"public","citation":{"mla":"Amaro, Pedro, et al. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3, 032502, American Physical Society, 2016, doi:10.1103/PhysRevA.93.032502.","chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Jorge Machado, Mauro Guerra, Paul Indelicato, and José Santos. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.032502.","ama":"Amaro P, Fratini F, Safari L, et al. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3). doi:10.1103/PhysRevA.93.032502","ista":"Amaro P, Fratini F, Safari L, Machado J, Guerra M, Indelicato P, Santos J. 2016. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 032502.","short":"P. Amaro, F. Fratini, L. Safari, J. Machado, M. Guerra, P. Indelicato, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).","apa":"Amaro, P., Fratini, F., Safari, L., Machado, J., Guerra, M., Indelicato, P., & Santos, J. (2016). Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.93.032502","ieee":"P. Amaro et al., “Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3. American Physical Society, 2016."},"author":[{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"},{"last_name":"Safari","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh"},{"last_name":"Machado","first_name":"Jorge","full_name":"Machado, Jorge"},{"first_name":"Mauro","last_name":"Guerra","full_name":"Guerra, Mauro"},{"first_name":"Paul","last_name":"Indelicato","full_name":"Indelicato, Paul"},{"last_name":"Santos","first_name":"José","full_name":"Santos, José"}],"publist_id":"5683","language":[{"iso":"eng"}],"intvolume":" 93","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","doi":"10.1103/PhysRevA.93.032502","acknowledgement":"This research was supported in part by FCT, Portugal, through Project No. PTDC/FIS/117606/2010, financed by the European Community Fund FEDER through the COMPETE. ","scopus_import":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"abstract":[{"text":"The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is theoretically investigated within a fully relativistic framework and a second-order perturbation theory. We focus our analysis on how electron correlation, as well as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For this purpose, we include the electronic correlation via an effective local potential and within a single configuration-state model. Due to its experimental interest, evaluations of decay rates are performed for berylliumlike xenon and uranium. We find that the negative-energy contribution can be neglected at the present level of accuracy in the evaluation of the decay rate. On the other hand, if contributions of electronic correlation are not carefully taken into account, it may change the lifetime of the metastable state by up to 20%. By performing a full-relativistic jj-coupling calculation, we found a decrease of the decay rate by two orders of magnitude compared to non-relativistic LS-coupling calculations, for the selected heavy ions.","lang":"eng"}],"oa_version":"Preprint","quality_controlled":"1","title":"Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","issue":"3","main_file_link":[{"url":"http://arxiv.org/abs/1508.06169","open_access":"1"}],"date_created":"2018-12-11T11:52:21Z","ec_funded":1,"oa":1},{"scopus_import":1,"abstract":[{"text":"Turbulence is one of the most frequently encountered non-equilibrium phenomena in nature, yet characterizing the transition that gives rise to turbulence in basic shear flows has remained an elusive task. Although, in recent studies, critical points marking the onset of sustained turbulence have been determined for several such flows, the physical nature of the transition could not be fully explained. In extensive experimental and computational studies we show for the example of Couette flow that the onset of turbulence is a second-order phase transition and falls into the directed percolation universality class. Consequently, the complex laminar–turbulent patterns distinctive for the onset of turbulence in shear flows result from short-range interactions of turbulent domains and are characterized by universal critical exponents. More generally, our study demonstrates that even high-dimensional systems far from equilibrium such as turbulence exhibit universality at onset and that here the collective dynamics obeys simple rules.","lang":"eng"}],"page":"254 - 258","project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"name":"Astrophysical instability of currents and turbulences","grant_number":"SFB 963 TP A8","_id":"2511D90C-B435-11E9-9278-68D0E5697425"}],"title":"Directed percolation phase transition to sustained turbulence in Couette flow","publisher":"Nature Publishing Group","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","quality_controlled":"1","issue":"3","date_created":"2018-12-11T11:52:21Z","ec_funded":1,"day":"15","year":"2016","date_updated":"2021-01-12T06:51:08Z","date_published":"2016-02-15T00:00:00Z","month":"02","department":[{"_id":"BjHo"}],"_id":"1494","type":"journal_article","volume":12,"status":"public","publication_status":"published","citation":{"apa":"Lemoult, G. M., Shi, L., Avila, K., Jalikop, S. V., Avila, M., & Hof, B. (2016). Directed percolation phase transition to sustained turbulence in Couette flow. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3675","short":"G.M. Lemoult, L. Shi, K. Avila, S.V. Jalikop, M. Avila, B. Hof, Nature Physics 12 (2016) 254–258.","ieee":"G. M. Lemoult, L. Shi, K. Avila, S. V. Jalikop, M. Avila, and B. Hof, “Directed percolation phase transition to sustained turbulence in Couette flow,” Nature Physics, vol. 12, no. 3. Nature Publishing Group, pp. 254–258, 2016.","chicago":"Lemoult, Grégoire M, Liang Shi, Kerstin Avila, Shreyas V Jalikop, Marc Avila, and Björn Hof. “Directed Percolation Phase Transition to Sustained Turbulence in Couette Flow.” Nature Physics. Nature Publishing Group, 2016. https://doi.org/10.1038/nphys3675.","mla":"Lemoult, Grégoire M., et al. “Directed Percolation Phase Transition to Sustained Turbulence in Couette Flow.” Nature Physics, vol. 12, no. 3, Nature Publishing Group, 2016, pp. 254–58, doi:10.1038/nphys3675.","ista":"Lemoult GM, Shi L, Avila K, Jalikop SV, Avila M, Hof B. 2016. Directed percolation phase transition to sustained turbulence in Couette flow. Nature Physics. 12(3), 254–258.","ama":"Lemoult GM, Shi L, Avila K, Jalikop SV, Avila M, Hof B. Directed percolation phase transition to sustained turbulence in Couette flow. Nature Physics. 2016;12(3):254-258. doi:10.1038/nphys3675"},"publist_id":"5685","author":[{"last_name":"Lemoult","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","first_name":"Grégoire M","full_name":"Lemoult, Grégoire M"},{"full_name":"Shi, Liang","last_name":"Shi","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang"},{"full_name":"Avila, Kerstin","last_name":"Avila","first_name":"Kerstin"},{"full_name":"Jalikop, Shreyas V","id":"44A1D772-F248-11E8-B48F-1D18A9856A87","first_name":"Shreyas V","last_name":"Jalikop"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"publication":"Nature Physics","doi":"10.1038/nphys3675","acknowledgement":"We thank P. Maier for providing valuable ideas and supporting us in the technical aspects. Discussions with D. Barkley, Y. Duguet, B. Eckhart, N. Goldenfeld, P. Manneville and K. Takeuchi are gratefully acknowledged. 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. L.S. and B.H. acknowledge research funding by Deutsche Forschungsgemeinschaft (DFG) under Grant No. SFB 963/1 (project A8). Numerical simulations were performed thanks to the CPU time allocations of JUROPA in Juelich Supercomputing Center (project HGU17) and of the Max Planck Computing and Data Facility (Garching, Germany). Excellent technical support from M. Rampp on the hybrid code nsCouette is appreciated.","intvolume":" 12","language":[{"iso":"eng"}]},{"publist_id":"5692","author":[{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"full_name":"Nam, Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"},{"first_name":"Nicolas","last_name":"Rougerie","full_name":"Rougerie, Nicolas"}],"acknowledgement":"The authors acknowledge financial support from the European Research Council (FP7/2007-2013 Grant Agreement MNIQS 258023) and the ANR (Mathostaq project, ANR-13-JS01-0005-01). The second and third authors have benefited from the hospitality of the Institute for Mathematical Science of the National University of Singapore.","doi":"10.1090/tran/6537","publication":"Transactions of the American Mathematical Society","language":[{"iso":"eng"}],"intvolume":" 368","status":"public","volume":368,"type":"journal_article","publication_status":"published","citation":{"short":"M. Lewin, P. Nam, N. Rougerie, Transactions of the American Mathematical Society 368 (2016) 6131–6157.","apa":"Lewin, M., Nam, P., & Rougerie, N. (2016). The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6537","ieee":"M. Lewin, P. Nam, and N. Rougerie, “The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases,” Transactions of the American Mathematical Society, vol. 368, no. 9. American Mathematical Society, pp. 6131–6157, 2016.","mla":"Lewin, Mathieu, et al. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” Transactions of the American Mathematical Society, vol. 368, no. 9, American Mathematical Society, 2016, pp. 6131–57, doi:10.1090/tran/6537.","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” Transactions of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/tran/6537.","ista":"Lewin M, Nam P, Rougerie N. 2016. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. 368(9), 6131–6157.","ama":"Lewin M, Nam P, Rougerie N. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. 2016;368(9):6131-6157. doi:10.1090/tran/6537"},"month":"01","date_published":"2016-01-01T00:00:00Z","_id":"1491","department":[{"_id":"RoSe"}],"day":"01","year":"2016","date_updated":"2021-01-12T06:51:07Z","date_created":"2018-12-11T11:52:20Z","oa":1,"publisher":"American Mathematical Society","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases","quality_controlled":"1","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1405.3220"}],"issue":"9","abstract":[{"lang":"eng","text":"We study the ground state of a trapped Bose gas, starting from the full many-body Schrödinger Hamiltonian, and derive the non-linear Schrödinger energy functional in the limit of a large particle number, when the interaction potential converges slowly to a Dirac delta function. Our method is based on quantitative estimates on the discrepancy between the full many-body energy and its mean-field approximation using Hartree states. These are proved using finite dimensional localization and a quantitative version of the quantum de Finetti theorem. Our approach covers the case of attractive interactions in the regime of stability. In particular, our main new result is a derivation of the 2D attractive non-linear Schrödinger ground state."}],"page":"6131 - 6157","scopus_import":1},{"author":[{"last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Franek, Peter"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Krcál","full_name":"Krcál, Marek"}],"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5799","intvolume":" 56","language":[{"iso":"eng"}],"doi":"10.1007/s00454-016-9794-2","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","publication":"Discrete & Computational Geometry","publication_status":"published","pubrep_id":"614","status":"public","type":"journal_article","volume":56,"citation":{"ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” Discrete & Computational Geometry, vol. 56, no. 1. Springer, pp. 126–164, 2016.","short":"P. Franek, M. Krcál, Discrete & Computational Geometry 56 (2016) 126–164.","apa":"Franek, P., & Krcál, M. (2016). On computability and triviality of well groups. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9794-2","ista":"Franek P, Krcál M. 2016. On computability and triviality of well groups. Discrete & Computational Geometry. 56(1), 126–164.","ama":"Franek P, Krcál M. On computability and triviality of well groups. Discrete & Computational Geometry. 2016;56(1):126-164. doi:10.1007/s00454-016-9794-2","mla":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry, vol. 56, no. 1, Springer, 2016, pp. 126–64, doi:10.1007/s00454-016-9794-2.","chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry. Springer, 2016. https://doi.org/10.1007/s00454-016-9794-2."},"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)"},"month":"07","date_published":"2016-07-01T00:00:00Z","_id":"1408","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"related_material":{"record":[{"status":"public","id":"1510","relation":"earlier_version"}]},"day":"01","date_updated":"2023-02-23T10:02:11Z","year":"2016","ec_funded":1,"date_created":"2018-12-11T11:51:51Z","oa":1,"ddc":["510"],"oa_version":"Published Version","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"On computability and triviality of well groups","issue":"1","project":[{"name":"Robust invariants of Nonlinear Systems","call_identifier":"FWF","grant_number":"M01980","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map (Formula presented.) on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within (Formula presented.) distance r from f for a given (Formula presented.). The main drawback of the approach is that the computability of well groups was shown only when (Formula presented.) or (Formula presented.). Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of (Formula presented.) by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and (Formula presented.), our approximation of the (Formula presented.)th well group is exact. For the second part, we find examples of maps (Formula presented.) with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status.","lang":"eng"}],"file":[{"date_created":"2018-12-12T10:10:55Z","file_name":"IST-2016-614-v1+1_s00454-016-9794-2.pdf","content_type":"application/pdf","file_id":"4846","creator":"system","checksum":"e0da023abf6b72abd8c6a8c76740d53c","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","relation":"main_file","file_size":905303}],"has_accepted_license":"1","page":"126 - 164","scopus_import":1},{"intvolume":" 202","language":[{"iso":"eng"}],"doi":"10.1534/genetics.115.183814","acknowledgement":"We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.).","publication":"Genetics","author":[{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"first_name":"Simon","last_name":"Martin","full_name":"Martin, Simon"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5658","citation":{"apa":"Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.183814","short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","ieee":"K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016.","mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:10.1534/genetics.115.183814.","chicago":"Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814.","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.","ama":"Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786. doi:10.1534/genetics.115.183814"},"publication_status":"published","pubrep_id":"561","status":"public","type":"journal_article","volume":202,"_id":"1518","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"month":"02","date_published":"2016-02-01T00:00:00Z","date_updated":"2022-05-24T09:16:22Z","year":"2016","day":"01","oa":1,"article_type":"original","ddc":["570"],"ec_funded":1,"date_created":"2018-12-11T11:52:29Z","issue":"2","quality_controlled":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Genetics Society of America","title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"article_processing_charge":"No","abstract":[{"text":"The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno.","lang":"eng"}],"page":"775 - 786","has_accepted_license":"1","file":[{"file_size":957466,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:45:00Z","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","creator":"system","file_id":"5241","content_type":"application/pdf","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","date_created":"2018-12-12T10:16:51Z"}],"external_id":{"pmid":["26715666"]},"pmid":1,"scopus_import":"1"},{"scopus_import":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"abstract":[{"lang":"eng","text":"When designing genetic circuits, the typical primitives used in major existing modelling formalisms are gene interaction graphs, where edges between genes denote either an activation or inhibition relation. However, when designing experiments, it is important to be precise about the low-level mechanistic details as to how each such relation is implemented. The rule-based modelling language Kappa allows to unambiguously specify mechanistic details such as DNA binding sites, dimerisation of transcription factors, or co-operative interactions. Such a detailed description comes with complexity and computationally costly executions. We propose a general method for automatically transforming a rule-based program, by eliminating intermediate species and adjusting the rate constants accordingly. To the best of our knowledge, we show the first automated reduction of rule-based models based on equilibrium approximations.\r\nOur algorithm is an adaptation of an existing algorithm, which was designed for reducing reaction-based programs; our version of the algorithm scans the rule-based Kappa model in search for those interaction patterns known to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional checks are then performed in order to verify if the reduction is meaningful in the context of the full model. The reduced model is efficiently obtained by static inspection over the rule-set. The tool is tested on a detailed rule-based model of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has 11 rules and 5 agents, and provides a dramatic reduction in simulation time of several orders of magnitude."}],"page":"173 - 191","oa_version":"Preprint","quality_controlled":"1","title":"Efficient reduction of kappa models by static inspection of the rule-set","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://arxiv.org/abs/1501.00440","open_access":"1"}],"date_created":"2018-12-11T11:52:31Z","ec_funded":1,"oa":1,"day":"10","date_updated":"2021-01-12T06:51:22Z","year":"2016","alternative_title":["LNCS"],"date_published":"2016-01-10T00:00:00Z","month":"01","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"_id":"1524","conference":{"end_date":"2015-09-05","name":"HSB: Hybrid Systems Biology","location":"Madrid, Spain","start_date":"2015-09-04"},"publication_status":"published","volume":9271,"type":"conference","status":"public","citation":{"mla":"Beica, Andreea, et al. Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set. Vol. 9271, Springer, 2016, pp. 173–91, doi:10.1007/978-3-319-26916-0_10.","chicago":"Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set,” 9271:173–91. Springer, 2016. https://doi.org/10.1007/978-3-319-26916-0_10.","ama":"Beica A, Guet CC, Petrov T. Efficient reduction of kappa models by static inspection of the rule-set. In: Vol 9271. Springer; 2016:173-191. doi:10.1007/978-3-319-26916-0_10","ista":"Beica A, Guet CC, Petrov T. 2016. Efficient reduction of kappa models by static inspection of the rule-set. HSB: Hybrid Systems Biology, LNCS, vol. 9271, 173–191.","short":"A. Beica, C.C. Guet, T. Petrov, in:, Springer, 2016, pp. 173–191.","apa":"Beica, A., Guet, C. C., & Petrov, T. (2016). Efficient reduction of kappa models by static inspection of the rule-set (Vol. 9271, pp. 173–191). Presented at the HSB: Hybrid Systems Biology, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-26916-0_10","ieee":"A. Beica, C. C. Guet, and T. Petrov, “Efficient reduction of kappa models by static inspection of the rule-set,” presented at the HSB: Hybrid Systems Biology, Madrid, Spain, 2016, vol. 9271, pp. 173–191."},"author":[{"full_name":"Beica, Andreea","first_name":"Andreea","last_name":"Beica"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov"}],"publist_id":"5649","intvolume":" 9271","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-26916-0_10","acknowledgement":"This research was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734, and the SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2_148797."},{"year":"2016","date_updated":"2021-01-12T06:51:21Z","day":"01","scopus_import":1,"page":"892 - 901","abstract":[{"lang":"eng","text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. It is the largest protein assembly of respiratory chains and one of the most elaborate redox membrane proteins known. Bacterial enzyme is about half the size of mitochondrial and thus provides its important "minimal" model. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The L-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. We have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus, the membrane domain from Escherichia coli and recently of the intact, entire complex I from T. thermophilus (536. kDa, 16 subunits, 9 iron-sulphur clusters, 64 transmembrane helices). The 95. Å long electron transfer pathway through the enzyme proceeds from the primary electron acceptor flavin mononucleotide through seven conserved Fe-S clusters to the unusual elongated quinone-binding site at the interface with the membrane domain. Four putative proton translocation channels are found in the membrane domain, all linked by the central flexible axis containing charged residues. The redox energy of electron transfer is coupled to proton translocation by the as yet undefined mechanism proposed to involve long-range conformational changes. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt."}],"_id":"1521","department":[{"_id":"LeSa"}],"month":"07","date_published":"2016-07-01T00:00:00Z","issue":"7","citation":{"ieee":"J. Berrisford, R. Baradaran, and L. A. Sazanov, “Structure of bacterial respiratory complex I,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no. 7. Elsevier, pp. 892–901, 2016.","apa":"Berrisford, J., Baradaran, R., & Sazanov, L. A. (2016). Structure of bacterial respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2016.01.012","short":"J. Berrisford, R. Baradaran, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1857 (2016) 892–901.","ama":"Berrisford J, Baradaran R, Sazanov LA. Structure of bacterial respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 2016;1857(7):892-901. doi:10.1016/j.bbabio.2016.01.012","ista":"Berrisford J, Baradaran R, Sazanov LA. 2016. Structure of bacterial respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(7), 892–901.","chicago":"Berrisford, John, Rozbeh Baradaran, and Leonid A Sazanov. “Structure of Bacterial Respiratory Complex I.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2016. https://doi.org/10.1016/j.bbabio.2016.01.012.","mla":"Berrisford, John, et al. “Structure of Bacterial Respiratory Complex I.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no. 7, Elsevier, 2016, pp. 892–901, doi:10.1016/j.bbabio.2016.01.012."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","status":"public","title":"Structure of bacterial respiratory complex I","volume":1857,"type":"journal_article","oa_version":"None","publication_status":"published","quality_controlled":"1","doi":"10.1016/j.bbabio.2016.01.012","acknowledgement":"funded by the Medical Research Council (Grant number MC_U105674180)","publication":"Biochimica et Biophysica Acta - Bioenergetics","language":[{"iso":"eng"}],"intvolume":" 1857","publist_id":"5654","date_created":"2018-12-11T11:52:30Z","author":[{"full_name":"Berrisford, John","last_name":"Berrisford","first_name":"John"},{"full_name":"Baradaran, Rozbeh","last_name":"Baradaran","first_name":"Rozbeh"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}]},{"date_created":"2018-12-11T11:52:30Z","oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Independent University of Moscow","title":"The classification of certain linked 3-manifolds in 6-space","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.3918"}],"issue":"1","page":"1 - 25","abstract":[{"lang":"eng","text":"We classify smooth Brunnian (i.e., unknotted on both components) embeddings (S2 × S1) ⊔ S3 → ℝ6. Any Brunnian embedding (S2 × S1) ⊔ S3 → ℝ6 is isotopic to an explicitly constructed embedding fk,m,n for some integers k, m, n such that m ≡ n (mod 2). Two embeddings fk,m,n and fk′ ,m′,n′ are isotopic if and only if k = k′, m ≡ m′ (mod 2k) and n ≡ n′ (mod 2k). We use Haefliger’s classification of embeddings S3 ⊔ S3 → ℝ6 in our proof. The relation between the embeddings (S2 × S1) ⊔ S3 → ℝ6 and S3 ⊔ S3 → ℝ6 is not trivial, however. For example, we show that there exist embeddings f: (S2 ×S1) ⊔ S3 → ℝ6 and g, g′ : S3 ⊔ S3 → ℝ6 such that the componentwise embedded connected sum f # g is isotopic to f # g′ but g is not isotopic to g′."}],"article_processing_charge":"No","scopus_import":"1","external_id":{"arxiv":["1408.3918"]},"publist_id":"5652","author":[{"first_name":"Serhii","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","full_name":"Avvakumov, Serhii"}],"doi":"10.17323/1609-4514-2016-16-1-1-25","acknowledgement":"I thank A. Skopenkov for telling me about the problem and for his useful remarks. I also thank A. Sossinsky,\r\nA. Zhubr, M. Skopenkov, P. Akhmetiev, and an anonymous referee for their feedback. Author was partially\r\nsupported by Dobrushin fellowship, 2013, and by RFBR grant 15-01-06302.","publication":"Moscow Mathematical Journal","publication_identifier":{"eissn":["1609-4514"]},"language":[{"iso":"eng"}],"intvolume":" 16","status":"public","volume":16,"type":"journal_article","publication_status":"published","citation":{"apa":"Avvakumov, S. (2016). The classification of certain linked 3-manifolds in 6-space. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2016-16-1-1-25","short":"S. Avvakumov, Moscow Mathematical Journal 16 (2016) 1–25.","ieee":"S. Avvakumov, “The classification of certain linked 3-manifolds in 6-space,” Moscow Mathematical Journal, vol. 16, no. 1. Independent University of Moscow, pp. 1–25, 2016.","mla":"Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in 6-Space.” Moscow Mathematical Journal, vol. 16, no. 1, Independent University of Moscow, 2016, pp. 1–25, doi:10.17323/1609-4514-2016-16-1-1-25.","chicago":"Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in 6-Space.” Moscow Mathematical Journal. Independent University of Moscow, 2016. https://doi.org/10.17323/1609-4514-2016-16-1-1-25.","ama":"Avvakumov S. The classification of certain linked 3-manifolds in 6-space. Moscow Mathematical Journal. 2016;16(1):1-25. doi:10.17323/1609-4514-2016-16-1-1-25","ista":"Avvakumov S. 2016. The classification of certain linked 3-manifolds in 6-space. Moscow Mathematical Journal. 16(1), 1–25."},"month":"01","date_published":"2016-01-01T00:00:00Z","_id":"1522","department":[{"_id":"UlWa"}],"day":"01","year":"2016","date_updated":"2022-02-25T10:15:57Z"},{"publication_status":"published","type":"journal_article","volume":144,"status":"public","citation":{"ama":"Gundert A, Wagner U. On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. 2016;144(4):1815-1828. doi:10.1090/proc/12824","ista":"Gundert A, Wagner U. 2016. On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. 144(4), 1815–1828.","chicago":"Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial Complexes.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/12824.","mla":"Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial Complexes.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1815–28, doi:10.1090/proc/12824.","ieee":"A. Gundert and U. Wagner, “On topological minors in random simplicial complexes,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1815–1828, 2016.","short":"A. Gundert, U. Wagner, Proceedings of the American Mathematical Society 144 (2016) 1815–1828.","apa":"Gundert, A., & Wagner, U. (2016). On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12824"},"author":[{"full_name":"Gundert, Anna","last_name":"Gundert","first_name":"Anna"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"}],"publist_id":"5650","intvolume":" 144","language":[{"iso":"eng"}],"publication":"Proceedings of the American Mathematical Society","acknowledgement":"This research was supported by the Swiss National Science Foundation (SNF Projects 200021-125309 and 200020-138230","doi":"10.1090/proc/12824","day":"01","date_updated":"2021-01-12T06:51:22Z","year":"2016","date_published":"2016-04-01T00:00:00Z","month":"04","department":[{"_id":"UlWa"}],"_id":"1523","quality_controlled":"1","oa_version":"Preprint","title":"On topological minors in random simplicial complexes","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Mathematical Society","issue":"4","main_file_link":[{"url":"http://arxiv.org/abs/1404.2106","open_access":"1"}],"date_created":"2018-12-11T11:52:30Z","oa":1,"scopus_import":1,"abstract":[{"lang":"eng","text":"For random graphs, the containment problem considers the probability that a binomial random graph G(n, p) contains a given graph as a substructure. When asking for the graph as a topological minor, i.e., for a copy of a subdivision of the given graph, it is well known that the (sharp) threshold is at p = 1/n. We consider a natural analogue of this question for higher-dimensional random complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k = 2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold for containing a subdivision of any fixed complete 2-complex. For higher dimensions k > 2, we get that p = O(n−1/k) is an upper bound for the threshold probability of containing a subdivision of a fixed k-dimensional complex."}],"page":"1815 - 1828"},{"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"page":"250 - 267","abstract":[{"lang":"eng","text":"We present the first study of robustness of systems that are both timed as well as reactive (I/O). We study the behavior of such timed I/O systems in the presence of uncertain inputs and formalize their robustness using the analytic notion of Lipschitz continuity: a timed I/O system is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions over timed words such as the timed version of the Manhattan distance and the Skorokhod distance. We consider two models of timed I/O systems — timed transducers and asynchronous sequential circuits. We show that K-robustness of timed transducers can be decided in polynomial space under certain conditions. For asynchronous sequential circuits, we reduce K-robustness w.r.t. timed Manhattan distances to K-robustness of discrete letter-to-letter transducers and show PSpace-completeness of the problem."}],"scopus_import":1,"date_created":"2018-12-11T11:52:32Z","ec_funded":1,"oa":1,"quality_controlled":"1","oa_version":"Preprint","title":"Lipschitz robustness of timed I/O systems","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1506.01233"}],"alternative_title":["LNCS"],"date_published":"2016-01-01T00:00:00Z","month":"01","department":[{"_id":"ToHe"}],"_id":"1526","day":"01","date_updated":"2021-01-12T06:51:23Z","year":"2016","author":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha","last_name":"Samanta"}],"publist_id":"5647","language":[{"iso":"eng"}],"intvolume":" 9583","acknowledgement":"This research was supported in part 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 National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","doi":"10.1007/978-3-662-49122-5_12","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","location":"St. Petersburg, FL, USA","start_date":"2016-01-17","end_date":"2016-01-19"},"publication_status":"published","type":"conference","volume":9583,"status":"public","citation":{"ieee":"T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of timed I/O systems,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 250–267.","apa":"Henzinger, T. A., Otop, J., & Samanta, R. (2016). Lipschitz robustness of timed I/O systems (Vol. 9583, pp. 250–267). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. https://doi.org/10.1007/978-3-662-49122-5_12","short":"T.A. Henzinger, J. Otop, R. Samanta, in:, Springer, 2016, pp. 250–267.","ista":"Henzinger TA, Otop J, Samanta R. 2016. Lipschitz robustness of timed I/O systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583, 250–267.","ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of timed I/O systems. In: Vol 9583. Springer; 2016:250-267. doi:10.1007/978-3-662-49122-5_12","chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Timed I/O Systems,” 9583:250–67. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_12.","mla":"Henzinger, Thomas A., et al. Lipschitz Robustness of Timed I/O Systems. Vol. 9583, Springer, 2016, pp. 250–67, doi:10.1007/978-3-662-49122-5_12."}},{"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"page":"4340 - 4368","abstract":[{"lang":"eng","text":"We provide general conditions for which bosonic quadratic Hamiltonians on Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover the case when quantum systems have infinite degrees of freedom and the associated one-body kinetic and paring operators are unbounded. Our sufficient conditions are optimal in the sense that they become necessary when the relevant one-body operators commute."}],"scopus_import":1,"date_created":"2018-12-11T11:52:38Z","ec_funded":1,"oa":1,"oa_version":"Submitted Version","quality_controlled":"1","title":"Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations","publisher":"Academic Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"11","main_file_link":[{"url":"http://arxiv.org/abs/1508.07321","open_access":"1"}],"date_published":"2016-06-01T00:00:00Z","month":"06","department":[{"_id":"RoSe"}],"_id":"1545","day":"01","date_updated":"2021-01-12T06:51:30Z","year":"2016","author":[{"full_name":"Nam, Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"},{"first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"},{"full_name":"Solovej, Jan","last_name":"Solovej","first_name":"Jan"}],"publist_id":"5626","intvolume":" 270","language":[{"iso":"eng"}],"publication":"Journal of Functional Analysis","doi":"10.1016/j.jfa.2015.12.007","acknowledgement":"We thank Jan Dereziński for several inspiring discussions and useful remarks. We thank the referee for helpful comments. J.P.S. thanks the Erwin Schrödinger Institute for the hospitality during the thematic programme “Quantum many-body systems, random matrices, and disorder”. We gratefully acknowledge the financial supports by the European Union's Seventh Framework Programme under the ERC Advanced Grant ERC-2012-AdG 321029 (J.P.S.) and the REA grant agreement No. 291734 (P.T.N.), as well as the support of the National Science Center (NCN) grant No. 2012/07/N/ST1/03185 and the Austrian Science Fund (FWF) project No. P 27533-N27 (M.N.).","publication_status":"published","volume":270,"type":"journal_article","status":"public","citation":{"short":"P. Nam, M.M. Napiórkowski, J. Solovej, Journal of Functional Analysis 270 (2016) 4340–4368.","apa":"Nam, P., Napiórkowski, M. M., & Solovej, J. (2016). Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2015.12.007","ieee":"P. Nam, M. M. Napiórkowski, and J. Solovej, “Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations,” Journal of Functional Analysis, vol. 270, no. 11. Academic Press, pp. 4340–4368, 2016.","mla":"Nam, Phan, et al. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” Journal of Functional Analysis, vol. 270, no. 11, Academic Press, 2016, pp. 4340–68, doi:10.1016/j.jfa.2015.12.007.","chicago":"Nam, Phan, Marcin M Napiórkowski, and Jan Solovej. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” Journal of Functional Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2015.12.007.","ista":"Nam P, Napiórkowski MM, Solovej J. 2016. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 270(11), 4340–4368.","ama":"Nam P, Napiórkowski MM, Solovej J. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 2016;270(11):4340-4368. doi:10.1016/j.jfa.2015.12.007"}},{"file":[{"file_name":"IST-2016-488-v1+1_20152452.full.pdf","date_created":"2018-12-12T10:11:43Z","file_id":"4899","content_type":"application/pdf","checksum":"78ffe70c1c88af3856d31ca6b7195a27","creator":"system","date_updated":"2020-07-14T12:45:02Z","access_level":"open_access","relation":"main_file","file_size":626804}],"abstract":[{"text":"Antibiotic resistance carries a fitness cost that must be overcome in order for resistance to persist over the long term. Compensatory mutations that recover the functional defects associated with resistance mutations have been argued to play a key role in overcoming the cost of resistance, but compensatory mutations are expected to be rare relative to generally beneficial mutations that increase fitness, irrespective of antibiotic resistance. Given this asymmetry, population genetics theory predicts that populations should adapt by compensatory mutations when the cost of resistance is large, whereas generally beneficial mutations should drive adaptation when the cost of resistance is small. We tested this prediction by determining the genomic mechanisms underpinning adaptation to antibiotic-free conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that carry costly antibiotic resistance mutations. Whole-genome sequencing revealed that populations founded by high-cost rifampicin-resistant mutants adapted via compensatory mutations in three genes of the RNA polymerase core enzyme, whereas populations founded by low-cost mutants adapted by generally beneficial mutations, predominantly in the quorum-sensing transcriptional regulator gene lasR. Even though the importance of compensatory evolution in maintaining resistance has been widely recognized, our study shows that the roles of general adaptation in maintaining resistance should not be underestimated and highlights the need to understand how selection at other sites in the genome influences the dynamics of resistance alleles in clinical settings.","lang":"eng"}],"has_accepted_license":"1","scopus_import":1,"ddc":["570"],"oa":1,"date_created":"2018-12-11T11:52:40Z","issue":"1822","title":"The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa","publisher":"Royal Society, The","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"ToBo"}],"_id":"1552","date_published":"2016-01-13T00:00:00Z","month":"01","article_number":"20152452","year":"2016","date_updated":"2021-01-12T06:51:33Z","day":"13","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","acknowledgement":"We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics funded by Wellcome\r\nTrust grant reference 090532/Z/09/Z and Medical Research Council Hub grant no. G0900747 91070 for generation of the high-throughput sequencing data. We thank Wook Kim and two anonymous reviewers for their constructive feedback on previous versions of our manuscript.","doi":"10.1098/rspb.2015.2452","intvolume":" 283","language":[{"iso":"eng"}],"publist_id":"5619","file_date_updated":"2020-07-14T12:45:02Z","author":[{"last_name":"Qi","first_name":"Qin","id":"3B22D412-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6148-2416","full_name":"Qi, Qin"},{"last_name":"Toll Riera","first_name":"Macarena","full_name":"Toll Riera, Macarena"},{"full_name":"Heilbron, Karl","first_name":"Karl","last_name":"Heilbron"},{"full_name":"Preston, Gail","last_name":"Preston","first_name":"Gail"},{"full_name":"Maclean, R Craig","first_name":"R Craig","last_name":"Maclean"}],"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)"},"citation":{"ama":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. 2016;283(1822). doi:10.1098/rspb.2015.2452","ista":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. 2016. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1822), 20152452.","mla":"Qi, Qin, et al. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1822, 20152452, Royal Society, The, 2016, doi:10.1098/rspb.2015.2452.","chicago":"Qi, Qin, Macarena Toll Riera, Karl Heilbron, Gail Preston, and R Craig Maclean. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2016. https://doi.org/10.1098/rspb.2015.2452.","ieee":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, and R. C. Maclean, “The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1822. Royal Society, The, 2016.","short":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, R.C. Maclean, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016).","apa":"Qi, Q., Toll Riera, M., Heilbron, K., Preston, G., & Maclean, R. C. (2016). The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2015.2452"},"volume":283,"type":"journal_article","status":"public","pubrep_id":"488","publication_status":"published"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., Malkova, D., Kuvaev, R., & Kashin, S. (2016). The classification of endoscopy images with persistent homology. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2015.12.012","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, R. Kuvaev, S. Kashin, Pattern Recognition Letters 83 (2016) 13–22.","ieee":"O. Dunaeva et al., “The classification of endoscopy images with persistent homology,” Pattern Recognition Letters, vol. 83, no. 1. Elsevier, pp. 13–22, 2016.","chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, Daria Malkova, Roman Kuvaev, and Sergey Kashin. “The Classification of Endoscopy Images with Persistent Homology.” Pattern Recognition Letters. Elsevier, 2016. https://doi.org/10.1016/j.patrec.2015.12.012.","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” Pattern Recognition Letters, vol. 83, no. 1, Elsevier, 2016, pp. 13–22, doi:10.1016/j.patrec.2015.12.012.","ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, et al. The classification of endoscopy images with persistent homology. Pattern Recognition Letters. 2016;83(1):13-22. doi:10.1016/j.patrec.2015.12.012","ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D, Kuvaev R, Kashin S. 2016. The classification of endoscopy images with persistent homology. Pattern Recognition Letters. 83(1), 13–22."},"status":"public","type":"journal_article","volume":83,"pubrep_id":"975","publication_status":"published","doi":"10.1016/j.patrec.2015.12.012","publication":"Pattern Recognition Letters","language":[{"iso":"eng"}],"intvolume":" 83","publist_id":"6027","author":[{"full_name":"Dunaeva, Olga","first_name":"Olga","last_name":"Dunaeva"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"full_name":"Lukyanov, Anton","first_name":"Anton","last_name":"Lukyanov"},{"full_name":"Machin, Michael","last_name":"Machin","first_name":"Michael"},{"full_name":"Malkova, Daria","first_name":"Daria","last_name":"Malkova"},{"first_name":"Roman","last_name":"Kuvaev","full_name":"Kuvaev, Roman"},{"last_name":"Kashin","first_name":"Sergey","full_name":"Kashin, Sergey"}],"file_date_updated":"2020-07-14T12:44:42Z","year":"2016","date_updated":"2023-02-23T10:04:40Z","day":"01","related_material":{"record":[{"id":"1568","relation":"earlier_version","status":"public"}]},"_id":"1289","department":[{"_id":"HeEd"}],"month":"11","date_published":"2016-11-01T00:00:00Z","issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","title":"The classification of endoscopy images with persistent homology","oa_version":"Submitted Version","quality_controlled":"1","oa":1,"ddc":["004","514"],"date_created":"2018-12-11T11:51:10Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI) magnifying endoscopic (ME) images of the stomach, we combine methods from image processing, topology, geometry, and machine learning to classify patterns into three classes: oval, tubular and irregular. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions."}],"file":[{"access_level":"open_access","relation":"main_file","file_size":1921113,"checksum":"33458bbb8c32a339e1adeca6d5a1112d","creator":"dernst","date_updated":"2020-07-14T12:44:42Z","content_type":"application/pdf","file_id":"6334","date_created":"2019-04-17T07:55:51Z","file_name":"2016-Edelsbrunner_The_classification.pdf"}],"has_accepted_license":"1","page":"13 - 22","article_processing_charge":"No"},{"external_id":{"arxiv":["1608.08662"]},"scopus_import":1,"article_processing_charge":"No","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"abstract":[{"text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, … , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. A pair of edges e and f in a graph is independent if e and f do not share a vertex. We show that a graph G is radial planar if G has a radial drawing in which every two independent edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the strong Hanani-Tutte theorem for radial planarity. This characterization yields a very simple algorithm for radial planarity testing.","lang":"eng"}],"page":"468 - 481","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.08662"}],"oa_version":"Preprint","quality_controlled":"1","title":"Hanani-Tutte for radial planarity II","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","oa":1,"date_created":"2018-12-11T11:50:29Z","ec_funded":1,"date_updated":"2023-02-23T10:05:57Z","year":"2016","related_material":{"record":[{"status":"public","id":"1113","relation":"later_version"},{"status":"public","id":"1595","relation":"earlier_version"}]},"day":"08","department":[{"_id":"UlWa"}],"_id":"1164","alternative_title":["LNCS"],"date_published":"2016-12-08T00:00:00Z","month":"12","citation":{"short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2016). Hanani-Tutte for radial planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_36","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity II,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 468–481.","mla":"Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity II. Vol. 9801, Springer, 2016, pp. 468–81, doi:10.1007/978-3-319-50106-2_36.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity II,” 9801:468–81. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_36.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In: Vol 9801. Springer; 2016:468-481. doi:10.1007/978-3-319-50106-2_36","ista":"Fulek R, Pelsmajer M, Schaefer M. 2016. Hanani-Tutte for radial planarity II. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 468–481."},"publication_status":"published","conference":{"end_date":"2016-09-21","name":"GD: Graph Drawing and Network Visualization","start_date":"2016-09-19","location":"Athens, Greece"},"volume":9801,"type":"conference","status":"public","language":[{"iso":"eng"}],"intvolume":" 9801","doi":"10.1007/978-3-319-50106-2_36","author":[{"last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Pelsmajer, Michael","last_name":"Pelsmajer","first_name":"Michael"},{"first_name":"Marcus","last_name":"Schaefer","full_name":"Schaefer, Marcus"}],"publist_id":"6193"},{"day":"01","scopus_import":1,"year":"2016","date_updated":"2021-01-12T06:51:49Z","month":"04","date_published":"2016-04-01T00:00:00Z","page":"363 - 421","abstract":[{"lang":"eng","text":"A modular approach to constructing cryptographic protocols leads to simple designs but often inefficient instantiations. On the other hand, ad hoc constructions may yield efficient protocols at the cost of losing conceptual simplicity. We suggest a new design paradigm, structure-preserving cryptography, that provides a way to construct modular protocols with reasonable efficiency while retaining conceptual simplicity. A cryptographic scheme over a bilinear group is called structure-preserving if its public inputs and outputs consist of elements from the bilinear groups and their consistency can be verified by evaluating pairing-product equations. As structure-preserving schemes smoothly interoperate with each other, they are useful as building blocks in modular design of cryptographic applications. This paper introduces structure-preserving commitment and signature schemes over bilinear groups with several desirable properties. The commitment schemes include homomorphic, trapdoor and length-reducing commitments to group elements, and the structure-preserving signature schemes are the first ones that yield constant-size signatures on multiple group elements. A structure-preserving signature scheme is called automorphic if the public keys lie in the message space, which cannot be achieved by compressing inputs via a cryptographic hash function, as this would destroy the mathematical structure we are trying to preserve. Automorphic signatures can be used for building certification chains underlying privacy-preserving protocols. Among a vast number of applications of structure-preserving protocols, we present an efficient round-optimal blind-signature scheme and a group signature scheme with an efficient and concurrently secure protocol for enrolling new members."}],"_id":"1592","department":[{"_id":"KrPi"}],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","type":"journal_article","title":"Structure preserving signatures and commitments to group elements","volume":29,"publication_status":"published","quality_controlled":"1","oa_version":"None","issue":"2","citation":{"chicago":"Abe, Masayuki, Georg Fuchsbauer, Jens Groth, Kristiyan Haralambiev, and Miyako Ohkubo. “Structure Preserving Signatures and Commitments to Group Elements.” Journal of Cryptology. Springer, 2016. https://doi.org/10.1007/s00145-014-9196-7.","mla":"Abe, Masayuki, et al. “Structure Preserving Signatures and Commitments to Group Elements.” Journal of Cryptology, vol. 29, no. 2, Springer, 2016, pp. 363–421, doi:10.1007/s00145-014-9196-7.","ama":"Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. Structure preserving signatures and commitments to group elements. Journal of Cryptology. 2016;29(2):363-421. doi:10.1007/s00145-014-9196-7","ista":"Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. 2016. Structure preserving signatures and commitments to group elements. Journal of Cryptology. 29(2), 363–421.","apa":"Abe, M., Fuchsbauer, G., Groth, J., Haralambiev, K., & Ohkubo, M. (2016). Structure preserving signatures and commitments to group elements. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-014-9196-7","short":"M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, M. Ohkubo, Journal of Cryptology 29 (2016) 363–421.","ieee":"M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, and M. Ohkubo, “Structure preserving signatures and commitments to group elements,” Journal of Cryptology, vol. 29, no. 2. Springer, pp. 363–421, 2016."},"publist_id":"5579","date_created":"2018-12-11T11:52:54Z","author":[{"last_name":"Abe","first_name":"Masayuki","full_name":"Abe, Masayuki"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"last_name":"Groth","first_name":"Jens","full_name":"Groth, Jens"},{"first_name":"Kristiyan","last_name":"Haralambiev","full_name":"Haralambiev, Kristiyan"},{"first_name":"Miyako","last_name":"Ohkubo","full_name":"Ohkubo, Miyako"}],"acknowledgement":"The authors would like to thank the anonymous reviewers of this paper. We also would like to express our appreciation to the program committee and the anonymous reviewers for CRYPTO 2010. The first author thanks Sherman S. M. Chow for his comment on group signatures in Sect. 7.1.","doi":"10.1007/s00145-014-9196-7","publication":"Journal of Cryptology","intvolume":" 29","language":[{"iso":"eng"}]},{"intvolume":" 351","language":[{"iso":"eng"}],"publication":"Science","doi":"10.1126/science.aad0512","acknowledgement":"We thank S. Schüchner and E. Ogris for kindly providing the antibody to GFP, M. Helmbrecht and A. Huber for providing Nrp2−/− mice, the IST Scientific Support Facilities for excellent services, and J. Renkawitz and K. Vaahtomeri for critically reading the manuscript. ","author":[{"full_name":"Kiermaier, Eva","orcid":"0000-0001-6165-5738","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Kiermaier"},{"full_name":"Moussion, Christine","last_name":"Moussion","id":"3356F664-F248-11E8-B48F-1D18A9856A87","first_name":"Christine"},{"first_name":"Christopher","last_name":"Veldkamp","full_name":"Veldkamp, Christopher"},{"full_name":"Gerardy Schahn, Rita","last_name":"Gerardy Schahn","first_name":"Rita"},{"full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","last_name":"De Vries"},{"full_name":"Williams, Larry","first_name":"Larry","last_name":"Williams"},{"last_name":"Chaffee","first_name":"Gary","full_name":"Chaffee, Gary"},{"first_name":"Andrew","last_name":"Phillips","full_name":"Phillips, Andrew"},{"last_name":"Freiberger","first_name":"Friedrich","full_name":"Freiberger, Friedrich"},{"last_name":"Imre","first_name":"Richard","full_name":"Imre, Richard"},{"full_name":"Taleski, Deni","last_name":"Taleski","first_name":"Deni"},{"last_name":"Payne","first_name":"Richard","full_name":"Payne, Richard"},{"full_name":"Braun, Asolina","last_name":"Braun","first_name":"Asolina"},{"last_name":"Förster","first_name":"Reinhold","full_name":"Förster, Reinhold"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"last_name":"Mühlenhoff","first_name":"Martina","full_name":"Mühlenhoff, Martina"},{"last_name":"Volkman","first_name":"Brian","full_name":"Volkman, Brian"},{"last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"publist_id":"5570","citation":{"chicago":"Kiermaier, Eva, Christine Moussion, Christopher Veldkamp, Rita Gerardy Schahn, Ingrid de Vries, Larry Williams, Gary Chaffee, et al. “Polysialylation Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aad0512.","mla":"Kiermaier, Eva, et al. “Polysialylation Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” Science, vol. 351, no. 6269, American Association for the Advancement of Science, 2016, pp. 186–90, doi:10.1126/science.aad0512.","ista":"Kiermaier E, Moussion C, Veldkamp C, Gerardy Schahn R, de Vries I, Williams L, Chaffee G, Phillips A, Freiberger F, Imre R, Taleski D, Payne R, Braun A, Förster R, Mechtler K, Mühlenhoff M, Volkman B, Sixt MK. 2016. Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. 351(6269), 186–190.","ama":"Kiermaier E, Moussion C, Veldkamp C, et al. Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. 2016;351(6269):186-190. doi:10.1126/science.aad0512","apa":"Kiermaier, E., Moussion, C., Veldkamp, C., Gerardy Schahn, R., de Vries, I., Williams, L., … Sixt, M. K. (2016). Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aad0512","short":"E. Kiermaier, C. Moussion, C. Veldkamp, R. Gerardy Schahn, I. de Vries, L. Williams, G. Chaffee, A. Phillips, F. Freiberger, R. Imre, D. Taleski, R. Payne, A. Braun, R. Förster, K. Mechtler, M. Mühlenhoff, B. Volkman, M.K. Sixt, Science 351 (2016) 186–190.","ieee":"E. Kiermaier et al., “Polysialylation controls dendritic cell trafficking by regulating chemokine recognition,” Science, vol. 351, no. 6269. American Association for the Advancement of Science, pp. 186–190, 2016."},"publication_status":"published","volume":351,"type":"journal_article","status":"public","department":[{"_id":"MiSi"}],"_id":"1599","date_published":"2016-01-08T00:00:00Z","month":"01","date_updated":"2021-01-12T06:51:52Z","year":"2016","day":"08","article_type":"original","oa":1,"date_created":"2018-12-11T11:52:57Z","ec_funded":1,"issue":"6269","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583642/","open_access":"1"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Submitted Version","quality_controlled":"1","title":"Polysialylation controls dendritic cell trafficking by regulating chemokine recognition","publisher":"American Association for the Advancement of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"name":"Stromal Cell-immune Cell Interactions in Health and Disease","call_identifier":"FP7","grant_number":"289720","_id":"25A76F58-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"page":"186 - 190","abstract":[{"text":"The addition of polysialic acid to N- and/or O-linked glycans, referred to as polysialylation, is a rare posttranslational modification that is mainly known to control the developmental plasticity of the nervous system. Here we show that CCR7, the central chemokine receptor controlling immune cell trafficking to secondary lymphatic organs, carries polysialic acid. This modification is essential for the recognition of the CCR7 ligand CCL21. As a consequence, dendritic cell trafficking is abrogated in polysialyltransferase-deficient mice, manifesting as disturbed lymph node homeostasis and unresponsiveness to inflammatory stimuli. Structure-function analysis of chemokine-receptor interactions reveals that CCL21 adopts an autoinhibited conformation, which is released upon interaction with polysialic acid. Thus, we describe a glycosylation-mediated immune cell trafficking disorder and its mechanistic basis.\r\n","lang":"eng"}],"pmid":1,"external_id":{"pmid":["26657283"]},"scopus_import":1},{"language":[{"iso":"eng"}],"intvolume":" 570","publication":"Methods in Enzymology","doi":"10.1016/bs.mie.2015.11.004","acknowledgement":"This work was supported by the Boehringer Ingelheim Fonds, the European Research Council (ERC StG 281556), and a START Award of the Austrian Science Foundation (FWF). We thank Robert Hauschild, Anne Reversat, and Jack Merrin for valuable input and the Imaging Facility of IST Austria for excellent support.","author":[{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz","full_name":"Schwarz, Jan"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"}],"publist_id":"5573","citation":{"chicago":"Schwarz, Jan, and Michael K Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” Methods in Enzymology. Elsevier, 2016. https://doi.org/10.1016/bs.mie.2015.11.004.","mla":"Schwarz, Jan, and Michael K. Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” Methods in Enzymology, vol. 570, Elsevier, 2016, pp. 567–81, doi:10.1016/bs.mie.2015.11.004.","ama":"Schwarz J, Sixt MK. Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. 2016;570:567-581. doi:10.1016/bs.mie.2015.11.004","ista":"Schwarz J, Sixt MK. 2016. Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. 570, 567–581.","apa":"Schwarz, J., & Sixt, M. K. (2016). Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. Elsevier. https://doi.org/10.1016/bs.mie.2015.11.004","short":"J. Schwarz, M.K. Sixt, Methods in Enzymology 570 (2016) 567–581.","ieee":"J. Schwarz and M. K. Sixt, “Quantitative analysis of dendritic cell haptotaxis,” Methods in Enzymology, vol. 570. Elsevier, pp. 567–581, 2016."},"publication_status":"published","volume":570,"type":"journal_article","status":"public","department":[{"_id":"MiSi"}],"_id":"1597","date_published":"2016-01-01T00:00:00Z","month":"01","date_updated":"2021-01-12T06:51:51Z","year":"2016","day":"01","article_type":"original","date_created":"2018-12-11T11:52:56Z","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"None","quality_controlled":"1","title":"Quantitative analysis of dendritic cell haptotaxis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","article_processing_charge":"No","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"}],"abstract":[{"lang":"eng","text":"Chemokines are the main guidance cues directing leukocyte migration. Opposed to early assumptions, chemokines do not necessarily act as soluble cues but are often immobilized within tissues, e.g., dendritic cell migration toward lymphatic vessels is guided by a haptotactic gradient of the chemokine CCL21. Controlled assay systems to quantitatively study haptotaxis in vitro are still missing. In this chapter, we describe an in vitro haptotaxis assay optimized for the unique properties of dendritic cells. The chemokine CCL21 is immobilized in a bioactive state, using laser-assisted protein adsorption by photobleaching. The cells follow this immobilized CCL21 gradient in a haptotaxis chamber, which provides three dimensionally confined migration conditions."}],"page":"567 - 581","pmid":1,"external_id":{"pmid":["26921962"]},"scopus_import":1},{"department":[{"_id":"LaEr"}],"_id":"1608","date_published":"2016-07-01T00:00:00Z","month":"07","date_updated":"2021-01-12T06:51:58Z","year":"2016","day":"01","intvolume":" 17","language":[{"iso":"eng"}],"publication":"Annales Henri Poincare","doi":"10.1007/s00023-015-0456-3","author":[{"first_name":"Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","last_name":"Sadel","full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968"}],"publist_id":"5558","citation":{"chicago":"Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees and Spectral Theory for Operators with One Propagating Channel.” Annales Henri Poincare. Birkhäuser, 2016. https://doi.org/10.1007/s00023-015-0456-3.","mla":"Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees and Spectral Theory for Operators with One Propagating Channel.” Annales Henri Poincare, vol. 17, no. 7, Birkhäuser, 2016, pp. 1631–75, doi:10.1007/s00023-015-0456-3.","ista":"Sadel C. 2016. Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. 17(7), 1631–1675.","ama":"Sadel C. Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. 2016;17(7):1631-1675. doi:10.1007/s00023-015-0456-3","apa":"Sadel, C. (2016). Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-015-0456-3","short":"C. Sadel, Annales Henri Poincare 17 (2016) 1631–1675.","ieee":"C. Sadel, “Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel,” Annales Henri Poincare, vol. 17, no. 7. Birkhäuser, pp. 1631–1675, 2016."},"publication_status":"published","volume":17,"type":"journal_article","status":"public","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"page":"1631 - 1675","abstract":[{"text":"We show that the Anderson model has a transition from localization to delocalization at exactly 2 dimensional growth rate on antitrees with normalized edge weights which are certain discrete graphs. The kinetic part has a one-dimensional structure allowing a description through transfer matrices which involve some Schur complement. For such operators we introduce the notion of having one propagating channel and extend theorems from the theory of one-dimensional Jacobi operators that relate the behavior of transfer matrices with the spectrum. These theorems are then applied to the considered model. In essence, in a certain energy region the kinetic part averages the random potentials along shells and the transfer matrices behave similar as for a one-dimensional operator with random potential of decaying variance. At d dimensional growth for d>2 this effective decay is strong enough to obtain absolutely continuous spectrum, whereas for some uniform d dimensional growth with d<2 one has pure point spectrum in this energy region. At exactly uniform 2 dimensional growth also some singular continuous spectrum appears, at least at small disorder. As a corollary we also obtain a change from singular spectrum (d≤2) to absolutely continuous spectrum (d≥3) for random operators of the type rΔdr+λ on ℤd, where r is an orthogonal radial projection, Δd the discrete adjacency operator (Laplacian) on ℤd and λ a random potential. ","lang":"eng"}],"scopus_import":1,"oa":1,"date_created":"2018-12-11T11:53:00Z","ec_funded":1,"issue":"7","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.04287"}],"oa_version":"Preprint","quality_controlled":"1","title":"Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel","publisher":"Birkhäuser","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2016-02-01T00:00:00Z","month":"02","department":[{"_id":"VlKo"}],"_id":"1612","page":"75 - 84","abstract":[{"text":"We prove that whenever A is a 3-conservative relational structure with only binary and unary relations,then the algebra of polymorphisms of A either has no Taylor operation (i.e.,CSP(A)is NP-complete),or it generates an SD(∧) variety (i.e.,CSP(A)has bounded width).","lang":"eng"}],"scopus_import":1,"day":"01","date_updated":"2021-01-12T06:52:00Z","year":"2016","author":[{"last_name":"Kazda","first_name":"Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr"}],"date_created":"2018-12-11T11:53:01Z","publist_id":"5554","intvolume":" 75","language":[{"iso":"eng"}],"oa":1,"publication":"Algebra Universalis","doi":"10.1007/s00012-015-0358-8","publication_status":"published","oa_version":"Preprint","quality_controlled":"1","type":"journal_article","volume":75,"title":"CSP for binary conservative relational structures","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","citation":{"ieee":"A. Kazda, “CSP for binary conservative relational structures,” Algebra Universalis, vol. 75, no. 1. Springer, pp. 75–84, 2016.","short":"A. Kazda, Algebra Universalis 75 (2016) 75–84.","apa":"Kazda, A. (2016). CSP for binary conservative relational structures. Algebra Universalis. Springer. https://doi.org/10.1007/s00012-015-0358-8","ista":"Kazda A. 2016. CSP for binary conservative relational structures. Algebra Universalis. 75(1), 75–84.","ama":"Kazda A. CSP for binary conservative relational structures. Algebra Universalis. 2016;75(1):75-84. doi:10.1007/s00012-015-0358-8","chicago":"Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra Universalis. Springer, 2016. https://doi.org/10.1007/s00012-015-0358-8.","mla":"Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra Universalis, vol. 75, no. 1, Springer, 2016, pp. 75–84, doi:10.1007/s00012-015-0358-8."},"issue":"1","main_file_link":[{"url":"http://arxiv.org/abs/1112.1099","open_access":"1"}]},{"abstract":[{"lang":"eng","text":"We study the discrepancy of jittered sampling sets: such a set P⊂ [0,1]d is generated for fixed m∈ℕ by partitioning [0,1]d into md axis aligned cubes of equal measure and placing a random point inside each of the N=md cubes. We prove that, for N sufficiently large, 1/10 d/N1/2+1/2d ≤EDN∗(P)≤ √d(log N) 1/2/N1/2+1/2d, where the upper bound with an unspecified constant Cd was proven earlier by Beck. Our proof makes crucial use of the sharp Dvoretzky-Kiefer-Wolfowitz inequality and a suitably taylored Bernstein inequality; we have reasons to believe that the upper bound has the sharp scaling in N. Additional heuristics suggest that jittered sampling should be able to improve known bounds on the inverse of the star-discrepancy in the regime N≳dd. We also prove a partition principle showing that every partition of [0,1]d combined with a jittered sampling construction gives rise to a set whose expected squared L2-discrepancy is smaller than that of purely random points."}],"page":"199 - 216","_id":"1617","department":[{"_id":"HeEd"}],"month":"04","date_published":"2016-04-01T00:00:00Z","year":"2016","date_updated":"2021-01-12T06:52:02Z","day":"01","scopus_import":1,"acknowledgement":"We are grateful to the referee whose suggestions greatly improved the quality and clarity of the exposition.","doi":"10.1016/j.jco.2015.11.003","publication":"Journal of Complexity","oa":1,"intvolume":" 33","language":[{"iso":"eng"}],"publist_id":"5549","date_created":"2018-12-11T11:53:03Z","author":[{"full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pausinger"},{"first_name":"Stefan","last_name":"Steinerberger","full_name":"Steinerberger, Stefan"}],"main_file_link":[{"url":"http://arxiv.org/abs/1510.00251","open_access":"1"}],"citation":{"short":"F. Pausinger, S. Steinerberger, Journal of Complexity 33 (2016) 199–216.","apa":"Pausinger, F., & Steinerberger, S. (2016). On the discrepancy of jittered sampling. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.11.003","ieee":"F. Pausinger and S. Steinerberger, “On the discrepancy of jittered sampling,” Journal of Complexity, vol. 33. Academic Press, pp. 199–216, 2016.","mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” Journal of Complexity, vol. 33, Academic Press, 2016, pp. 199–216, doi:10.1016/j.jco.2015.11.003.","chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” Journal of Complexity. Academic Press, 2016. https://doi.org/10.1016/j.jco.2015.11.003.","ama":"Pausinger F, Steinerberger S. On the discrepancy of jittered sampling. Journal of Complexity. 2016;33:199-216. doi:10.1016/j.jco.2015.11.003","ista":"Pausinger F, Steinerberger S. 2016. On the discrepancy of jittered sampling. Journal of Complexity. 33, 199–216."},"publisher":"Academic Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","title":"On the discrepancy of jittered sampling","volume":33,"publication_status":"published","quality_controlled":"1","oa_version":"Submitted Version"},{"oa":1,"date_created":"2018-12-11T11:53:04Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.2352"}],"issue":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"The external field dependence of the BCS critical temperature","quality_controlled":"1","oa_version":"Submitted Version","page":"189 - 216","abstract":[{"lang":"eng","text":"We consider the Bardeen–Cooper–Schrieffer free energy functional for particles interacting via a two-body potential on a microscopic scale and in the presence of weak external fields varying on a macroscopic scale. We study the influence of the external fields on the critical temperature. We show that in the limit where the ratio between the microscopic and macroscopic scale tends to zero, the next to leading order of the critical temperature is determined by the lowest eigenvalue of the linearization of the Ginzburg–Landau equation."}],"scopus_import":1,"doi":"10.1007/s00220-015-2526-2","acknowledgement":"The authors are grateful to I. M. Sigal for useful discussions. Financial support from the US National Science Foundation through Grants PHY-1347399 and DMS-1363432 (R.L.F.), from the Danish council for independent research and from ERC Advanced Grant 321029 (J.P.S.) is acknowledged.","publication":"Communications in Mathematical Physics","intvolume":" 342","language":[{"iso":"eng"}],"publist_id":"5546","author":[{"last_name":"Frank","first_name":"Rupert","full_name":"Frank, Rupert"},{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Solovej, Jan","first_name":"Jan","last_name":"Solovej"}],"citation":{"apa":"Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2016). The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2526-2","short":"R. Frank, C. Hainzl, R. Seiringer, J. Solovej, Communications in Mathematical Physics 342 (2016) 189–216.","ieee":"R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “The external field dependence of the BCS critical temperature,” Communications in Mathematical Physics, vol. 342, no. 1. Springer, pp. 189–216, 2016.","mla":"Frank, Rupert, et al. “The External Field Dependence of the BCS Critical Temperature.” Communications in Mathematical Physics, vol. 342, no. 1, Springer, 2016, pp. 189–216, doi:10.1007/s00220-015-2526-2.","chicago":"Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “The External Field Dependence of the BCS Critical Temperature.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-015-2526-2.","ama":"Frank R, Hainzl C, Seiringer R, Solovej J. The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. 2016;342(1):189-216. doi:10.1007/s00220-015-2526-2","ista":"Frank R, Hainzl C, Seiringer R, Solovej J. 2016. The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. 342(1), 189–216."},"status":"public","volume":342,"type":"journal_article","publication_status":"published","_id":"1620","department":[{"_id":"RoSe"}],"month":"02","date_published":"2016-02-01T00:00:00Z","year":"2016","date_updated":"2021-01-12T06:52:03Z","day":"01"},{"publist_id":"5542","author":[{"last_name":"Lundholm","first_name":"Douglas","full_name":"Lundholm, Douglas"},{"first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","full_name":"Nam, Phan"},{"first_name":"Fabian","last_name":"Portmann","full_name":"Portmann, Fabian"}],"doi":"10.1007/s00205-015-0923-5","acknowledgement":"We thank Jan Philip Solovej, Robert Seiringer and Vladimir Maz’ya for helpful discussions, as well as Rupert Frank\r\nand the anonymous referee for useful comments. Part of this work has been carried out during a visit at the Institut Mittag-Leffler (Stockholm). D.L. acknowledges financial support by the grant KAW 2010.0063 from the Knut and Alice Wallenberg Foundation and the Swedish Research Council grant no. 2013-4734. P.T.N. is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. F.P. acknowledges support from the ERC project no. 321029 “The\r\nmathematics of the structure of matter”.","publication":"Archive for Rational Mechanics and Analysis","language":[{"iso":"eng"}],"intvolume":" 219","status":"public","volume":219,"type":"journal_article","publication_status":"published","citation":{"ama":"Lundholm D, Nam P, Portmann F. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. 2016;219(3):1343-1382. doi:10.1007/s00205-015-0923-5","ista":"Lundholm D, Nam P, Portmann F. 2016. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. 219(3), 1343–1382.","chicago":"Lundholm, Douglas, Phan Nam, and Fabian Portmann. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics and Analysis. Springer, 2016. https://doi.org/10.1007/s00205-015-0923-5.","mla":"Lundholm, Douglas, et al. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics and Analysis, vol. 219, no. 3, Springer, 2016, pp. 1343–82, doi:10.1007/s00205-015-0923-5.","ieee":"D. Lundholm, P. Nam, and F. Portmann, “Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems,” Archive for Rational Mechanics and Analysis, vol. 219, no. 3. Springer, pp. 1343–1382, 2016.","short":"D. Lundholm, P. Nam, F. Portmann, Archive for Rational Mechanics and Analysis 219 (2016) 1343–1382.","apa":"Lundholm, D., Nam, P., & Portmann, F. (2016). Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-015-0923-5"},"month":"03","date_published":"2016-03-01T00:00:00Z","_id":"1622","department":[{"_id":"RoSe"}],"day":"01","year":"2016","date_updated":"2021-01-12T06:52:04Z","ec_funded":1,"date_created":"2018-12-11T11:53:05Z","oa":1,"publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems","quality_controlled":"1","oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1501.04570","open_access":"1"}],"issue":"3","page":"1343 - 1382","abstract":[{"text":"We prove analogues of the Lieb–Thirring and Hardy–Lieb–Thirring inequalities for many-body quantum systems with fractional kinetic operators and homogeneous interaction potentials, where no anti-symmetry on the wave functions is assumed. These many-body inequalities imply interesting one-body interpolation inequalities, and we show that the corresponding one- and many-body inequalities are actually equivalent in certain cases.","lang":"eng"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"scopus_import":1},{"quality_controlled":"1","oa_version":"Published Version","title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","publisher":"Academic Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:53:08Z","ec_funded":1,"ddc":["576"],"oa":1,"scopus_import":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"abstract":[{"text":"Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.","lang":"eng"}],"page":"1 - 12","file":[{"file_id":"4865","content_type":"application/pdf","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","date_created":"2018-12-12T10:11:12Z","file_size":1684043,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:07Z","creator":"system","checksum":"6a65ba187994d4ad86c1c509e0ff482a"}],"has_accepted_license":"1","pubrep_id":"465","publication_status":"published","volume":108,"type":"journal_article","status":"public","citation":{"ieee":"J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” Theoretical Population Biology, vol. 108. Academic Press, pp. 1–12, 2016.","apa":"Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12.","ista":"Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12.","ama":"Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 2016;108:1-12. doi:10.1016/j.tpb.2015.10.008","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008.","mla":"Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology, vol. 108, Academic Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008."},"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_updated":"2020-07-14T12:45:07Z","author":[{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5524","intvolume":" 108","language":[{"iso":"eng"}],"publication":"Theoretical Population Biology","doi":"10.1016/j.tpb.2015.10.008","day":"01","date_updated":"2021-01-12T06:52:07Z","year":"2016","date_published":"2016-04-01T00:00:00Z","month":"04","department":[{"_id":"NiBa"}],"_id":"1631"},{"citation":{"ieee":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana,” Journal of Plant Growth Regulation, vol. 35, no. 2. Springer, pp. 465–476, 2016.","apa":"Zemová, R., Zwiewka, M., Bielach, A., Robert, H., & Friml, J. (2016). A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. Springer. https://doi.org/10.1007/s00344-015-9553-2","short":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant Growth Regulation 35 (2016) 465–476.","ista":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476.","ama":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 2016;35(2):465-476. doi:10.1007/s00344-015-9553-2","mla":"Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:10.1007/s00344-015-9553-2.","chicago":"Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation. Springer, 2016. https://doi.org/10.1007/s00344-015-9553-2."},"status":"public","type":"journal_article","volume":35,"pubrep_id":"1001","publication_status":"published","acknowledgement":"European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to JF. ","doi":"10.1007/s00344-015-9553-2","publication":"Journal of Plant Growth Regulation","language":[{"iso":"eng"}],"intvolume":" 35","publist_id":"5512","author":[{"full_name":"Zemová, Radka","last_name":"Zemová","first_name":"Radka"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"last_name":"Robert","first_name":"Hélène","full_name":"Robert, Hélène"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:45:08Z","year":"2016","date_updated":"2021-01-12T06:52:11Z","day":"01","_id":"1641","department":[{"_id":"JiFr"}],"month":"06","date_published":"2016-06-01T00:00:00Z","issue":"2","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana","oa_version":"Preprint","quality_controlled":"1","oa":1,"ddc":["581"],"date_created":"2018-12-11T11:53:12Z","scopus_import":1,"abstract":[{"text":"The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant growth and development including embryo and root patterning, lateral organ formation and growth responses to environmental stimuli. Auxin is directionally transported from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)] and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations are aligned with the direction of the auxin flow. Auxin itself regulates its own transport by modulation of the expression and subcellular localization of the auxin transporters. Increased auxin levels promote the transcription of PIN2 and AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged auxin exposure increases the turnover of PIN proteins and their degradation in the vacuole. In this study, we applied a forward genetic approach, to identify molecular components playing a role in the auxin-mediated degradation. We generated EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations and designed a screen for mutants with persistently strong fluorescent signals of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and established a role for auxin-mediated degradation in plant development.","lang":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","file_size":5637591,"checksum":"0dc6a300cde6536ceedd2bcdd2060efb","creator":"system","date_updated":"2020-07-14T12:45:08Z","content_type":"application/pdf","file_id":"4695","file_name":"IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf","date_created":"2018-12-12T10:08:34Z"}],"has_accepted_license":"1","page":"465 - 476"},{"_id":"1225","department":[{"_id":"KrPi"}],"month":"08","date_published":"2016-08-11T00:00:00Z","alternative_title":["LNCS"],"year":"2016","date_updated":"2023-02-23T10:08:16Z","day":"11","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1647"}]},"doi":"10.1007/978-3-319-44618-9_21","intvolume":" 9841","language":[{"iso":"eng"}],"publist_id":"6109","author":[{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"full_name":"Hanser, Christian","last_name":"Hanser","first_name":"Christian"},{"last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"first_name":"Daniel","last_name":"Slamanig","full_name":"Slamanig, Daniel"}],"citation":{"ieee":"G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, and D. Slamanig, “Practical round-optimal blind signatures in the standard model from weaker assumptions,” presented at the SCN: Security and Cryptography for Networks, Amalfi, Italy, 2016, vol. 9841, pp. 391–408.","short":"G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, D. Slamanig, in:, Springer, 2016, pp. 391–408.","apa":"Fuchsbauer, G., Hanser, C., Kamath Hosdurg, C., & Slamanig, D. (2016). Practical round-optimal blind signatures in the standard model from weaker assumptions (Vol. 9841, pp. 391–408). Presented at the SCN: Security and Cryptography for Networks, Amalfi, Italy: Springer. https://doi.org/10.1007/978-3-319-44618-9_21","ama":"Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. Practical round-optimal blind signatures in the standard model from weaker assumptions. In: Vol 9841. Springer; 2016:391-408. doi:10.1007/978-3-319-44618-9_21","ista":"Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. 2016. Practical round-optimal blind signatures in the standard model from weaker assumptions. SCN: Security and Cryptography for Networks, LNCS, vol. 9841, 391–408.","mla":"Fuchsbauer, Georg, et al. Practical Round-Optimal Blind Signatures in the Standard Model from Weaker Assumptions. Vol. 9841, Springer, 2016, pp. 391–408, doi:10.1007/978-3-319-44618-9_21.","chicago":"Fuchsbauer, Georg, Christian Hanser, Chethan Kamath Hosdurg, and Daniel Slamanig. “Practical Round-Optimal Blind Signatures in the Standard Model from Weaker Assumptions,” 9841:391–408. Springer, 2016. https://doi.org/10.1007/978-3-319-44618-9_21."},"status":"public","volume":9841,"type":"conference","conference":{"name":"SCN: Security and Cryptography for Networks","start_date":"2016-08-31","location":"Amalfi, Italy","end_date":"2016-09-02"},"publication_status":"published","abstract":[{"text":"At Crypto 2015 Fuchsbauer, Hanser and Slamanig (FHS) presented the first standard-model construction of efficient roundoptimal blind signatures that does not require complexity leveraging. It is conceptually simple and builds on the primitive of structure-preserving signatures on equivalence classes (SPS-EQ). FHS prove the unforgeability of their scheme assuming EUF-CMA security of the SPS-EQ scheme and hardness of a version of the DH inversion problem. Blindness under adversarially chosen keys is proven under an interactive variant of the DDH assumption. We propose a variant of their scheme whose blindness can be proven under a non-interactive assumption, namely a variant of the bilinear DDH assumption. We moreover prove its unforgeability assuming only unforgeability of the underlying SPS-EQ but no additional assumptions as needed for the FHS scheme.","lang":"eng"}],"page":"391 - 408","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"scopus_import":1,"oa":1,"ec_funded":1,"date_created":"2018-12-11T11:50:49Z","main_file_link":[{"url":"https://eprint.iacr.org/2016/662","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"Practical round-optimal blind signatures in the standard model from weaker assumptions","oa_version":"Submitted Version","quality_controlled":"1"},{"title":"New realizations of somewhere statistically binding hashing and positional accumulators","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","oa_version":"Submitted Version","quality_controlled":"1","date_created":"2018-12-11T11:53:16Z","ec_funded":1,"ddc":["000"],"oa":1,"scopus_import":1,"page":"121 - 145","has_accepted_license":"1","abstract":[{"text":"A somewhere statistically binding (SSB) hash, introduced by Hubáček and Wichs (ITCS ’15), can be used to hash a long string x to a short digest y = H hk (x) using a public hashing-key hk. Furthermore, there is a way to set up the hash key hk to make it statistically binding on some arbitrary hidden position i, meaning that: (1) the digest y completely determines the i’th bit (or symbol) of x so that all pre-images of y have the same value in the i’th position, (2) it is computationally infeasible to distinguish the position i on which hk is statistically binding from any other position i’. Lastly, the hash should have a local opening property analogous to Merkle-Tree hashing, meaning that given x and y = H hk (x) it should be possible to create a short proof π that certifies the value of the i’th bit (or symbol) of x without having to provide the entire input x. A similar primitive called a positional accumulator, introduced by Koppula, Lewko and Waters (STOC ’15) further supports dynamic updates of the hashed value. These tools, which are interesting in their own right, also serve as one of the main technical components in several recent works building advanced applications from indistinguishability obfuscation (iO).\r\n\r\nThe prior constructions of SSB hashing and positional accumulators required fully homomorphic encryption (FHE) and iO respectively. In this work, we give new constructions of these tools based on well studied number-theoretic assumptions such as DDH, Phi-Hiding and DCR, as well as a general construction from lossy/injective functions.","lang":"eng"}],"file":[{"date_created":"2018-12-12T10:12:05Z","file_name":"IST-2016-677-v1+1_869.pdf","file_id":"4923","content_type":"application/pdf","creator":"system","checksum":"a57711cb660c5b17b42bb47275a00180","date_updated":"2020-07-14T12:45:08Z","access_level":"open_access","relation":"main_file","file_size":580088}],"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"volume":9452,"type":"conference","status":"public","conference":{"end_date":"2015-12-03","start_date":"2015-11-29","location":"Auckland, New Zealand","name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"pubrep_id":"677","publication_status":"published","citation":{"short":"T. Okamoto, K.Z. Pietrzak, B. Waters, D. Wichs, in:, Springer, 2016, pp. 121–145.","apa":"Okamoto, T., Pietrzak, K. Z., Waters, B., & Wichs, D. (2016). New realizations of somewhere statistically binding hashing and positional accumulators (Vol. 9452, pp. 121–145). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48797-6_6","ieee":"T. Okamoto, K. Z. Pietrzak, B. Waters, and D. Wichs, “New realizations of somewhere statistically binding hashing and positional accumulators,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand, 2016, vol. 9452, pp. 121–145.","chicago":"Okamoto, Tatsuaki, Krzysztof Z Pietrzak, Brent Waters, and Daniel Wichs. “New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators,” 9452:121–45. Springer, 2016. https://doi.org/10.1007/978-3-662-48797-6_6.","mla":"Okamoto, Tatsuaki, et al. New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators. Vol. 9452, Springer, 2016, pp. 121–45, doi:10.1007/978-3-662-48797-6_6.","ista":"Okamoto T, Pietrzak KZ, Waters B, Wichs D. 2016. New realizations of somewhere statistically binding hashing and positional accumulators. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 9452, 121–145.","ama":"Okamoto T, Pietrzak KZ, Waters B, Wichs D. New realizations of somewhere statistically binding hashing and positional accumulators. In: Vol 9452. Springer; 2016:121-145. doi:10.1007/978-3-662-48797-6_6"},"publist_id":"5497","file_date_updated":"2020-07-14T12:45:08Z","author":[{"full_name":"Okamoto, Tatsuaki","last_name":"Okamoto","first_name":"Tatsuaki"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"full_name":"Waters, Brent","last_name":"Waters","first_name":"Brent"},{"full_name":"Wichs, Daniel","first_name":"Daniel","last_name":"Wichs"}],"doi":"10.1007/978-3-662-48797-6_6","intvolume":" 9452","language":[{"iso":"eng"}],"day":"08","year":"2016","date_updated":"2021-01-12T06:52:16Z","date_published":"2016-01-08T00:00:00Z","month":"01","alternative_title":["LNCS"],"department":[{"_id":"KrPi"}],"_id":"1653"},{"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"page":"15 - 25","abstract":[{"lang":"eng","text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd"}],"scopus_import":1,"ec_funded":1,"date_created":"2018-12-11T11:50:24Z","oa_version":"None","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","title":"Adaptive moment closure for parameter inference of biochemical reaction networks","month":"11","date_published":"2016-11-01T00:00:00Z","_id":"1148","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"related_material":{"record":[{"relation":"earlier_version","id":"1658","status":"public"}]},"day":"01","date_updated":"2023-02-23T10:08:46Z","year":"2016","author":[{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling"},{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"full_name":"Podelski, Andreas","first_name":"Andreas","last_name":"Podelski"},{"last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob"}],"publist_id":"6210","language":[{"iso":"eng"}],"intvolume":" 149","doi":"10.1016/j.biosystems.2016.07.005","acknowledgement":"This work is based on the CMSB 2015 paper “Adaptive moment closure for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015). The work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","publication":"Biosystems","publication_status":"published","status":"public","type":"journal_article","volume":149,"citation":{"ama":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 2016;149:15-25. doi:10.1016/j.biosystems.2016.07.005","ista":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.","mla":"Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Biosystems, vol. 149, Elsevier, 2016, pp. 15–25, doi:10.1016/j.biosystems.2016.07.005.","chicago":"Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Biosystems. Elsevier, 2016. https://doi.org/10.1016/j.biosystems.2016.07.005.","ieee":"C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” Biosystems, vol. 149. Elsevier, pp. 15–25, 2016.","apa":"Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., & Ruess, J. (2016). Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2016.07.005","short":"C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25."}},{"issue":"4","oa_version":"Published Version","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"Guided search for hybrid systems based on coarse-grained space abstractions","oa":1,"ddc":["000"],"ec_funded":1,"date_created":"2018-12-11T11:53:34Z","scopus_import":1,"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file":[{"file_id":"5146","content_type":"application/pdf","file_name":"IST-2016-457-v1+1_s10009-015-0393-y.pdf","date_created":"2018-12-12T10:15:26Z","date_updated":"2020-07-14T12:45:13Z","creator":"system","checksum":"31561d7705599a9bd4ea816accc0752e","file_size":2296522,"relation":"main_file","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search. Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential."}],"page":"449 - 467","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)"},"citation":{"ieee":"S. Bogomolov et al., “Guided search for hybrid systems based on coarse-grained space abstractions,” International Journal on Software Tools for Technology Transfer, vol. 18, no. 4. Springer, pp. 449–467, 2016.","short":"S. Bogomolov, A. Donzé, G. Frehse, R. Grosu, T. Johnson, H. Ladan, A. Podelski, M. Wehrle, International Journal on Software Tools for Technology Transfer 18 (2016) 449–467.","apa":"Bogomolov, S., Donzé, A., Frehse, G., Grosu, R., Johnson, T., Ladan, H., … Wehrle, M. (2016). Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. Springer. https://doi.org/10.1007/s10009-015-0393-y","ista":"Bogomolov S, Donzé A, Frehse G, Grosu R, Johnson T, Ladan H, Podelski A, Wehrle M. 2016. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 18(4), 449–467.","ama":"Bogomolov S, Donzé A, Frehse G, et al. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 2016;18(4):449-467. doi:10.1007/s10009-015-0393-y","chicago":"Bogomolov, Sergiy, Alexandre Donzé, Goran Frehse, Radu Grosu, Taylor Johnson, Hamed Ladan, Andreas Podelski, and Martin Wehrle. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” International Journal on Software Tools for Technology Transfer. Springer, 2016. https://doi.org/10.1007/s10009-015-0393-y.","mla":"Bogomolov, Sergiy, et al. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” International Journal on Software Tools for Technology Transfer, vol. 18, no. 4, Springer, 2016, pp. 449–67, doi:10.1007/s10009-015-0393-y."},"pubrep_id":"457","publication_status":"published","status":"public","type":"journal_article","volume":18,"intvolume":" 18","language":[{"iso":"eng"}],"doi":"10.1007/s10009-015-0393-y","publication":"International Journal on Software Tools for Technology Transfer","author":[{"last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"last_name":"Donzé","first_name":"Alexandre","full_name":"Donzé, Alexandre"},{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"},{"full_name":"Johnson, Taylor","first_name":"Taylor","last_name":"Johnson"},{"full_name":"Ladan, Hamed","last_name":"Ladan","first_name":"Hamed"},{"full_name":"Podelski, Andreas","last_name":"Podelski","first_name":"Andreas"},{"full_name":"Wehrle, Martin","first_name":"Martin","last_name":"Wehrle"}],"file_date_updated":"2020-07-14T12:45:13Z","publist_id":"5431","date_updated":"2021-01-12T06:52:38Z","year":"2016","day":"01","_id":"1705","department":[{"_id":"ToHe"}],"month":"08","date_published":"2016-08-01T00:00:00Z"},{"type":"conference","title":"Optimal geospatial allocation of volunteers for crisis management","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","quality_controlled":"1","oa_version":"None","publication_status":"published","conference":{"start_date":"2015-11-30","location":"Rennes, France","name":"ICT-DM: Information and Communication Technologies for Disaster Management","end_date":"2015-12-02"},"citation":{"chicago":"Pielorz, Jasmin, and Christoph Lampert. “Optimal Geospatial Allocation of Volunteers for Crisis Management.” IEEE, 2016. https://doi.org/10.1109/ICT-DM.2015.7402041.","mla":"Pielorz, Jasmin, and Christoph Lampert. Optimal Geospatial Allocation of Volunteers for Crisis Management. 7402041, IEEE, 2016, doi:10.1109/ICT-DM.2015.7402041.","ista":"Pielorz J, Lampert C. 2016. Optimal geospatial allocation of volunteers for crisis management. ICT-DM: Information and Communication Technologies for Disaster Management, 7402041.","ama":"Pielorz J, Lampert C. Optimal geospatial allocation of volunteers for crisis management. In: IEEE; 2016. doi:10.1109/ICT-DM.2015.7402041","short":"J. Pielorz, C. Lampert, in:, IEEE, 2016.","apa":"Pielorz, J., & Lampert, C. (2016). Optimal geospatial allocation of volunteers for crisis management. Presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France: IEEE. https://doi.org/10.1109/ICT-DM.2015.7402041","ieee":"J. Pielorz and C. Lampert, “Optimal geospatial allocation of volunteers for crisis management,” presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France, 2016."},"date_created":"2018-12-11T11:53:35Z","publist_id":"5429","author":[{"id":"49BC895A-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Pielorz","full_name":"Pielorz, Jasmin"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"acknowledgement":"The DRIVER FP7 project has received funding from the European Unions Seventh Framework Programme for research, technological development and demonstration under grant agreement no 607798. RE-ACTA was funded within the framework of the Austrian Security Research Programme KIRAS by the Federal Ministry for Transport, Innovation and Technology.","doi":"10.1109/ICT-DM.2015.7402041","language":[{"iso":"eng"}],"day":"11","scopus_import":1,"year":"2016","date_updated":"2021-01-12T06:52:39Z","date_published":"2016-02-11T00:00:00Z","month":"02","article_number":"7402041","abstract":[{"text":"Volunteer supporters play an important role in modern crisis and disaster management. In the times of mobile Internet devices, help from thousands of volunteers can be requested within a short time span, thus relieving professional helpers from minor chores or geographically spread-out tasks. However, the simultaneous availability of many volunteers also poses new problems. In particular, the volunteer efforts must be well coordinated, or otherwise situations might emerge in which too many idle volunteers at one location become more of a burden than a relief to the professionals.\r\nIn this work, we study the task of optimally assigning volunteers to selected locations, e.g. in order to perform regular measurements, to report on damage, or to distribute information or resources to the population in a crisis situation. We formulate the assignment tasks as an optimization problem and propose an effective and efficient solution procedure. Experiments on real data of the Team Österreich, consisting of over 36,000 Austrian volunteers, show the effectiveness and efficiency of our approach.","lang":"eng"}],"department":[{"_id":"ChLa"}],"_id":"1707"},{"main_file_link":[{"url":"http://arxiv.org/abs/1501.00600","open_access":"1"}],"citation":{"ieee":"A. Klimova and T. Rudas, “On the closure of relational models,” Journal of Multivariate Analysis, vol. 143. Elsevier, pp. 440–452, 2016.","short":"A. Klimova, T. Rudas, Journal of Multivariate Analysis 143 (2016) 440–452.","apa":"Klimova, A., & Rudas, T. (2016). On the closure of relational models. Journal of Multivariate Analysis. Elsevier. https://doi.org/10.1016/j.jmva.2015.10.005","ista":"Klimova A, Rudas T. 2016. On the closure of relational models. Journal of Multivariate Analysis. 143, 440–452.","ama":"Klimova A, Rudas T. On the closure of relational models. Journal of Multivariate Analysis. 2016;143:440-452. doi:10.1016/j.jmva.2015.10.005","chicago":"Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” Journal of Multivariate Analysis. Elsevier, 2016. https://doi.org/10.1016/j.jmva.2015.10.005.","mla":"Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” Journal of Multivariate Analysis, vol. 143, Elsevier, 2016, pp. 440–52, doi:10.1016/j.jmva.2015.10.005."},"type":"journal_article","title":"On the closure of relational models","volume":143,"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","oa_version":"Preprint","publication_status":"published","quality_controlled":"1","publication":"Journal of Multivariate Analysis","doi":"10.1016/j.jmva.2015.10.005","language":[{"iso":"eng"}],"intvolume":" 143","oa":1,"date_created":"2018-12-11T11:54:15Z","publist_id":"5270","author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova","full_name":"Klimova, Anna"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"year":"2016","date_updated":"2021-01-12T06:53:30Z","day":"01","scopus_import":1,"abstract":[{"text":"Relational models for contingency tables are generalizations of log-linear models, allowing effects associated with arbitrary subsets of cells in the table, and not necessarily containing the overall effect, that is, a common parameter in every cell. Similarly to log-linear models, relational models can be extended to non-negative distributions, but the extension requires more complex methods. An extended relational model is defined as an algebraic variety, and it turns out to be the closure of the original model with respect to the Bregman divergence. In the extended relational model, the MLE of the cell parameters always exists and is unique, but some of its properties may be different from those of the MLE under log-linear models. The MLE can be computed using a generalized iterative scaling procedure based on Bregman projections. ","lang":"eng"}],"page":"440 - 452","department":[{"_id":"CaUh"}],"_id":"1833","date_published":"2016-01-01T00:00:00Z","month":"01"},{"quality_controlled":"1","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"Extremal eigenvalues and eigenvectors of deformed Wigner matrices","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.7057"}],"issue":"1-2","ec_funded":1,"date_created":"2018-12-11T11:54:31Z","oa":1,"scopus_import":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"abstract":[{"lang":"eng","text":"We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal random matrix of size N with i.i.d.\\ entries that are independent of W. We assume subexponential decay for the matrix entries of W and we choose λ∼1, so that the eigenvalues of W and λV are typically of the same order. Further, we assume that the density of the entries of V is supported on a single interval and is convex near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such that the largest eigenvalues of H are in the limit of large N determined by the order statistics of V for λ>λ+. In particular, the largest eigenvalue of H has a Weibull distribution in the limit N→∞ if λ>λ+. Moreover, for N sufficiently large, we show that the eigenvectors associated to the largest eigenvalues are partially localized for λ>λ+, while they are completely delocalized for λ<λ+. Similar results hold for the lowest eigenvalues. "}],"page":"165 - 241","publication_status":"published","status":"public","volume":164,"type":"journal_article","citation":{"ista":"Lee J, Schnelli K. 2016. Extremal eigenvalues and eigenvectors of deformed Wigner matrices. Probability Theory and Related Fields. 164(1–2), 165–241.","ama":"Lee J, Schnelli K. Extremal eigenvalues and eigenvectors of deformed Wigner matrices. Probability Theory and Related Fields. 2016;164(1-2):165-241. doi:10.1007/s00440-014-0610-8","mla":"Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed Wigner Matrices.” Probability Theory and Related Fields, vol. 164, no. 1–2, Springer, 2016, pp. 165–241, doi:10.1007/s00440-014-0610-8.","chicago":"Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer, 2016. https://doi.org/10.1007/s00440-014-0610-8.","ieee":"J. Lee and K. Schnelli, “Extremal eigenvalues and eigenvectors of deformed Wigner matrices,” Probability Theory and Related Fields, vol. 164, no. 1–2. Springer, pp. 165–241, 2016.","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 164 (2016) 165–241.","apa":"Lee, J., & Schnelli, K. (2016). Extremal eigenvalues and eigenvectors of deformed Wigner matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-014-0610-8"},"author":[{"last_name":"Lee","first_name":"Jioon","full_name":"Lee, Jioon"},{"full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin","last_name":"Schnelli"}],"publist_id":"5215","intvolume":" 164","language":[{"iso":"eng"}],"doi":"10.1007/s00440-014-0610-8","acknowledgement":"Most of the presented work was obtained while Kevin Schnelli was staying at the IAS with the support of\r\nThe Fund For Math.","publication":"Probability Theory and Related Fields","day":"01","date_updated":"2021-01-12T06:53:49Z","year":"2016","month":"02","date_published":"2016-02-01T00:00:00Z","_id":"1881","department":[{"_id":"LaEr"}]},{"citation":{"short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Israel Journal of Mathematics 212 (2016) 37–79.","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2016). Untangling two systems of noncrossing curves. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1294-9","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Untangling two systems of noncrossing curves,” Israel Journal of Mathematics, vol. 212, no. 1. Springer, pp. 37–79, 2016.","mla":"Matoušek, Jiří, et al. “Untangling Two Systems of Noncrossing Curves.” Israel Journal of Mathematics, vol. 212, no. 1, Springer, 2016, pp. 37–79, doi:10.1007/s11856-016-1294-9.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Untangling Two Systems of Noncrossing Curves.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1294-9.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2016. Untangling two systems of noncrossing curves. Israel Journal of Mathematics. 212(1), 37–79.","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Untangling two systems of noncrossing curves. Israel Journal of Mathematics. 2016;212(1):37-79. doi:10.1007/s11856-016-1294-9"},"publication_status":"published","status":"public","volume":212,"type":"journal_article","language":[{"iso":"eng"}],"intvolume":" 212","acknowledgement":"Supported by the ERC Adv anced Grant No. 267165. ","doi":"10.1007/s11856-016-1294-9","publication":"Israel Journal of Mathematics","author":[{"first_name":"Jiří","last_name":"Matoušek","full_name":"Matoušek, Jiří"},{"last_name":"Sedgwick","first_name":"Eric","full_name":"Sedgwick, Eric"},{"orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner"}],"publist_id":"5796","date_updated":"2023-02-23T10:34:31Z","year":"2016","related_material":{"record":[{"status":"public","id":"2244","relation":"earlier_version"}]},"day":"01","_id":"1411","department":[{"_id":"UlWa"}],"month":"05","date_published":"2016-05-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1302.6475"}],"issue":"1","oa_version":"Preprint","quality_controlled":"1","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Untangling two systems of noncrossing curves","oa":1,"date_created":"2018-12-11T11:51:52Z","scopus_import":1,"project":[{"grant_number":"PP00P2_138948","_id":"25FA3206-B435-11E9-9278-68D0E5697425","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics"}],"abstract":[{"text":"We consider two systems (α1, …, αm) and (β1, …,βn) of simple curves drawn on a compact two-dimensional surface M with boundary. Each αi and each βj is either an arc meeting the boundary of M at its two endpoints, or a closed curve. The αi are pairwise disjoint except for possibly sharing endpoints, and similarly for the βj. We want to “untangle” the βj from the ai by a self-homeomorphism of M; more precisely, we seek a homeomorphism φ:M→M fixing the boundary of M pointwise such that the total number of crossings of the ai with the φ(βj) is as small as possible. This problem is motivated by an application in the algorithmic theory of embeddings and 3-manifolds. We prove that if M is planar, i.e., a sphere with h ≥ 0 boundary components (“holes”), then O(mn) crossings can be achieved (independently of h), which is asymptotically tight, as an easy lower bound shows. In general, for an arbitrary (orientable or nonorientable) surface M with h holes and of (orientable or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent of h and g. The proofs rely, among other things, on a result concerning simultaneous planar drawings of graphs by Erten and Kobourov.","lang":"eng"}],"page":"37 - 79"},{"scopus_import":1,"page":"567 - 605","abstract":[{"lang":"eng","text":"Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That is, by conditioning on A the entropy of X can decrease by at most the bitlength |A| of A. Such chain rules are known to hold for some computational entropy notions like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue of min-entropy, the chain rule is of special interest and has found many applications, including leakage-resilient cryptography, deterministic encryption, and memory delegation. These applications rely on restricted special cases of the chain rule. Whether the chain rule for conditional HILL entropy holds in general was an open problem for which we give a strong negative answer: we construct joint distributions (X,Z,A), where A is a distribution over a single bit, such that the HILL entropy H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero.\r\n\r\nOur counterexample just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption that injective one-way function exist, we can make all the distributions efficiently samplable.\r\n\r\nFinally, we show that some more sophisticated cryptographic objects like lossy functions can be used to sample a distribution constituting a counterexample to the chain rule making only a single invocation to the underlying object."}],"file":[{"file_size":483258,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:44:56Z","creator":"system","checksum":"7659296174fa75f5f0364f31f46f4bcf","file_name":"IST-2017-766-v1+1_678.pdf","date_created":"2018-12-12T10:13:29Z","content_type":"application/pdf","file_id":"5012"}],"has_accepted_license":"1","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"A counterexample to the chain rule for conditional HILL entropy","quality_controlled":"1","oa_version":"Submitted Version","issue":"3","ec_funded":1,"date_created":"2018-12-11T11:52:16Z","oa":1,"ddc":["004"],"day":"01","related_material":{"record":[{"id":"2940","relation":"earlier_version","status":"public"}]},"year":"2016","date_updated":"2023-02-23T11:05:09Z","month":"09","date_published":"2016-09-01T00:00:00Z","_id":"1479","department":[{"_id":"KrPi"}],"status":"public","volume":25,"type":"journal_article","pubrep_id":"766","publication_status":"published","citation":{"ama":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. 2016;25(3):567-605. doi:10.1007/s00037-015-0120-9","ista":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. 2016. A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. 25(3), 567–605.","mla":"Krenn, Stephan, et al. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” Computational Complexity, vol. 25, no. 3, Springer, 2016, pp. 567–605, doi:10.1007/s00037-015-0120-9.","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, Akshay Wadia, and Daniel Wichs. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” Computational Complexity. Springer, 2016. https://doi.org/10.1007/s00037-015-0120-9.","ieee":"S. Krenn, K. Z. Pietrzak, A. Wadia, and D. Wichs, “A counterexample to the chain rule for conditional HILL entropy,” Computational Complexity, vol. 25, no. 3. Springer, pp. 567–605, 2016.","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, D. Wichs, Computational Complexity 25 (2016) 567–605.","apa":"Krenn, S., Pietrzak, K. Z., Wadia, A., & Wichs, D. (2016). A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. Springer. https://doi.org/10.1007/s00037-015-0120-9"},"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)"},"publist_id":"5715","author":[{"full_name":"Krenn, Stephan","orcid":"0000-0003-2835-9093","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","last_name":"Krenn"},{"last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Wadia, Akshay","last_name":"Wadia","first_name":"Akshay"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"file_date_updated":"2020-07-14T12:44:56Z","doi":"10.1007/s00037-015-0120-9","acknowledgement":"This work was partly funded by the European Research Council under ERC Starting Grant 259668-PSPC and ERC Advanced Grant 321310-PERCY.\r\n","publication":"Computational Complexity","intvolume":" 25","language":[{"iso":"eng"}]},{"publist_id":"7342","file_date_updated":"2020-07-14T12:46:35Z","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen"}],"doi":"10.3233/978-1-61499-672-9-1432","intvolume":" 285","language":[{"iso":"eng"}],"type":"conference","volume":285,"status":"public","conference":{"name":"ECAI: European Conference on Artificial Intelligence","start_date":"2016-08-29","location":"The Hague, Netherlands","end_date":"2016-09-02"},"pubrep_id":"950","publication_status":"published","citation":{"ieee":"K. Chatterjee and R. Ibsen-Jensen, “The complexity of deciding legality of a single step of magic: The gathering,” presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands, 2016, vol. 285, pp. 1432–1439.","apa":"Chatterjee, K., & Ibsen-Jensen, R. (2016). The complexity of deciding legality of a single step of magic: The gathering (Vol. 285, pp. 1432–1439). Presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands: IOS Press. https://doi.org/10.3233/978-1-61499-672-9-1432","short":"K. Chatterjee, R. Ibsen-Jensen, in:, IOS Press, 2016, pp. 1432–1439.","ista":"Chatterjee K, Ibsen-Jensen R. 2016. The complexity of deciding legality of a single step of magic: The gathering. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 285, 1432–1439.","ama":"Chatterjee K, Ibsen-Jensen R. The complexity of deciding legality of a single step of magic: The gathering. In: Vol 285. IOS Press; 2016:1432-1439. doi:10.3233/978-1-61499-672-9-1432","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Deciding Legality of a Single Step of Magic: The Gathering,” 285:1432–39. IOS Press, 2016. https://doi.org/10.3233/978-1-61499-672-9-1432.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Deciding Legality of a Single Step of Magic: The Gathering. Vol. 285, IOS Press, 2016, pp. 1432–39, doi:10.3233/978-1-61499-672-9-1432."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"date_published":"2016-01-01T00:00:00Z","month":"01","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"department":[{"_id":"KrCh"}],"_id":"478","day":"01","year":"2016","date_updated":"2021-01-12T08:00:54Z","date_created":"2018-12-11T11:46:41Z","ddc":["004"],"oa":1,"title":"The complexity of deciding legality of a single step of magic: The gathering","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IOS Press","oa_version":"Published Version","quality_controlled":"1","file":[{"checksum":"848043c812ace05e459579c923f3d3cf","creator":"system","date_updated":"2020-07-14T12:46:35Z","relation":"main_file","access_level":"open_access","file_size":2116225,"content_type":"application/pdf","file_id":"4658","file_name":"IST-2018-950-v1+1_2016_Chatterjee_The_complexity.pdf","date_created":"2018-12-12T10:07:59Z"}],"abstract":[{"text":"Magic: the Gathering is a game about magical combat for any number of players. Formally it is a zero-sum, imperfect information stochastic game that consists of a potentially unbounded number of steps. We consider the problem of deciding if a move is legal in a given single step of Magic. We show that the problem is (a) coNP-complete in general; and (b) in P if either of two small sets of cards are not used. Our lower bound holds even for single-player Magic games. The significant aspects of our results are as follows: First, in most real-life game problems, the task of deciding whether a given move is legal in a single step is trivial, and the computationally hard task is to find the best sequence of legal moves in the presence of multiple players. In contrast, quite uniquely our hardness result holds for single step and with only one-player. Second, we establish efficient algorithms for important special cases of Magic.","lang":"eng"}],"page":"1432 - 1439","has_accepted_license":"1","scopus_import":1},{"language":[{"iso":"eng"}],"acknowledgement":"This work is supported by NSF CNS 13-30077, NSF CNS 13-29886, NSF CNS 15-45002, and NSFC 61303014.\r\nThe authors thank Dr. Bobby and Dr. Hill at Carle Hospital, Urbana, IL for their help with the discussion on medical knowledge.\r\n\r\n","doi":"10.1145/2889160.2889233","publication":"Proceedings of the 38th International Conference on Software Engineering Companion ","author":[{"last_name":"Jiang","first_name":"Yu","full_name":"Jiang, Yu"},{"last_name":"Liu","first_name":"Han","full_name":"Liu, Han"},{"orcid":"0000-0002-3066-6941","full_name":"Kong, Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui"},{"full_name":"Wang, Rui","first_name":"Rui","last_name":"Wang"},{"full_name":"Hosseini, Mohamad","first_name":"Mohamad","last_name":"Hosseini"},{"first_name":"Jiaguang","last_name":"Sun","full_name":"Sun, Jiaguang"},{"full_name":"Sha, Lui","last_name":"Sha","first_name":"Lui"}],"publist_id":"7341","date_created":"2018-12-11T11:46:42Z","citation":{"mla":"Jiang, Yu, et al. “Use Runtime Verification to Improve the Quality of Medical Care Practice.” Proceedings of the 38th International Conference on Software Engineering Companion , IEEE, 2016, pp. 112–21, doi:10.1145/2889160.2889233.","chicago":"Jiang, Yu, Han Liu, Hui Kong, Rui Wang, Mohamad Hosseini, Jiaguang Sun, and Lui Sha. “Use Runtime Verification to Improve the Quality of Medical Care Practice.” In Proceedings of the 38th International Conference on Software Engineering Companion , 112–21. IEEE, 2016. https://doi.org/10.1145/2889160.2889233.","ista":"Jiang Y, Liu H, Kong H, Wang R, Hosseini M, Sun J, Sha L. 2016. Use runtime verification to improve the quality of medical care practice. Proceedings of the 38th International Conference on Software Engineering Companion . ICSE: International Conference on Software Engineering, Proceedings International Conference on Software Engineering, , 112–121.","ama":"Jiang Y, Liu H, Kong H, et al. Use runtime verification to improve the quality of medical care practice. In: Proceedings of the 38th International Conference on Software Engineering Companion . IEEE; 2016:112-121. doi:10.1145/2889160.2889233","short":"Y. Jiang, H. Liu, H. Kong, R. Wang, M. Hosseini, J. Sun, L. Sha, in:, Proceedings of the 38th International Conference on Software Engineering Companion , IEEE, 2016, pp. 112–121.","apa":"Jiang, Y., Liu, H., Kong, H., Wang, R., Hosseini, M., Sun, J., & Sha, L. (2016). Use runtime verification to improve the quality of medical care practice. In Proceedings of the 38th International Conference on Software Engineering Companion (pp. 112–121). Austin, TX, USA: IEEE. https://doi.org/10.1145/2889160.2889233","ieee":"Y. Jiang et al., “Use runtime verification to improve the quality of medical care practice,” in Proceedings of the 38th International Conference on Software Engineering Companion , Austin, TX, USA, 2016, pp. 112–121."},"quality_controlled":"1","oa_version":"None","conference":{"end_date":"2016-05-22","name":"ICSE: International Conference on Software Engineering","start_date":"2016-05-14","location":"Austin, TX, USA"},"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"IEEE","title":"Use runtime verification to improve the quality of medical care practice","type":"conference","_id":"479","department":[{"_id":"ToHe"}],"abstract":[{"text":"Clinical guidelines and decision support systems (DSS) play an important role in daily practices of medicine. Many text-based guidelines have been encoded for work-flow simulation of DSS to automate health care. During the collaboration with Carle hospital to develop a DSS, we identify that, for some complex and life-critical diseases, it is highly desirable to automatically rigorously verify some complex temporal properties in guidelines, which brings new challenges to current simulation based DSS with limited support of automatical formal verification and real-time data analysis. In this paper, we conduct the first study on applying runtime verification to cooperate with current DSS based on real-time data. Within the proposed technique, a user-friendly domain specific language, named DRTV, is designed to specify vital real-time data sampled by medical devices and temporal properties originated from clinical guidelines. Some interfaces are developed for data acquisition and communication. Then, for medical practice scenarios described in DRTV model, we will automatically generate event sequences and runtime property verifier automata. If a temporal property violates, real-time warnings will be produced by the formal verifier and passed to medical DSS. We have used DRTV to specify different kinds of medical care scenarios, and applied the proposed technique to assist existing DSS. As presented in experiment results, in terms of warning detection, it outperforms the only use of DSS or human inspection, and improves the quality of clinical health care of hospital","lang":"eng"}],"page":"112 - 121","alternative_title":["Proceedings International Conference on Software Engineering"],"month":"05","date_published":"2016-05-14T00:00:00Z","date_updated":"2021-01-12T08:00:55Z","year":"2016","scopus_import":1,"day":"14"},{"scopus_import":1,"page":"247 - 256","abstract":[{"text":"Graph games provide the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic reactive processes, the traditional model is perfect-information stochastic games, where some transitions of the game graph are controlled by two adversarial players, and the other transitions are executed probabilistically. We consider such games where the objective is the conjunction of several quantitative objectives (specified as mean-payoff conditions), which we refer to as generalized mean-payoff objectives. The basic decision problem asks for the existence of a finite-memory strategy for a player that ensures the generalized mean-payoff objective be satisfied with a desired probability against all strategies of the opponent. A special case of the decision problem is the almost-sure problem where the desired probability is 1. Previous results presented a semi-decision procedure for -approximations of the almost-sure problem. In this work, we show that both the almost-sure problem as well as the general basic decision problem are coNP-complete, significantly improving the previous results. Moreover, we show that in the case of 1-player stochastic games, randomized memoryless strategies are sufficient and the problem can be solved in polynomial time. In contrast, in two-player stochastic games, we show that even with randomized strategies exponential memory is required in general, and present a matching exponential upper bound. We also study the basic decision problem with infinite-memory strategies and present computational complexity results for the problem. Our results are relevant in the synthesis of stochastic reactive systems with multiple quantitative requirements.","lang":"eng"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","title":"Perfect-information stochastic games with generalized mean-payoff objectives","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06376"}],"ec_funded":1,"date_created":"2018-12-11T11:46:42Z","oa":1,"day":"05","year":"2016","date_updated":"2021-01-12T08:00:56Z","month":"07","date_published":"2016-07-05T00:00:00Z","alternative_title":["Proceedings Symposium on Logic in Computer Science"],"_id":"480","department":[{"_id":"KrCh"}],"status":"public","type":"conference","volume":"05-08-July-2016","publication_status":"published","conference":{"location":"New York, NY, USA","start_date":"2016-07-05","name":"LICS: Logic in Computer Science","end_date":"2016-07-08"},"citation":{"chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Perfect-Information Stochastic Games with Generalized Mean-Payoff Objectives,” 05-08-July-2016:247–56. IEEE, 2016. https://doi.org/10.1145/2933575.2934513.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Perfect-Information Stochastic Games with Generalized Mean-Payoff Objectives. Vol. 05-08-July-2016, IEEE, 2016, pp. 247–56, doi:10.1145/2933575.2934513.","ista":"Chatterjee K, Doyen L. 2016. Perfect-information stochastic games with generalized mean-payoff objectives. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, vol. 05-08-July-2016, 247–256.","ama":"Chatterjee K, Doyen L. Perfect-information stochastic games with generalized mean-payoff objectives. In: Vol 05-08-July-2016. IEEE; 2016:247-256. doi:10.1145/2933575.2934513","short":"K. Chatterjee, L. Doyen, in:, IEEE, 2016, pp. 247–256.","apa":"Chatterjee, K., & Doyen, L. (2016). Perfect-information stochastic games with generalized mean-payoff objectives (Vol. 05-08-July-2016, pp. 247–256). Presented at the LICS: Logic in Computer Science, New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934513","ieee":"K. Chatterjee and L. Doyen, “Perfect-information stochastic games with generalized mean-payoff objectives,” presented at the LICS: Logic in Computer Science, New York, NY, USA, 2016, vol. 05-08-July-2016, pp. 247–256."},"publist_id":"7340","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"doi":"10.1145/2933575.2934513","language":[{"iso":"eng"}]},{"pubrep_id":"622","publication_status":"published","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2016-06-14","location":"Medford, MA, USA","end_date":"2016-06-17"},"type":"conference","volume":51,"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)"},"citation":{"short":"B. Burton, A.N. de Mesmay, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15.","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2016). Finding non-orientable surfaces in 3-manifolds (Vol. 51, p. 24.1-24.15). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.24","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 24.1-24.15.","mla":"Burton, Benjamin, et al. Finding Non-Orientable Surfaces in 3-Manifolds. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15, doi:10.4230/LIPIcs.SoCG.2016.24.","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds,” 51:24.1-24.15. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.24.","ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-manifolds. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing; 2016:24.1-24.15. doi:10.4230/LIPIcs.SoCG.2016.24","ista":"Burton B, de Mesmay AN, Wagner U. 2016. Finding non-orientable surfaces in 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 24.1-24.15."},"file_date_updated":"2020-07-14T12:44:47Z","author":[{"full_name":"Burton, Benjamin","last_name":"Burton","first_name":"Benjamin"},{"full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay","first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner"}],"publist_id":"5832","language":[{"iso":"eng"}],"intvolume":" 51","doi":"10.4230/LIPIcs.SoCG.2016.24","related_material":{"record":[{"status":"public","relation":"later_version","id":"534"}]},"day":"01","date_updated":"2023-02-23T12:23:20Z","year":"2016","alternative_title":["LIPIcs"],"date_published":"2016-06-01T00:00:00Z","month":"06","department":[{"_id":"UlWa"}],"_id":"1379","oa_version":"Published Version","quality_controlled":"1","title":"Finding non-orientable surfaces in 3-manifolds","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing","date_created":"2018-12-11T11:51:41Z","ddc":["510"],"oa":1,"scopus_import":1,"file":[{"relation":"main_file","access_level":"open_access","file_size":574770,"creator":"system","checksum":"f04248a61c24297cfabd30c5f8e0deb9","date_updated":"2020-07-14T12:44:47Z","content_type":"application/pdf","file_id":"4930","date_created":"2018-12-12T10:12:12Z","file_name":"IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf"}],"abstract":[{"lang":"eng","text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case."}],"has_accepted_license":"1","page":"24.1 - 24.15"},{"citation":{"ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with ω-regular objectives,” Journal of Computer and System Sciences, vol. 82, no. 5. Elsevier, pp. 878–911, 2016.","short":"K. Chatterjee, M. Chmelik, M. Tracol, Journal of Computer and System Sciences 82 (2016) 878–911.","apa":"Chatterjee, K., Chmelik, M., & Tracol, M. (2016). What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.02.009","ama":"Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. 2016;82(5):878-911. doi:10.1016/j.jcss.2016.02.009","ista":"Chatterjee K, Chmelik M, Tracol M. 2016. What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. 82(5), 878–911.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” Journal of Computer and System Sciences. Elsevier, 2016. https://doi.org/10.1016/j.jcss.2016.02.009.","mla":"Chatterjee, Krishnendu, et al. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” Journal of Computer and System Sciences, vol. 82, no. 5, Elsevier, 2016, pp. 878–911, doi:10.1016/j.jcss.2016.02.009."},"publication_status":"published","status":"public","type":"journal_article","volume":82,"intvolume":" 82","language":[{"iso":"eng"}],"doi":"10.1016/j.jcss.2016.02.009","publication":"Journal of Computer and System Sciences","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","first_name":"Mathieu","last_name":"Tracol","full_name":"Tracol, Mathieu"}],"publist_id":"5718","date_updated":"2023-02-23T12:24:38Z","year":"2016","related_material":{"record":[{"status":"public","id":"2295","relation":"earlier_version"},{"status":"public","id":"5400","relation":"earlier_version"}]},"day":"01","_id":"1477","department":[{"_id":"KrCh"}],"month":"08","date_published":"2016-08-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1309.2802","open_access":"1"}],"issue":"5","oa_version":"Preprint","quality_controlled":"1","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","oa":1,"ec_funded":1,"date_created":"2018-12-11T11:52:15Z","external_id":{"arxiv":["1309.2802"]},"scopus_import":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples.","lang":"eng"}],"page":"878 - 911"},{"volume":234,"type":"journal_article","status":"public","publication_status":"published","citation":{"ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 2016;234:26-48. doi:10.1016/j.artint.2016.01.007","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 234, 26–48.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Artificial Intelligence, vol. 234, Elsevier, 2016, pp. 26–48, doi:10.1016/j.artint.2016.01.007.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” Artificial Intelligence. Elsevier, 2016. https://doi.org/10.1016/j.artint.2016.01.007.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” Artificial Intelligence, vol. 234. Elsevier, pp. 26–48, 2016.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2016). Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2016.01.007","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence 234 (2016) 26–48."},"publist_id":"5642","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"full_name":"Gupta, Raghav","last_name":"Gupta","first_name":"Raghav"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"}],"publication":"Artificial Intelligence","acknowledgement":"We thank Blai Bonet for helping us with RTDP-Bel. 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.","doi":"10.1016/j.artint.2016.01.007","intvolume":" 234","language":[{"iso":"eng"}],"day":"01","related_material":{"record":[{"relation":"earlier_version","id":"1820","status":"public"},{"id":"5425","relation":"earlier_version","status":"public"}]},"year":"2016","date_updated":"2023-02-23T12:25:49Z","date_published":"2016-05-01T00:00:00Z","month":"05","department":[{"_id":"KrCh"}],"_id":"1529","title":"Optimal cost almost-sure reachability in POMDPs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"date_created":"2018-12-11T11:52:33Z","ec_funded":1,"oa":1,"scopus_import":1,"external_id":{"arxiv":["1411.3880"]},"page":"26 - 48","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and an integer cost associated with every transition. The optimization objective we study asks to minimize the expected total cost of reaching a state in the target set, 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, both double exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation 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 also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest."}],"article_processing_charge":"No","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}]},{"language":[{"iso":"eng"}],"ddc":["005"],"publication_identifier":{"issn":["2664-1690"]},"oa":1,"doi":"10.15479/AT:IST-2016-523-v1-1","file_date_updated":"2020-07-14T12:46:58Z","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"date_created":"2018-12-12T11:39:22Z","citation":{"ama":"Chatterjee K, Pavlogiannis A, Velner Y. Quantitative Interprocedural Analysis. IST Austria; 2016. doi:10.15479/AT:IST-2016-523-v1-1","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural analysis, IST Austria, 33p.","mla":"Chatterjee, Krishnendu, et al. Quantitative Interprocedural Analysis. IST Austria, 2016, doi:10.15479/AT:IST-2016-523-v1-1.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. Quantitative Interprocedural Analysis. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-523-v1-1.","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, Quantitative interprocedural analysis. IST Austria, 2016.","apa":"Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2016). Quantitative interprocedural analysis. IST Austria. https://doi.org/10.15479/AT:IST-2016-523-v1-1","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis, IST Austria, 2016."},"oa_version":"Published Version","publication_status":"published","pubrep_id":"523","type":"technical_report","title":"Quantitative interprocedural analysis","publisher":"IST Austria","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"_id":"5445","has_accepted_license":"1","file":[{"file_size":1012204,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:58Z","creator":"system","checksum":"cef516fa091925b5868813e355268fb4","date_created":"2018-12-12T11:53:52Z","file_name":"IST-2016-523-v1+1_main.pdf","content_type":"application/pdf","file_id":"5513"}],"page":"33","abstract":[{"lang":"eng","text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. "}],"alternative_title":["IST Austria Technical Report"],"date_published":"2016-03-31T00:00:00Z","month":"03","date_updated":"2023-02-23T10:06:22Z","year":"2016","related_material":{"record":[{"status":"public","id":"1604","relation":"later_version"}]},"day":"31"},{"oa_version":"None","quality_controlled":"1","publication_status":"published","conference":{"name":"AAAI: Conference on Artificial Intelligence","location":"Phoenix, AZ, USA","start_date":"2016-02-12","end_date":"2016-02-17"},"publisher":"AAAI Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","type":"conference","title":"A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps","volume":2016,"citation":{"short":"K. Chatterjee, M. Chmelik, J. Davies, in:, Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, AAAI Press, 2016, pp. 3225–3232.","apa":"Chatterjee, K., Chmelik, M., & Davies, J. (2016). A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. In Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (Vol. 2016, pp. 3225–3232). Phoenix, AZ, USA: AAAI Press.","ieee":"K. Chatterjee, M. Chmelik, and J. Davies, “A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps,” in Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, Phoenix, AZ, USA, 2016, vol. 2016, pp. 3225–3232.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. “A Symbolic SAT Based Algorithm for Almost Sure Reachability with Small Strategies in Pomdps.” In Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, 2016:3225–32. AAAI Press, 2016.","mla":"Chatterjee, Krishnendu, et al. “A Symbolic SAT Based Algorithm for Almost Sure Reachability with Small Strategies in Pomdps.” Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, vol. 2016, AAAI Press, 2016, pp. 3225–32.","ama":"Chatterjee K, Chmelik M, Davies J. A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. In: Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence. Vol 2016. AAAI Press; 2016:3225-3232.","ista":"Chatterjee K, Chmelik M, Davies J. 2016. A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 2016, 3225–3232."},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"full_name":"Davies, Jessica","last_name":"Davies","first_name":"Jessica","id":"378E0060-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"publist_id":"6191","date_created":"2018-12-11T11:50:30Z","intvolume":" 2016","language":[{"iso":"eng"}],"publication":"Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5443"}],"link":[{"url":"https://dl.acm.org/citation.cfm?id=3016355","relation":"table_of_contents"}]},"day":"02","date_updated":"2023-02-23T12:26:41Z","year":"2016","month":"12","date_published":"2016-12-02T00:00:00Z","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"_id":"1166","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"page":"3225 - 3232","abstract":[{"lang":"eng","text":"POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIMEcomplete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. In this work, we first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. © 2016, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved."}]},{"has_accepted_license":"1","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.","lang":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","file_size":1264221,"creator":"system","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:54:07Z","file_name":"IST-2016-648-v1+1_tr.pdf","file_id":"5529","content_type":"application/pdf"}],"page":"22","_id":"5449","department":[{"_id":"KrCh"}],"month":"11","date_published":"2016-11-09T00:00:00Z","alternative_title":["IST Austria Technical Report"],"year":"2016","date_updated":"2023-02-23T12:22:21Z","day":"09","related_material":{"record":[{"id":"512","relation":"later_version","status":"public"}]},"doi":"10.15479/AT:IST-2016-648-v1-1","oa":1,"publication_identifier":{"issn":["2664-1690"]},"ddc":["519"],"language":[{"iso":"eng"}],"date_created":"2018-12-12T11:39:24Z","author":[{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"file_date_updated":"2020-07-14T12:46:58Z","citation":{"ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Amplification on undirected population structures: Comets beat stars. IST Austria, 2016.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Amplification on undirected population structures: Comets beat stars. IST Austria. https://doi.org/10.15479/AT:IST-2016-648-v1-1","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on Undirected Population Structures: Comets Beat Stars. IST Austria; 2016. doi:10.15479/AT:IST-2016-648-v1-1","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p.","mla":"Pavlogiannis, Andreas, et al. Amplification on Undirected Population Structures: Comets Beat Stars. IST Austria, 2016, doi:10.15479/AT:IST-2016-648-v1-1.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. Amplification on Undirected Population Structures: Comets Beat Stars. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-648-v1-1."},"publisher":"IST Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Amplification on undirected population structures: Comets beat stars","type":"technical_report","oa_version":"Updated Version","pubrep_id":"648","publication_status":"published"},{"_id":"5453","department":[{"_id":"KrCh"}],"has_accepted_license":"1","page":"34","file":[{"checksum":"83b0313dab3bff4bdb6ac38695026fda","creator":"system","date_updated":"2020-07-14T12:46:59Z","access_level":"open_access","relation":"main_file","file_size":1015647,"file_name":"IST-2017-749-v3+1_main.pdf","date_created":"2018-12-12T11:53:13Z","content_type":"application/pdf","file_id":"5474"}],"alternative_title":["IST Austria Technical Report"],"month":"12","date_published":"2016-12-30T00:00:00Z","date_updated":"2023-02-23T12:27:07Z","year":"2016","related_material":{"record":[{"status":"public","id":"5452","relation":"earlier_version"}]},"day":"30","oa":1,"publication_identifier":{"issn":["2664-1690"]},"ddc":["000"],"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2017-749-v3-1","author":[{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"file_date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:39:25Z","citation":{"apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Arbitrarily strong amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2017-749-v3-1","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Arbitrarily strong amplifiers of natural selection. IST Austria, 2016.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2017-749-v3-1.","mla":"Pavlogiannis, Andreas, et al. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria, 2016, doi:10.15479/AT:IST-2017-749-v3-1.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria; 2016. doi:10.15479/AT:IST-2017-749-v3-1","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p."},"pubrep_id":"755","oa_version":"Published Version","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"IST Austria","title":"Arbitrarily strong amplifiers of natural selection","type":"technical_report"},{"publication_identifier":{"issn":["2664-1690"]},"oa":1,"language":[{"iso":"eng"}],"ddc":["000"],"doi":"10.15479/AT:IST-2016-728-v1-1","author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"file_date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:39:24Z","citation":{"ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Strong Amplifiers of Natural Selection. IST Austria; 2016. doi:10.15479/AT:IST-2016-728-v1-1","mla":"Pavlogiannis, Andreas, et al. Strong Amplifiers of Natural Selection. IST Austria, 2016, doi:10.15479/AT:IST-2016-728-v1-1.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. Strong Amplifiers of Natural Selection. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-728-v1-1.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Strong amplifiers of natural selection. IST Austria, 2016.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Strong amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2016-728-v1-1","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of Natural Selection, IST Austria, 2016."},"pubrep_id":"728","publication_status":"published","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"IST Austria","title":"Strong amplifiers of natural selection","type":"technical_report","_id":"5451","department":[{"_id":"KrCh"}],"has_accepted_license":"1","page":"34","file":[{"date_updated":"2020-07-14T12:46:59Z","checksum":"7b8bb17c322c0556acba6ac169fa71c1","creator":"system","file_size":1014732,"relation":"main_file","access_level":"open_access","date_created":"2018-12-12T11:53:04Z","file_name":"IST-2016-728-v1+1_main.pdf","content_type":"application/pdf","file_id":"5465"}],"alternative_title":["IST Austria Technical Report"],"month":"12","date_published":"2016-12-30T00:00:00Z","date_updated":"2023-02-23T12:27:05Z","year":"2016","day":"30"},{"page":"256-267","abstract":[{"lang":"eng","text":"Although the concept of functional plane for naive plane is studied and reported in the literature in great detail, no similar study is yet found for naive sphere. This article exposes the first study in this line, opening up further prospects of analyzing the topological properties of sphere in the discrete space. We show that each quadraginta octant Q of a naive sphere forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as the functional plane of Q, and hence gives rise to merely mono-jumps during back projection. The other two coordinate planes serve as para-functional and dia-functional planes for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds neither of the two. Owing to this, the quadraginta octants form symmetry groups and subgroups with equivalent jump conditions. We also show a potential application in generating a special class of discrete 3D circles based on back projection and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry, uniqueness, and bounded distance from the underlying real sphere and real plane."}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Springer Nature","title":"On functionality of quadraginta octants of naive sphere with application to circle drawing","oa_version":"None","quality_controlled":"1","date_created":"2019-01-08T20:44:37Z","day":"09","year":"2016","date_updated":"2022-01-28T08:10:11Z","month":"04","date_published":"2016-04-09T00:00:00Z","place":"Cham","alternative_title":["LNCS"],"_id":"5806","department":[{"_id":"HeEd"}],"status":"public","type":"conference","volume":9647,"publication_status":"published","conference":{"end_date":"2016-04-20","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","start_date":"2016-04-18","location":"Nantes, France"},"citation":{"ama":"Biswas R, Bhowmick P. On functionality of quadraginta octants of naive sphere with application to circle drawing. In: Discrete Geometry for Computer Imagery. Vol 9647. Cham: Springer Nature; 2016:256-267. doi:10.1007/978-3-319-32360-2_20","ista":"Biswas R, Bhowmick P. 2016. On functionality of quadraginta octants of naive sphere with application to circle drawing. Discrete Geometry for Computer Imagery. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 9647, 256–267.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” In Discrete Geometry for Computer Imagery, 9647:256–67. Cham: Springer Nature, 2016. https://doi.org/10.1007/978-3-319-32360-2_20.","mla":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” Discrete Geometry for Computer Imagery, vol. 9647, Springer Nature, 2016, pp. 256–67, doi:10.1007/978-3-319-32360-2_20.","ieee":"R. Biswas and P. Bhowmick, “On functionality of quadraginta octants of naive sphere with application to circle drawing,” in Discrete Geometry for Computer Imagery, Nantes, France, 2016, vol. 9647, pp. 256–267.","short":"R. Biswas, P. Bhowmick, in:, Discrete Geometry for Computer Imagery, Springer Nature, Cham, 2016, pp. 256–267.","apa":"Biswas, R., & Bhowmick, P. (2016). On functionality of quadraginta octants of naive sphere with application to circle drawing. In Discrete Geometry for Computer Imagery (Vol. 9647, pp. 256–267). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-32360-2_20"},"author":[{"orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","last_name":"Biswas","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"}],"doi":"10.1007/978-3-319-32360-2_20","publication":"Discrete Geometry for Computer Imagery","publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["978-3-319-32359-6"],"eisbn":["978-3-319-32360-2"]},"language":[{"iso":"eng"}],"extern":"1","intvolume":" 9647"},{"date_updated":"2022-01-28T08:01:22Z","year":"2016","day":"02","department":[{"_id":"HeEd"}],"_id":"5805","alternative_title":["LNCS"],"place":"Cham","date_published":"2016-06-02T00:00:00Z","month":"06","citation":{"apa":"Sen, N., Biswas, R., & Bhowmick, P. (2016). On some local topological properties of naive discrete sphere. In Computational Topology in Image Context (Vol. 9667, pp. 253–264). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-39441-1_23","short":"N. Sen, R. Biswas, P. Bhowmick, in:, Computational Topology in Image Context, Springer Nature, Cham, 2016, pp. 253–264.","ieee":"N. Sen, R. Biswas, and P. Bhowmick, “On some local topological properties of naive discrete sphere,” in Computational Topology in Image Context, vol. 9667, Cham: Springer Nature, 2016, pp. 253–264.","chicago":"Sen, Nabhasmita, Ranita Biswas, and Partha Bhowmick. “On Some Local Topological Properties of Naive Discrete Sphere.” In Computational Topology in Image Context, 9667:253–64. Cham: Springer Nature, 2016. https://doi.org/10.1007/978-3-319-39441-1_23.","mla":"Sen, Nabhasmita, et al. “On Some Local Topological Properties of Naive Discrete Sphere.” Computational Topology in Image Context, vol. 9667, Springer Nature, 2016, pp. 253–64, doi:10.1007/978-3-319-39441-1_23.","ama":"Sen N, Biswas R, Bhowmick P. On some local topological properties of naive discrete sphere. In: Computational Topology in Image Context. Vol 9667. Cham: Springer Nature; 2016:253-264. doi:10.1007/978-3-319-39441-1_23","ista":"Sen N, Biswas R, Bhowmick P. 2016.On some local topological properties of naive discrete sphere. In: Computational Topology in Image Context. LNCS, vol. 9667, 253–264."},"publication_status":"published","conference":{"end_date":"2016-06-17","name":"CTIC: Computational Topology in Image Context","start_date":"2016-06-15","location":"Marseille, France"},"type":"book_chapter","volume":9667,"status":"public","extern":"1","language":[{"iso":"eng"}],"intvolume":" 9667","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-319-39440-4"],"eisbn":["978-3-319-39441-1"]},"publication":"Computational Topology in Image Context","doi":"10.1007/978-3-319-39441-1_23","author":[{"full_name":"Sen, Nabhasmita","last_name":"Sen","first_name":"Nabhasmita"},{"full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"article_processing_charge":"No","abstract":[{"text":"Discretization of sphere in the integer space follows a particular discretization scheme, which, in principle, conforms to some topological model. This eventually gives rise to interesting topological properties of a discrete spherical surface, which need to be investigated for its analytical characterization. This paper presents some novel results on the local topological properties of the naive model of discrete sphere. They follow from the bijection of each quadraginta octant of naive sphere with its projection map called f -map on the corresponding functional plane and from the characterization of certain jumps in the f-map. As an application, we have shown how these properties can be used in designing an efficient reconstruction algorithm for a naive spherical surface from an input voxel set when it is sparse or noisy.","lang":"eng"}],"page":"253-264","oa_version":"None","quality_controlled":"1","title":"On some local topological properties of naive discrete sphere","publisher":"Springer Nature","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2019-01-08T20:44:24Z"},{"abstract":[{"text":"A discrete spherical circle is a topologically well-connected 3D circle in the integer space, which belongs to a discrete sphere as well as a discrete plane. It is one of the most important 3D geometric primitives, but has not possibly yet been studied up to its merit. This paper is a maiden exposition of some of its elementary properties, which indicates a sense of its profound theoretical prospects in the framework of digital geometry. We have shown how different types of discretization can lead to forbidden and admissible classes, when one attempts to define the discretization of a spherical circle in terms of intersection between a discrete sphere and a discrete plane. Several fundamental theoretical results have been presented, the algorithm for construction of discrete spherical circles has been discussed, and some test results have been furnished to demonstrate its practicality and usefulness.","lang":"eng"}],"page":"86-100","department":[{"_id":"HeEd"}],"article_processing_charge":"No","_id":"5809","date_published":"2016-01-06T00:00:00Z","month":"01","place":"Cham","year":"2016","date_updated":"2022-01-28T08:13:03Z","day":"06","publication":"Combinatorial image analysis","doi":"10.1007/978-3-319-26145-4_7","language":[{"iso":"eng"}],"intvolume":" 9448","extern":"1","publication_identifier":{"eisbn":["978-3-319-26145-4"],"isbn":["978-3-319-26144-7"],"eissn":["1611-3349"],"issn":["0302-9743"]},"date_created":"2019-01-08T20:45:19Z","author":[{"full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"},{"first_name":"Valentin E.","last_name":"Brimkov","full_name":"Brimkov, Valentin E."}],"citation":{"ama":"Biswas R, Bhowmick P, Brimkov VE. On the connectivity and smoothness of discrete spherical circles. In: Combinatorial Image Analysis. Vol 9448. Cham: Springer Nature; 2016:86-100. doi:10.1007/978-3-319-26145-4_7","ista":"Biswas R, Bhowmick P, Brimkov VE. 2016.On the connectivity and smoothness of discrete spherical circles. In: Combinatorial image analysis. vol. 9448, 86–100.","mla":"Biswas, Ranita, et al. “On the Connectivity and Smoothness of Discrete Spherical Circles.” Combinatorial Image Analysis, vol. 9448, Springer Nature, 2016, pp. 86–100, doi:10.1007/978-3-319-26145-4_7.","chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Connectivity and Smoothness of Discrete Spherical Circles.” In Combinatorial Image Analysis, 9448:86–100. Cham: Springer Nature, 2016. https://doi.org/10.1007/978-3-319-26145-4_7.","ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the connectivity and smoothness of discrete spherical circles,” in Combinatorial image analysis, vol. 9448, Cham: Springer Nature, 2016, pp. 86–100.","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2016, pp. 86–100.","apa":"Biswas, R., Bhowmick, P., & Brimkov, V. E. (2016). On the connectivity and smoothness of discrete spherical circles. In Combinatorial image analysis (Vol. 9448, pp. 86–100). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-26145-4_7"},"title":"On the connectivity and smoothness of discrete spherical circles","type":"book_chapter","volume":9448,"publisher":"Springer Nature","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","oa_version":"None","conference":{"start_date":"2015-11-24","location":"Kolkata, India","name":"IWCIA: International Workshop on Combinatorial Image Analysis","end_date":"2015-11-27"},"quality_controlled":"1","publication_status":"published"},{"doi":"10.7551/978-0-262-33936-0-ch029","publication":"Proceedings of the Artificial Life Conference 2016","publication_identifier":{"isbn":["9780262339360"]},"intvolume":" 28","language":[{"iso":"eng"}],"author":[{"last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S"},{"last_name":"Hostettler","first_name":"Rafael","full_name":"Hostettler, Rafael"},{"first_name":"Alois","last_name":"Knoll","full_name":"Knoll, Alois"},{"last_name":"Der","first_name":"Ralf","full_name":"Der, Ralf"}],"file_date_updated":"2020-07-14T12:48:09Z","citation":{"ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in Proceedings of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","apa":"Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In Proceedings of the Artificial Life Conference 2016 (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: Proceedings of the Artificial Life Conference 2016. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” Proceedings of the Artificial Life Conference 2016, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029.","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029."},"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","volume":28,"type":"conference","conference":{"name":"ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems","location":"Cancun, Mexico","start_date":"2016-07-04","end_date":"2016-07-08"},"publication_status":"published","_id":"8094","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"month":"09","date_published":"2016-09-01T00:00:00Z","year":"2016","date_updated":"2021-01-12T08:16:53Z","day":"01","oa":1,"ddc":["610"],"ec_funded":1,"date_created":"2020-07-05T22:00:47Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"MIT Press","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","quality_controlled":"1","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:48:09Z","creator":"cziletti","checksum":"cff63e7a4b8ac466ba51a9c84153a940","file_size":678670,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"8096","file_name":"2016_ProcALIFE_Martius.pdf","date_created":"2020-07-06T12:59:09Z"}],"has_accepted_license":"1","page":"142-143","abstract":[{"lang":"eng","text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with."}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"article_processing_charge":"No","scopus_import":1},{"scopus_import":1,"abstract":[{"text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.","lang":"eng"}],"file":[{"content_type":"application/pdf","file_id":"5884","date_created":"2019-01-25T10:35:00Z","file_name":"2016_PLOS_Prentice.pdf","file_size":4492021,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:38Z","checksum":"47b08cbd4dbf32b25ba161f5f4b262cc","creator":"kschuh"}],"has_accepted_license":"1","project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"title":"Error-robust modes of the retinal population code","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","quality_controlled":"1","oa_version":"Published Version","issue":"11","date_created":"2018-12-11T11:50:40Z","ddc":["570"],"oa":1,"day":"17","related_material":{"record":[{"relation":"research_data","id":"9709","status":"public"}]},"year":"2016","date_updated":"2023-02-23T14:05:40Z","date_published":"2016-11-17T00:00:00Z","month":"11","article_number":"e1005855","department":[{"_id":"GaTk"}],"_id":"1197","volume":12,"type":"journal_article","status":"public","publication_status":"published","citation":{"ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. PLoS Computational Biology. 2016;12(11). doi:10.1371/journal.pcbi.1005148","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.","mla":"Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148.","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2016). Error-robust modes of the retinal population code. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148"},"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)"},"publist_id":"6153","file_date_updated":"2020-07-14T12:44:38Z","author":[{"first_name":"Jason","last_name":"Prentice","full_name":"Prentice, Jason"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"first_name":"Mark","last_name":"Ioffe","full_name":"Ioffe, Mark"},{"last_name":"Loback","first_name":"Adrianna","full_name":"Loback, Adrianna"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Berry, Michael","first_name":"Michael","last_name":"Berry"}],"publication":"PLoS Computational Biology","acknowledgement":"JSP was supported by a C.V. Starr Fellowship from the Starr Foundation (http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation (https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler for helpful comments on the manuscript.","doi":"10.1371/journal.pcbi.1005148","language":[{"iso":"eng"}],"intvolume":" 12"},{"date_created":"2021-07-26T09:14:19Z","author":[{"full_name":"Mcmahon, Dino","first_name":"Dino","last_name":"Mcmahon"},{"orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"full_name":"Caspar, Jesicca","last_name":"Caspar","first_name":"Jesicca"},{"full_name":"Theodorou, Panagiotis","last_name":"Theodorou","first_name":"Panagiotis"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"first_name":"Robert","last_name":"Paxton","full_name":"Paxton, Robert"}],"doi":"10.5061/dryad.4b565","oa":1,"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","type":"research_data_reference","title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.4b565","open_access":"1"}],"citation":{"mla":"Mcmahon, Dino, et al. Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees. Dryad, 2016, doi:10.5061/dryad.4b565.","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. https://doi.org/10.5061/dryad.4b565.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. 2016. doi:10.5061/dryad.4b565","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees, Dryad, 10.5061/dryad.4b565.","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton, R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Dryad. https://doi.org/10.5061/dryad.4b565","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees.” Dryad, 2016."},"month":"01","date_published":"2016-01-22T00:00:00Z","abstract":[{"lang":"eng","text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline."}],"_id":"9720","department":[{"_id":"SyCr"}],"article_processing_charge":"No","day":"22","related_material":{"record":[{"id":"1855","relation":"used_in_publication","status":"public"}]},"year":"2016","date_updated":"2023-02-23T10:17:25Z"},{"publist_id":"6200","author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"file_date_updated":"2020-07-14T12:44:36Z","acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","doi":"10.1371/journal.pbio.2000234","publication":"PLoS Biology","intvolume":" 14","language":[{"iso":"eng"}],"status":"public","volume":14,"type":"journal_article","publication_status":"published","pubrep_id":"742","citation":{"apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234."},"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)"},"month":"12","date_published":"2016-12-27T00:00:00Z","article_number":"e2000234","_id":"1158","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"day":"27","related_material":{"record":[{"id":"9862","relation":"research_data","status":"public"},{"id":"9863","relation":"research_data","status":"public"}]},"year":"2016","date_updated":"2023-02-23T14:11:16Z","date_created":"2018-12-11T11:50:28Z","oa":1,"ddc":["576"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","oa_version":"Published Version","quality_controlled":"1","issue":"12","abstract":[{"lang":"eng","text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation."}],"file":[{"checksum":"2bab63b068a9840efd532b9ae583f9bb","creator":"system","date_updated":"2020-07-14T12:44:36Z","relation":"main_file","access_level":"open_access","file_size":2494348,"content_type":"application/pdf","file_id":"5164","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","date_created":"2018-12-12T10:15:42Z"}],"has_accepted_license":"1","scopus_import":1},{"date_created":"2018-12-11T11:50:30Z","ddc":["570"],"oa":1,"title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","oa_version":"Published Version","quality_controlled":"1","issue":"12","has_accepted_license":"1","file":[{"file_size":3822299,"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:37Z","checksum":"84f44ae92866c52ff1ca8a574558dca7","creator":"system","date_created":"2018-12-12T10:12:08Z","file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf","content_type":"application/pdf","file_id":"4926"}],"abstract":[{"lang":"eng","text":"Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph. However, it is unclear how these results translate to the biologically relevant case in which genotypes are represented by sequences of more than two units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the mutational graph is not the hypercube. Here we investigate accessibility of the best-adapted genotype in the general case of K > 2 units. Using computer generated and experimental fitness landscapes we show that accessibility of the global fitness maximum increases with K and can be much higher than for binary sequences. The increase in accessibility comes from the increase in the number of indirect trajectories exploited by evolution for higher K. As one of the consequences, the fraction of genotypes that are accessible increases by three orders of magnitude when the number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes. This suggests that evolution can follow many different trajectories on such landscapes and the reconstruction of evolutionary pathways from experimental data might be an extremely difficult task."}],"article_processing_charge":"No","scopus_import":"1","publist_id":"6190","file_date_updated":"2020-07-14T12:44:37Z","author":[{"last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P"},{"full_name":"Burda, Zdzisław","first_name":"Zdzisław","last_name":"Burda"},{"first_name":"Bartłomiej","last_name":"Wacław","full_name":"Wacław, Bartłomiej"}],"publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1005218","acknowledgement":"MZ acknowledges the Polish National Science Centre grant no. DEC-2012/07/N/NZ2/00107. BW was supported by the Scottish Government/Royal Society of Edinburgh Personal Research Fellowship. We thank Marjon de Vos and Oliver Martin for critically reading the manuscript.","language":[{"iso":"eng"}],"intvolume":" 12","type":"journal_article","volume":12,"status":"public","publication_status":"published","pubrep_id":"740","citation":{"ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks,” PLoS Computational Biology, vol. 12, no. 12. Public Library of Science, 2016.","apa":"Zagórski, M. P., Burda, Z., & Wacław, B. (2016). Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218","short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016).","ama":"Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. 2016;12(12). doi:10.1371/journal.pcbi.1005218","ista":"Zagórski MP, Burda Z, Wacław B. 2016. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. 12(12), e1005218.","mla":"Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational Biology, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005218."},"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)"},"date_published":"2016-12-09T00:00:00Z","month":"12","article_number":"e1005218","department":[{"_id":"AnKi"}],"_id":"1167","day":"09","related_material":{"record":[{"status":"public","relation":"research_data","id":"9866"}]},"year":"2016","date_updated":"2023-02-23T14:11:22Z"},{"month":"10","article_processing_charge":"No","department":[{"_id":"KrCh"}],"_id":"9867","abstract":[{"lang":"eng","text":"In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German."}],"related_material":{"record":[{"relation":"used_in_publication","id":"1322","status":"public"}]},"day":"04","date_updated":"2023-02-21T16:59:01Z","year":"2016","author":[{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe"},{"full_name":"Hagel, Kristin","last_name":"Hagel","first_name":"Kristin"},{"full_name":"Milinski, Manfred","last_name":"Milinski","first_name":"Manfred"}],"date_created":"2021-08-10T08:42:00Z","doi":"10.1371/journal.pone.0163867.s008","oa_version":"Published Version","type":"research_data_reference","title":"Experimental game instructions","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","citation":{"ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public Library of Science, 2016.","apa":"Hilbe, C., Hagel, K., & Milinski, M. (2016). Experimental game instructions. Public Library of Science. https://doi.org/10.1371/journal.pone.0163867.s008","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","ama":"Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:10.1371/journal.pone.0163867.s008","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public Library of Science, 10.1371/journal.pone.0163867.s008.","mla":"Hilbe, Christian, et al. Experimental Game Instructions. Public Library of Science, 2016, doi:10.1371/journal.pone.0163867.s008.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game Instructions.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.s008."}},{"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"Public Library of Science","type":"research_data_reference","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","citation":{"ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:10.1371/journal.pbio.2000234.s016","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, 10.1371/journal.pbio.2000234.s016.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s016.","mla":"Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016."},"author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"date_created":"2021-08-10T08:20:17Z","doi":"10.1371/journal.pbio.2000234.s016","related_material":{"record":[{"id":"1158","relation":"used_in_publication","status":"public"}]},"day":"27","date_updated":"2023-02-21T16:21:20Z","year":"2016","month":"12","_id":"9862","article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}]},{"month":"12","_id":"9863","article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"day":"27","related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]},"year":"2016","date_updated":"2023-02-21T16:21:20Z","date_created":"2021-08-10T08:22:52Z","author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"doi":"10.1371/journal.pbio.2000234.s017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"Public Library of Science","type":"research_data_reference","title":"Accessions of surveyed individuals, geographic locations and summary statistics","oa_version":"Published Version","citation":{"ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, 10.1371/journal.pbio.2000234.s017.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017.","mla":"Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017."}},{"date_published":"2016-12-09T00:00:00Z","month":"12","department":[{"_id":"AnKi"}],"article_processing_charge":"No","_id":"9866","day":"09","related_material":{"record":[{"id":"1167","relation":"used_in_publication","status":"public"}]},"year":"2016","date_updated":"2023-02-21T16:24:29Z","date_created":"2021-08-10T08:37:20Z","author":[{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","last_name":"Zagórski","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762"},{"full_name":"Burda, Zdzisław","first_name":"Zdzisław","last_name":"Burda"},{"first_name":"Bartłomiej","last_name":"Wacław","full_name":"Wacław, Bartłomiej"}],"doi":"10.1371/journal.pcbi.1005218.s009","type":"research_data_reference","title":"ZIP-archived directory containing all data and computer programs","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","status":"public","oa_version":"Published Version","citation":{"ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing all data and computer programs.” Public Library of Science, 2016.","short":"M.P. Zagórski, Z. Burda, B. Wacław, (2016).","apa":"Zagórski, M. P., Burda, Z., & Wacław, B. (2016). ZIP-archived directory containing all data and computer programs. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218.s009","ama":"Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data and computer programs. 2016. doi:10.1371/journal.pcbi.1005218.s009","ista":"Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all data and computer programs, Public Library of Science, 10.1371/journal.pcbi.1005218.s009.","mla":"Zagórski, Marcin P., et al. ZIP-Archived Directory Containing All Data and Computer Programs. Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.s009.","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived Directory Containing All Data and Computer Programs.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005218.s009."}},{"date_published":"2016-10-27T00:00:00Z","month":"10","department":[{"_id":"DaZi"}],"_id":"9456","day":"27","date_updated":"2021-12-14T07:55:30Z","year":"2016","author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"},{"full_name":"Roy, Scott W.","last_name":"Roy","first_name":"Scott W."}],"extern":"1","language":[{"iso":"eng"}],"intvolume":" 538","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication":"Nature","doi":"10.1038/nature20110","publication_status":"published","volume":538,"type":"journal_article","status":"public","citation":{"ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” Nature, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.","apa":"Huff, J. T., Zilberman, D., & Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. Nature. Springer Nature . https://doi.org/10.1038/nature20110","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536.","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110","chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature , 2016. https://doi.org/10.1038/nature20110.","mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” Nature, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:10.1038/nature20110."},"article_processing_charge":"No","abstract":[{"text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution.","lang":"eng"}],"page":"533-536","scopus_import":"1","pmid":1,"external_id":{"pmid":["27760113"]},"date_created":"2021-06-04T11:34:55Z","article_type":"letter_note","oa":1,"quality_controlled":"1","oa_version":"Submitted Version","title":"Mechanism for DNA transposons to generate introns on genomic scales","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Springer Nature ","issue":"7626","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/"}]},{"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"abstract":[{"text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations.","lang":"eng"}],"page":"4285 - 4293","scopus_import":1,"ec_funded":1,"date_created":"2018-12-11T11:49:21Z","oa_version":"None","quality_controlled":"1","publisher":"Neural Information Processing Systems","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics"}],"alternative_title":["Advances in Neural Information Processing Systems"],"month":"01","date_published":"2016-01-01T00:00:00Z","_id":"948","department":[{"_id":"GaTk"}],"day":"01","date_updated":"2021-01-12T08:22:08Z","year":"2016","author":[{"first_name":"Travis","last_name":"Monk","full_name":"Monk, Travis"},{"first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","full_name":"Savin, Cristina"},{"first_name":"Jörg","last_name":"Lücke","full_name":"Lücke, Jörg"}],"publist_id":"6469","language":[{"iso":"eng"}],"intvolume":" 29","acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","publication_status":"published","conference":{"end_date":"2016-12-10","start_date":"2016-12-05","location":"Barcelona, Spaine","name":"NIPS: Neural Information Processing Systems"},"status":"public","type":"conference","volume":29,"citation":{"short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.","apa":"Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016.","mla":"Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics. Vol. 29, Neural Information Processing Systems, 2016, pp. 4285–93.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems; 2016:4285-4293.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293."}},{"scopus_import":1,"has_accepted_license":"1","file":[{"date_created":"2018-12-12T10:08:46Z","file_name":"IST-2016-701-v1+1_20160811.full.pdf","file_id":"4708","content_type":"application/pdf","creator":"system","checksum":"0b0d1be38b497d004064650acb3baced","date_updated":"2020-07-14T12:44:42Z","relation":"main_file","access_level":"open_access","file_size":796872}],"abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline."}],"oa_version":"Published Version","quality_controlled":"1","title":"Elevated virulence of an emerging viral genotype as a driver of honeybee loss","publisher":"Royal Society, The","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"1833","date_created":"2018-12-11T11:51:00Z","ddc":["576","592"],"oa":1,"related_material":{"record":[{"id":"9704","relation":"research_data","status":"public"}]},"day":"29","date_updated":"2023-02-23T14:05:30Z","year":"2016","article_number":"20160811","date_published":"2016-06-29T00:00:00Z","month":"06","department":[{"_id":"SyCr"}],"_id":"1262","pubrep_id":"701","publication_status":"published","volume":283,"type":"journal_article","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)"},"citation":{"ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. 2016;283(1833). doi:10.1098/rspb.2016.0811","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1833), 20160811.","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2016. https://doi.org/10.1098/rspb.2016.0811.","mla":"Mcmahon, Dino, et al. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1833, 20160811, Royal Society, The, 2016, doi:10.1098/rspb.2016.0811.","ieee":"D. Mcmahon et al., “Elevated virulence of an emerging viral genotype as a driver of honeybee loss,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1833. Royal Society, The, 2016.","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.0811","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016)."},"file_date_updated":"2020-07-14T12:44:42Z","author":[{"last_name":"Mcmahon","first_name":"Dino","full_name":"Mcmahon, Dino"},{"last_name":"Natsopoulou","first_name":"Myrsini","full_name":"Natsopoulou, Myrsini"},{"last_name":"Doublet","first_name":"Vincent","full_name":"Doublet, Vincent"},{"full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Fürst"},{"first_name":"Silvio","last_name":"Weging","full_name":"Weging, Silvio"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"first_name":"Andreas","last_name":"Gogol Döring","full_name":"Gogol Döring, Andreas"},{"first_name":"Robert","last_name":"Paxton","full_name":"Paxton, Robert"}],"publist_id":"6060","language":[{"iso":"eng"}],"intvolume":" 283","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","doi":"10.1098/rspb.2016.0811","acknowledgement":"This work was supported by the Federal Ministry of Food, Agriculture and Consumer Protection (Germany): Fit Bee project (grant 511-06.01-28-1-71.007-10), the EU: BeeDoc (grant 244956), iDiv (2013 NGS-Fast Track grant W47004118) and the Insect Pollinators Initiative (IPI grant BB/I000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, the Scottish Government and the Wellcome Trust, under the Living with Environmental Change Partnership. We thank A. Abrahams, M. Husemann and A. Soro\r\nfor support in obtaining\r\nV. destructor\r\n-free honeybees; and BBKA\r\nPresident D. Aston for access to records of colony overwinter\r\n2011–2012 mortality in the UK. We also thank the anonymous refe-\r\nrees and Stephen Martin for comments that led to substantial\r\nimprovement of the manuscript."},{"date_updated":"2023-02-21T16:54:31Z","year":"2016","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1262"}]},"day":"06","_id":"9704","article_processing_charge":"No","department":[{"_id":"SyCr"}],"abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline."}],"month":"05","date_published":"2016-05-06T00:00:00Z","citation":{"chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. https://doi.org/10.5061/dryad.cq7t1.","mla":"Mcmahon, Dino, et al. Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss. Dryad, 2016, doi:10.5061/dryad.cq7t1.","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:10.5061/dryad.cq7t1","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, 10.5061/dryad.cq7t1.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016).","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. https://doi.org/10.5061/dryad.cq7t1","ieee":"D. Mcmahon et al., “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cq7t1"}],"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","status":"public","title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","type":"research_data_reference","oa":1,"doi":"10.5061/dryad.cq7t1","author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"full_name":"Natsopoulou, Myrsini","last_name":"Natsopoulou","first_name":"Myrsini"},{"full_name":"Doublet, Vincent","first_name":"Vincent","last_name":"Doublet"},{"orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"last_name":"Weging","first_name":"Silvio","full_name":"Weging, Silvio"},{"full_name":"Brown, Mark","last_name":"Brown","first_name":"Mark"},{"full_name":"Gogol Döring, Andreas","last_name":"Gogol Döring","first_name":"Andreas"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"}],"date_created":"2021-07-23T08:30:38Z"},{"issue":"10","quality_controlled":"1","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","title":"Asymmetric power boosts extortion in an economic experiment","oa":1,"ddc":["004","006"],"date_created":"2018-12-11T11:51:22Z","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:44:44Z","checksum":"6b33e394003dfe8b4ca6be1858aaa8e3","creator":"system","file_size":2077905,"relation":"main_file","access_level":"open_access","file_id":"4668","content_type":"application/pdf","file_name":"IST-2016-716-v1+1_journal.pone.0163867.PDF","date_created":"2018-12-12T10:08:08Z"}],"abstract":[{"lang":"eng","text":"Direct reciprocity is a major mechanism for the evolution of cooperation. Several classical studies have suggested that humans should quickly learn to adopt reciprocal strategies to establish mutual cooperation in repeated interactions. On the other hand, the recently discovered theory of ZD strategies has found that subjects who use extortionate strategies are able to exploit and subdue cooperators. Although such extortioners have been predicted to succeed in any population of adaptive opponents, theoretical follow-up studies questioned whether extortion can evolve in reality. However, most of these studies presumed that individuals have similar strategic possibilities and comparable outside options, whereas asymmetries are ubiquitous in real world applications. Here we show with a model and an economic experiment that extortionate strategies readily emerge once subjects differ in their strategic power. Our experiment combines a repeated social dilemma with asymmetric partner choice. In our main treatment there is one randomly chosen group member who is unilaterally allowed to exchange one of the other group members after every ten rounds of the social dilemma. We find that this asymmetric replacement opportunity generally promotes cooperation, but often the resulting payoff distribution reflects the underlying power structure. Almost half of the subjects in a better strategic position turn into extortioners, who quickly proceed to exploit their peers. By adapting their cooperation probabilities consistent with ZD theory, extortioners force their co-players to cooperate without being similarly cooperative themselves. Comparison to non-extortionate players under the same conditions indicates a substantial net gain to extortion. Our results thus highlight how power asymmetries can endanger mutually beneficial interactions, and transform them into exploitative relationships. In particular, our results indicate that the extortionate strategies predicted from ZD theory could play a more prominent role in our daily interactions than previously thought."}],"has_accepted_license":"1","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)"},"citation":{"short":"C. Hilbe, K. Hagel, M. Milinski, PLoS One 11 (2016).","apa":"Hilbe, C., Hagel, K., & Milinski, M. (2016). Asymmetric power boosts extortion in an economic experiment. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163867","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Asymmetric power boosts extortion in an economic experiment,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016.","mla":"Hilbe, Christian, et al. “Asymmetric Power Boosts Extortion in an Economic Experiment.” PLoS One, vol. 11, no. 10, e0163867, Public Library of Science, 2016, doi:10.1371/journal.pone.0163867.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Asymmetric Power Boosts Extortion in an Economic Experiment.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.","ista":"Hilbe C, Hagel K, Milinski M. 2016. Asymmetric power boosts extortion in an economic experiment. PLoS One. 11(10), e0163867.","ama":"Hilbe C, Hagel K, Milinski M. Asymmetric power boosts extortion in an economic experiment. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0163867"},"publication_status":"published","pubrep_id":"716","status":"public","volume":11,"type":"journal_article","language":[{"iso":"eng"}],"intvolume":" 11","doi":"10.1371/journal.pone.0163867","acknowledgement":"CH was funded by the Schrödinger program of the Austrian Science Fund (FWF) J3475. ","publication":"PLoS One","author":[{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe"},{"full_name":"Hagel, Kristin","last_name":"Hagel","first_name":"Kristin"},{"full_name":"Milinski, Manfred","first_name":"Manfred","last_name":"Milinski"}],"file_date_updated":"2020-07-14T12:44:44Z","publist_id":"5948","date_updated":"2023-02-23T14:11:27Z","year":"2016","related_material":{"record":[{"status":"public","id":"9867","relation":"research_data"},{"status":"public","id":"9868","relation":"research_data"}]},"day":"04","_id":"1322","department":[{"_id":"KrCh"}],"article_number":"e0163867","month":"10","date_published":"2016-10-04T00:00:00Z"},{"month":"09","date_published":"2016-09-27T00:00:00Z","article_number":"e0163628","_id":"1270","department":[{"_id":"GaTk"}],"day":"27","related_material":{"record":[{"relation":"research_data","id":"9869","status":"public"},{"status":"public","id":"9870","relation":"research_data"},{"relation":"research_data","id":"9871","status":"public"}]},"year":"2016","date_updated":"2023-02-23T14:11:37Z","publist_id":"6050","author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"full_name":"Gerland, Ulrich","last_name":"Gerland","first_name":"Ulrich"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"file_date_updated":"2020-07-14T12:44:42Z","acknowledgement":"The authors would like to thank Thomas Sokolowski and Filipe Tostevin for helpful discussions. PH and UG were funded by the German Excellence Initiative via the program \"Nanosystems Initiative Munich\" (https://www.nano-initiative-munich.de) and the German Research Foundation via the SFB 1032 \"Nanoagents for Spatiotemporal Control of Molecular and Cellular Reactions\" (http://www.sfb1032.physik.uni-muenchen.de). GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at).","doi":"10.1371/journal.pone.0163628","publication":"PLoS One","intvolume":" 11","language":[{"iso":"eng"}],"status":"public","volume":11,"type":"journal_article","pubrep_id":"696","publication_status":"published","citation":{"ama":"Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 2016;11(9). doi:10.1371/journal.pone.0163628","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 11(9), e0163628.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.","mla":"Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9. Public Library of Science, 2016.","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628","short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016)."},"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)"},"has_accepted_license":"1","abstract":[{"lang":"eng","text":"A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic "French Flag" model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call "Counter" patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework."}],"file":[{"file_size":4950415,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:44:42Z","checksum":"3d0d55d373096a033bd9cf79288c8586","creator":"system","file_id":"4837","content_type":"application/pdf","file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF","date_created":"2018-12-12T10:10:47Z"}],"project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"scopus_import":1,"date_created":"2018-12-11T11:51:03Z","oa":1,"ddc":["571"],"publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","quality_controlled":"1","oa_version":"Published Version","issue":"9"},{"abstract":[{"text":"In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded as an aging mother with a decreased potential for future survival and division, the other as a rejuvenated daughter. Here, we aimed at investigating some of the processes involved in aging in the bacterium Escherichia coli, where the two types of cells can be distinguished by the age of their cell poles. We found that certain changes in the regulation of the carbohydrate metabolism can affect aging. A mutation in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative lifespan; csrA mutants stop dividing once their pole exceeds an age of about five divisions. These old-pole cells accumulate glycogen at their old cell poles; after their last division, they do not contain a chromosome, presumably because of spatial exclusion by the glycogen aggregates. The new-pole daughters produced by these aging mothers are born young; they only express the deleterious phenotype once their pole is old. These results demonstrate how manipulations of nutrient allocation can lead to the exclusion of the chromosome and limit replicative lifespan in E. coli, and illustrate how mutations can have phenotypic effects that are specific for cells with old poles. This raises the question how bacteria can avoid the accumulation of such mutations in their genomes over evolutionary times, and how they can achieve the long replicative lifespans that have recently been reported.","lang":"eng"}],"file":[{"file_name":"IST-2016-705-v1+1_journal.pgen.1005974.PDF","date_created":"2018-12-12T10:14:17Z","content_type":"application/pdf","file_id":"5067","checksum":"53d22b2b39e5adc243d34f18b2615a85","creator":"system","date_updated":"2020-07-14T12:44:41Z","relation":"main_file","access_level":"open_access","file_size":6273249}],"has_accepted_license":"1","scopus_import":1,"ddc":["576","579"],"oa":1,"date_created":"2018-12-11T11:50:56Z","issue":"4","oa_version":"Published Version","quality_controlled":"1","title":"Genetic manipulation of glycogen allocation affects replicative lifespan in E coli","publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"}],"_id":"1250","article_number":"e1005974","date_published":"2016-04-19T00:00:00Z","month":"04","date_updated":"2023-02-23T14:11:39Z","year":"2016","related_material":{"record":[{"id":"9873","relation":"research_data","status":"public"}]},"day":"19","language":[{"iso":"eng"}],"intvolume":" 12","publication":"PLoS Genetics","acknowledgement":"This manuscript is dedicated to the memory of Alex Böhm, who was a great friend and a passionate biologist. Alex passed away after the initial submission of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and Nela Nikolic for helpful discussions. This work was supported by the Swiss National Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).","doi":"10.1371/journal.pgen.1005974","file_date_updated":"2020-07-14T12:44:41Z","author":[{"full_name":"Boehm, Alex","last_name":"Boehm","first_name":"Alex"},{"first_name":"Markus","last_name":"Arnoldini","full_name":"Arnoldini, Markus"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"first_name":"Thomas","last_name":"Röösli","full_name":"Röösli, Thomas"},{"first_name":"Colette","last_name":"Bigosch","full_name":"Bigosch, Colette"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"publist_id":"6077","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)"},"citation":{"chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics. Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974.","mla":"Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics, vol. 12, no. 4, e1005974, Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974.","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 2016;12(4). doi:10.1371/journal.pgen.1005974","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 12(4), e1005974.","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann, M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, PLoS Genetics 12 (2016).","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Genetic manipulation of glycogen allocation affects replicative lifespan in E coli,” PLoS Genetics, vol. 12, no. 4. Public Library of Science, 2016."},"publication_status":"published","pubrep_id":"705","volume":12,"type":"journal_article","status":"public"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"Public Library of Science","type":"research_data_reference","title":"Computation of positional information in an Ising model","oa_version":"Published Version","citation":{"short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s002","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s002.","mla":"Hillenbrand, Patrick, et al. Computation of Positional Information in an Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, 10.1371/journal.pone.0163628.s002."},"date_created":"2021-08-10T09:23:45Z","author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"full_name":"Gerland, Ulrich","last_name":"Gerland","first_name":"Ulrich"},{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"doi":"10.1371/journal.pone.0163628.s002","day":"27","related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"year":"2016","date_updated":"2023-02-21T16:56:40Z","month":"09","date_published":"2016-09-27T00:00:00Z","abstract":[{"lang":"eng","text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined."}],"_id":"9870","department":[{"_id":"GaTk"}],"article_processing_charge":"No"},{"month":"04","_id":"9873","article_processing_charge":"No","department":[{"_id":"CaGu"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1250"}]},"day":"19","date_updated":"2023-02-21T16:50:13Z","year":"2016","author":[{"full_name":"Boehm, Alex","first_name":"Alex","last_name":"Boehm"},{"first_name":"Markus","last_name":"Arnoldini","full_name":"Arnoldini, Markus"},{"last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Röösli, Thomas","last_name":"Röösli","first_name":"Thomas"},{"full_name":"Bigosch, Colette","first_name":"Colette","last_name":"Bigosch"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"}],"date_created":"2021-08-10T09:42:34Z","doi":"10.1371/journal.pgen.1005974.s015","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","status":"public","title":"Quantification of the growth rate reduction as a consequence of age-specific mortality","type":"research_data_reference","citation":{"apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann, M. (2016). Quantification of the growth rate reduction as a consequence of age-specific mortality. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974.s015","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, (2016).","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Quantification of the growth rate reduction as a consequence of age-specific mortality.” Public Library of Science, 2016.","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974.s015.","mla":"Boehm, Alex, et al. Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality. Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974.s015.","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification of the growth rate reduction as a consequence of age-specific mortality. 2016. doi:10.1371/journal.pgen.1005974.s015","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Quantification of the growth rate reduction as a consequence of age-specific mortality, Public Library of Science, 10.1371/journal.pgen.1005974.s015."}},{"department":[{"_id":"GaTk"}],"article_processing_charge":"No","_id":"9869","abstract":[{"text":"A lower bound on the error of a positional estimator with limited positional information is derived.","lang":"eng"}],"date_published":"2016-09-27T00:00:00Z","month":"09","date_updated":"2023-02-21T16:56:40Z","year":"2016","related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"day":"27","doi":"10.1371/journal.pone.0163628.s001","author":[{"first_name":"Patrick","last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick"},{"first_name":"Ulrich","last_name":"Gerland","full_name":"Gerland, Ulrich"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"date_created":"2021-08-10T08:53:48Z","citation":{"apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s001","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.","mla":"Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s001.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, 10.1371/journal.pone.0163628.s001.","ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:10.1371/journal.pone.0163628.s001"},"oa_version":"Published Version","title":"Error bound on an estimator of position","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","status":"public"},{"month":"09","abstract":[{"text":"The positional information in a discrete morphogen field with Gaussian noise is computed.","lang":"eng"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"_id":"9871","day":"27","related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"year":"2016","date_updated":"2023-02-21T16:56:40Z","date_created":"2021-08-10T09:27:35Z","author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"first_name":"Ulrich","last_name":"Gerland","full_name":"Gerland, Ulrich"},{"last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"doi":"10.1371/journal.pone.0163628.s003","type":"research_data_reference","title":"Computation of positional information in a discrete morphogen field","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","oa_version":"Published Version","citation":{"ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s003","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, 10.1371/journal.pone.0163628.s003.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s003.","mla":"Hillenbrand, Patrick, et al. Computation of Positional Information in a Discrete Morphogen Field. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s003."}},{"citation":{"mla":"Hilbe, Christian, et al. Experimental Data. Public Library of Science, 2016, doi:10.1371/journal.pone.0163867.s009.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.s009.","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science, 10.1371/journal.pone.0163867.s009.","ama":"Hilbe C, Hagel K, Milinski M. Experimental data. 2016. doi:10.1371/journal.pone.0163867.s009","apa":"Hilbe, C., Hagel, K., & Milinski, M. (2016). Experimental data. Public Library of Science. https://doi.org/10.1371/journal.pone.0163867.s009","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of Science, 2016."},"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publisher":"Public Library of Science","title":"Experimental data","type":"research_data_reference","doi":"10.1371/journal.pone.0163867.s009","author":[{"last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"last_name":"Hagel","first_name":"Kristin","full_name":"Hagel, Kristin"},{"full_name":"Milinski, Manfred","last_name":"Milinski","first_name":"Manfred"}],"date_created":"2021-08-10T08:45:00Z","date_updated":"2023-02-21T16:59:01Z","year":"2016","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1322"}]},"day":"04","_id":"9868","article_processing_charge":"No","department":[{"_id":"KrCh"}],"abstract":[{"text":"The raw data file containing the experimental decisions of all our study subjects.","lang":"eng"}],"month":"10","date_published":"2016-10-04T00:00:00Z"},{"title":"Rangefinder: A semisynthetic FRET sensor design algorithm","type":"journal_article","volume":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Chemical Society","status":"public","publication_status":"published","quality_controlled":"1","oa_version":"None","issue":"11","citation":{"mla":"Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” ACS SENSORS, vol. 1, no. 11, American Chemical Society, 2016, pp. 1286–90, doi:10.1021/acssensors.6b00576.","chicago":"Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” ACS SENSORS. American Chemical Society, 2016. https://doi.org/10.1021/acssensors.6b00576.","ama":"Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 2016;1(11):1286-1290. doi:10.1021/acssensors.6b00576","ista":"Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 1(11), 1286–1290.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290.","apa":"Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. American Chemical Society. https://doi.org/10.1021/acssensors.6b00576","ieee":"J. Mitchell et al., “Rangefinder: A semisynthetic FRET sensor design algorithm,” ACS SENSORS, vol. 1, no. 11. American Chemical Society, pp. 1286–1290, 2016."},"date_created":"2018-12-11T11:50:09Z","publist_id":"6274","author":[{"first_name":"Joshua","last_name":"Mitchell","full_name":"Mitchell, Joshua"},{"full_name":"Whitfield, Jason","first_name":"Jason","last_name":"Whitfield"},{"full_name":"Zhang, William","first_name":"William","last_name":"Zhang"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak"},{"full_name":"O'Mara, Megan","first_name":"Megan","last_name":"O'Mara"},{"first_name":"Colin","last_name":"Jackson","full_name":"Jackson, Colin"}],"publication":"ACS SENSORS","doi":"10.1021/acssensors.6b00576","acknowledgement":"J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships. C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator Award and a Discovery Project and Future\r\nFellowship from the Australian Research Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153) and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure.","language":[{"iso":"eng"}],"intvolume":" 1","day":"10","scopus_import":"1","year":"2016","date_updated":"2023-03-30T11:32:33Z","date_published":"2016-11-10T00:00:00Z","month":"11","abstract":[{"text":"Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of >300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest.","lang":"eng"}],"page":"1286 - 1290","article_processing_charge":"No","department":[{"_id":"HaJa"}],"_id":"1101"}]