[{"department":[{"_id":"ToHe"}],"_id":"1421","language":[{"iso":"eng"}],"doi":"10.1145/2883817.2883837","ec_funded":1,"title":"Scalable static hybridization methods for analysis of nonlinear systems","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 &quot;dynamic&quot; 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."}],"publication_status":"published","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bak","first_name":"Stanley","full_name":"Bak, Stanley"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Taylor","last_name":"Johnson","full_name":"Johnson, Taylor"},{"last_name":"Prakash","first_name":"Pradyot","full_name":"Prakash, Pradyot"}],"quality_controlled":"1","citation":{"mla":"Bak, Stanley, et al. <i>Scalable Static Hybridization Methods for Analysis of Nonlinear Systems</i>. Springer, 2016, pp. 155–64, doi:<a href=\"https://doi.org/10.1145/2883817.2883837\">10.1145/2883817.2883837</a>.","apa":"Bak, S., Bogomolov, S., Henzinger, T. A., Johnson, T., &#38; 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. <a href=\"https://doi.org/10.1145/2883817.2883837\">https://doi.org/10.1145/2883817.2883837</a>","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.","short":"S. Bak, S. Bogomolov, T.A. Henzinger, T. Johnson, P. Prakash, in:, Springer, 2016, pp. 155–164.","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. <a href=\"https://doi.org/10.1145/2883817.2883837\">https://doi.org/10.1145/2883817.2883837</a>.","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.","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:<a href=\"https://doi.org/10.1145/2883817.2883837\">10.1145/2883817.2883837</a>"},"year":"2016","day":"11","oa_version":"None","type":"conference","date_updated":"2021-01-12T06:50:37Z","scopus_import":1,"publist_id":"5786","status":"public","conference":{"end_date":"2016-04-14","name":"HSCC 2016: International Conference on Hybrid Systems: Computation and Control","start_date":"2016-04-12","location":"Vienna, Austria"},"month":"04","date_created":"2018-12-11T11:51:55Z","page":"155 - 164","date_published":"2016-04-11T00:00:00Z","publisher":"Springer"},{"page":"913 - 923","file":[{"date_created":"2018-12-12T10:15:57Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":458968,"file_id":"5181","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","file_name":"IST-2016-591-v1+1_s11005-016-0847-5.pdf","checksum":"fb404923d8ca9a1faeb949561f26cbea"}],"date_published":"2016-07-01T00:00:00Z","scopus_import":1,"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","date_updated":"2021-01-12T06:50:38Z","type":"journal_article","has_accepted_license":"1","department":[{"_id":"RoSe"}],"doi":"10.1007/s11005-016-0847-5","language":[{"iso":"eng"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","pubrep_id":"591","issue":"7","volume":106,"publisher":"Springer","file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5785","intvolume":"       106","status":"public","month":"07","date_created":"2018-12-11T11:51:56Z","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer"}],"quality_controlled":"1","citation":{"ieee":"R. Frank, C. Hainzl, B. Schlein, and R. Seiringer, “Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations,” <i>Letters in Mathematical Physics</i>, vol. 106, no. 7. Springer, pp. 913–923, 2016.","ama":"Frank R, Hainzl C, Schlein B, Seiringer R. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. <i>Letters in Mathematical Physics</i>. 2016;106(7):913-923. doi:<a href=\"https://doi.org/10.1007/s11005-016-0847-5\">10.1007/s11005-016-0847-5</a>","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.","chicago":"Frank, Rupert, Christian Hainzl, Benjamin Schlein, and Robert Seiringer. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” <i>Letters in Mathematical Physics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11005-016-0847-5\">https://doi.org/10.1007/s11005-016-0847-5</a>.","short":"R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923.","mla":"Frank, Rupert, et al. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” <i>Letters in Mathematical Physics</i>, vol. 106, no. 7, Springer, 2016, pp. 913–23, doi:<a href=\"https://doi.org/10.1007/s11005-016-0847-5\">10.1007/s11005-016-0847-5</a>.","apa":"Frank, R., Hainzl, C., Schlein, B., &#38; Seiringer, R. (2016). Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. <i>Letters in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s11005-016-0847-5\">https://doi.org/10.1007/s11005-016-0847-5</a>"},"year":"2016","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"1422","ddc":["510","530"],"oa":1,"publication":"Letters in Mathematical Physics","title":"Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations","abstract":[{"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.","lang":"eng"}],"publication_status":"published","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}]},{"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"}],"publication_status":"published","title":"Comparing reactive and memory-one strategies of direct reciprocity","publication":"Scientific Reports","_id":"1423","ddc":["000"],"oa":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","citation":{"ama":"Baek S, Jeong H, Hilbe C, Nowak M. Comparing reactive and memory-one strategies of direct reciprocity. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep25676\">10.1038/srep25676</a>","ieee":"S. Baek, H. Jeong, C. Hilbe, and M. Nowak, “Comparing reactive and memory-one strategies of direct reciprocity,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","chicago":"Baek, Seung, Hyeongchai Jeong, Christian Hilbe, and Martin Nowak. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep25676\">https://doi.org/10.1038/srep25676</a>.","short":"S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).","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., &#38; Nowak, M. (2016). Comparing reactive and memory-one strategies of direct reciprocity. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep25676\">https://doi.org/10.1038/srep25676</a>","mla":"Baek, Seung, et al. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” <i>Scientific Reports</i>, vol. 6, 25676, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep25676\">10.1038/srep25676</a>."},"quality_controlled":"1","author":[{"full_name":"Baek, Seung","last_name":"Baek","first_name":"Seung"},{"full_name":"Jeong, Hyeongchai","first_name":"Hyeongchai","last_name":"Jeong"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"month":"05","date_created":"2018-12-11T11:51:56Z","status":"public","article_number":"25676","intvolume":"         6","publist_id":"5784","file_date_updated":"2020-07-14T12:44:53Z","publisher":"Nature Publishing Group","pubrep_id":"590","volume":6,"acknowledgement":"C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475.","has_accepted_license":"1","department":[{"_id":"KrCh"}],"doi":"10.1038/srep25676","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"journal_article","date_updated":"2021-01-12T06:50:38Z","day":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"file":[{"access_level":"open_access","checksum":"ee17c482370d2e1b3add393710d3c696","file_name":"IST-2016-590-v1+1_srep25676.pdf","date_updated":"2020-07-14T12:44:53Z","file_id":"5327","content_type":"application/pdf","creator":"system","file_size":1349915,"date_created":"2018-12-12T10:18:08Z","relation":"main_file"}],"date_published":"2016-05-10T00:00:00Z"},{"year":"2016","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Chakra, Maria","last_name":"Chakra","first_name":"Maria"},{"last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"first_name":"Arne","last_name":"Traulsen","full_name":"Traulsen, Arne"}],"quality_controlled":"1","citation":{"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.","short":"M. Chakra, C. Hilbe, A. Traulsen, Royal Society Open Science 3 (2016).","chicago":"Chakra, Maria, Christian Hilbe, and Arne Traulsen. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” <i>Royal Society Open Science</i>. Royal Society, The, 2016. <a href=\"https://doi.org/10.1098/rsos.160036\">https://doi.org/10.1098/rsos.160036</a>.","ama":"Chakra M, Hilbe C, Traulsen A. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. <i>Royal Society Open Science</i>. 2016;3(5). doi:<a href=\"https://doi.org/10.1098/rsos.160036\">10.1098/rsos.160036</a>","ieee":"M. Chakra, C. Hilbe, and A. Traulsen, “Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites,” <i>Royal Society Open Science</i>, vol. 3, no. 5. Royal Society, The, 2016.","mla":"Chakra, Maria, et al. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” <i>Royal Society Open Science</i>, vol. 3, no. 5, 160036, Royal Society, The, 2016, doi:<a href=\"https://doi.org/10.1098/rsos.160036\">10.1098/rsos.160036</a>.","apa":"Chakra, M., Hilbe, C., &#38; Traulsen, A. (2016). Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. <i>Royal Society Open Science</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rsos.160036\">https://doi.org/10.1098/rsos.160036</a>"},"publication_status":"published","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"}],"ddc":["000"],"oa":1,"_id":"1426","publication":"Royal Society Open Science","title":"Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites","publisher":"Royal Society, The","file_date_updated":"2020-07-14T12:44:53Z","volume":3,"issue":"5","pubrep_id":"589","article_number":"160036","status":"public","date_created":"2018-12-11T11:51:57Z","month":"05","publist_id":"5776","intvolume":"         3","day":"01","date_updated":"2021-01-12T06:50:39Z","type":"journal_article","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"C.H. gratefully acknowledges funding by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","doi":"10.1098/rsos.160036","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"has_accepted_license":"1","date_published":"2016-05-01T00:00:00Z","file":[{"access_level":"open_access","checksum":"bf84211b31fe87451e738ba301d729c3","file_name":"IST-2016-589-v1+1_160036.full.pdf","file_id":"5104","date_updated":"2020-07-14T12:44:53Z","file_size":937002,"content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:14:49Z","relation":"main_file"}],"scopus_import":1},{"oa":1,"ddc":["570","576"],"_id":"1427","publication":"Molecular Biology and Evolution","title":"Epistatic interactions in the arabinose cis-regulatory element","publication_status":"published","abstract":[{"lang":"eng","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."}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","author":[{"last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","last_name":"Igler"},{"full_name":"Moreno, Anaisa","last_name":"Moreno","first_name":"Anaisa"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"citation":{"apa":"Lagator, M., Igler, C., Moreno, A., Guet, C. C., &#38; Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv269\">https://doi.org/10.1093/molbev/msv269</a>","mla":"Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:<a href=\"https://doi.org/10.1093/molbev/msv269\">10.1093/molbev/msv269</a>.","ama":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. <i>Molecular Biology and Evolution</i>. 2016;33(3):761-769. doi:<a href=\"https://doi.org/10.1093/molbev/msv269\">10.1093/molbev/msv269</a>","ieee":"M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016.","chicago":"Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv269\">https://doi.org/10.1093/molbev/msv269</a>.","short":"M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769.","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."},"year":"2016","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"5772","intvolume":"        33","status":"public","date_created":"2018-12-11T11:51:57Z","month":"03","issue":"3","volume":33,"pubrep_id":"588","publisher":"Oxford University Press","file_date_updated":"2020-07-14T12:44:53Z","language":[{"iso":"eng"}],"doi":"10.1093/molbev/msv269","has_accepted_license":"1","department":[{"_id":"CaGu"},{"_id":"JoBo"}],"ec_funded":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","date_updated":"2021-01-12T06:50:39Z","type":"journal_article","oa_version":"Published Version","scopus_import":1,"page":"761 - 769","date_published":"2016-03-01T00:00:00Z","file":[{"date_created":"2018-12-12T10:09:27Z","relation":"main_file","file_size":648115,"creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","file_id":"4751","access_level":"open_access","checksum":"1f456ce1d2aa2f67176a1709f9702ecf","file_name":"IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf"}]},{"file_date_updated":"2020-07-14T12:44:53Z","publisher":"IOP Publishing Ltd.","pubrep_id":"585","volume":691,"issue":"1","month":"03","conference":{"name":"24th International Laser Physics Workshop (LPHYS'15)","end_date":"2015-08-25","location":"Shanghai, China","start_date":"2015-08-21"},"date_created":"2018-12-11T11:51:58Z","status":"public","article_number":"012016","intvolume":"       691","publist_id":"5770","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","citation":{"chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” In <i>Journal of Physics: Conference Series</i>, Vol. 691. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1742-6596/691/1/012016\">https://doi.org/10.1088/1742-6596/691/1/012016</a>.","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.","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential,” in <i>Journal of Physics: Conference Series</i>, Shanghai, China, 2016, vol. 691, no. 1.","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In: <i>Journal of Physics: Conference Series</i>. Vol 691. IOP Publishing Ltd.; 2016. doi:<a href=\"https://doi.org/10.1088/1742-6596/691/1/012016\">10.1088/1742-6596/691/1/012016</a>","apa":"Könenberg, M., Moser, T., Seiringer, R., &#38; Yngvason, J. (2016). Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In <i>Journal of Physics: Conference Series</i> (Vol. 691). Shanghai, China: IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-6596/691/1/012016\">https://doi.org/10.1088/1742-6596/691/1/012016</a>","mla":"Könenberg, Martin, et al. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” <i>Journal of Physics: Conference Series</i>, vol. 691, no. 1, 012016, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1742-6596/691/1/012016\">10.1088/1742-6596/691/1/012016</a>."},"author":[{"first_name":"Martin","last_name":"Könenberg","full_name":"Könenberg, Martin"},{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas","first_name":"Thomas","last_name":"Moser"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer"},{"last_name":"Yngvason","first_name":"Jakob","full_name":"Yngvason, Jakob"}],"quality_controlled":"1","project":[{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"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"}],"publication_status":"published","title":"Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential","publication":"Journal of Physics: Conference Series","_id":"1428","ddc":["510","530"],"oa":1,"file":[{"creator":"system","content_type":"application/pdf","file_size":1434688,"date_created":"2018-12-12T10:10:55Z","relation":"main_file","access_level":"open_access","checksum":"109db801749072c3f6c8f1a1848700fa","file_name":"IST-2016-585-v1+1_JPCS_691_1_012016.pdf","date_updated":"2020-07-14T12:44:53Z","file_id":"4847"}],"date_published":"2016-03-07T00:00:00Z","scopus_import":1,"oa_version":"Published Version","date_updated":"2021-01-12T06:50:40Z","type":"conference","day":"07","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1088/1742-6596/691/1/012016"},{"intvolume":"         7","publist_id":"5769","month":"04","date_created":"2018-12-11T11:51:58Z","article_number":"11332 (2016)","status":"public","pubrep_id":"583","volume":7,"file_date_updated":"2020-07-14T12:44:53Z","publisher":"Nature Publishing Group","publication":"Nature Communications","title":"Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides","_id":"1429","ddc":["530"],"oa":1,"abstract":[{"lang":"eng","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."}],"publication_status":"published","citation":{"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).","short":"C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B. Eggleton, L. Kuipers, Nature Communications 7 (2016).","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.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11332\">https://doi.org/10.1038/ncomms11332</a>.","ieee":"C. Husko <i>et al.</i>, “Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ama":"Husko C, Wulf M, Lefrançois S, et al. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11332\">10.1038/ncomms11332</a>","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. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11332\">https://doi.org/10.1038/ncomms11332</a>","mla":"Husko, Chad, et al. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” <i>Nature Communications</i>, vol. 7, 11332 (2016), Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11332\">10.1038/ncomms11332</a>."},"author":[{"full_name":"Husko, Chad","first_name":"Chad","last_name":"Husko"},{"last_name":"Wulf","first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378"},{"full_name":"Lefrançois, Simon","last_name":"Lefrançois","first_name":"Simon"},{"full_name":"Combrié, Sylvain","first_name":"Sylvain","last_name":"Combrié"},{"first_name":"Gaëlle","last_name":"Lehoucq","full_name":"Lehoucq, Gaëlle"},{"last_name":"De Rossi","first_name":"Alfredo","full_name":"De Rossi, Alfredo"},{"last_name":"Eggleton","first_name":"Benjamin","full_name":"Eggleton, Benjamin"},{"full_name":"Kuipers, Laurens","last_name":"Kuipers","first_name":"Laurens"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","scopus_import":1,"file":[{"access_level":"open_access","checksum":"6484fa81a2e52e4fdd7935e1ae6091d4","file_name":"IST-2016-583-v1+1_ncomms11332.pdf","date_updated":"2020-07-14T12:44:53Z","file_id":"5177","file_size":965176,"creator":"system","content_type":"application/pdf","date_created":"2018-12-12T10:15:53Z","relation":"main_file"}],"date_published":"2016-04-15T00:00:00Z","has_accepted_license":"1","department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"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.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","date_updated":"2021-01-12T06:50:40Z","day":"15"},{"publication_status":"published","abstract":[{"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.","lang":"eng"}],"title":"Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon","publication":"PeerJ","ddc":["570"],"oa":1,"_id":"1431","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","citation":{"apa":"Tartally, A., Kelager, A., Fürst, M., &#38; Nash, D. (2016). Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.1865\">https://doi.org/10.7717/peerj.1865</a>","mla":"Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” <i>PeerJ</i>, vol. 2016, no. 3, 1865, PeerJ, 2016, doi:<a href=\"https://doi.org/10.7717/peerj.1865\">10.7717/peerj.1865</a>.","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.” <i>PeerJ</i>. PeerJ, 2016. <a href=\"https://doi.org/10.7717/peerj.1865\">https://doi.org/10.7717/peerj.1865</a>.","short":"A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).","ama":"Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. <i>PeerJ</i>. 2016;2016(3). doi:<a href=\"https://doi.org/10.7717/peerj.1865\">10.7717/peerj.1865</a>","ieee":"A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon,” <i>PeerJ</i>, vol. 2016, no. 3. PeerJ, 2016."},"author":[{"full_name":"Tartally, András","first_name":"András","last_name":"Tartally"},{"full_name":"Kelager, Andreas","last_name":"Kelager","first_name":"Andreas"},{"last_name":"Fürst","first_name":"Matthias","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nash, David","first_name":"David","last_name":"Nash"}],"quality_controlled":"1","date_created":"2018-12-11T11:51:59Z","month":"01","article_number":"1865","status":"public","intvolume":"      2016","publist_id":"5767","file_date_updated":"2020-07-14T12:44:53Z","publisher":"PeerJ","volume":2016,"issue":"3","pubrep_id":"584","doi":"10.7717/peerj.1865","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"has_accepted_license":"1","date_updated":"2021-01-12T06:50:41Z","type":"journal_article","oa_version":"Published Version","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"date_published":"2016-01-01T00:00:00Z","file":[{"date_created":"2018-12-12T10:17:19Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1216360,"file_id":"5272","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","file_name":"IST-2016-584-v1+1_peerj-1865.pdf","checksum":"c27d898598a1e3d7f629607a309254e1"}]},{"ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1038/ncomms11552","department":[{"_id":"PeJo"}],"has_accepted_license":"1","acknowledgement":"We thank Jozsef Csicsvari and Nelson Spruston for critically reading the manuscript. We also thank A. Schlögl for programming, F. Marr for technical assistance and E. Kramberger for manuscript editing. ","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2023-09-07T11:55:25Z","oa_version":"Published Version","day":"13","scopus_import":1,"date_published":"2016-05-13T00:00:00Z","file":[{"file_id":"5355","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","file_name":"IST-2016-582-v1+1_ncomms11552.pdf","checksum":"7e84d0392348c874d473b62f1042de22","date_created":"2018-12-12T10:18:33Z","relation":"main_file","file_size":4510512,"content_type":"application/pdf","creator":"system"}],"title":"Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks","publication":"Nature Communications","oa":1,"ddc":["570"],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1396"}]},"_id":"1432","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548"}],"publication_status":"published","abstract":[{"text":"CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network.","lang":"eng"}],"citation":{"apa":"Mishra, R. K., Kim, S., Guzmán, J., &#38; Jonas, P. M. (2016). Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>","mla":"Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>, vol. 7, 11552, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>.","ista":"Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 7, 11552.","short":"R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).","chicago":"Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>.","ama":"Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>","ieee":"R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016."},"author":[{"last_name":"Mishra","first_name":"Rajiv Kumar","full_name":"Mishra, Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87"},{"id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun","first_name":"Sooyun","last_name":"Kim"},{"first_name":"José","last_name":"Guzmán","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","intvolume":"         7","publist_id":"5766","date_created":"2018-12-11T11:51:59Z","month":"05","article_number":"11552","status":"public","volume":7,"pubrep_id":"582","file_date_updated":"2020-07-14T12:44:53Z","publisher":"Nature Publishing Group"},{"publication":"Journal of Functional Analysis","title":"Local stability of the free additive convolution","_id":"1434","oa":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"abstract":[{"lang":"eng","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."}],"publication_status":"published","main_file_link":[{"url":"http://arxiv.org/abs/1508.05905","open_access":"1"}],"citation":{"apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2016). Local stability of the free additive convolution. <i>Journal of Functional Analysis</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">https://doi.org/10.1016/j.jfa.2016.04.006</a>","mla":"Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” <i>Journal of Functional Analysis</i>, vol. 271, no. 3, Academic Press, 2016, pp. 672–719, doi:<a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">10.1016/j.jfa.2016.04.006</a>.","ama":"Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution. <i>Journal of Functional Analysis</i>. 2016;271(3):672-719. doi:<a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">10.1016/j.jfa.2016.04.006</a>","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,” <i>Journal of Functional Analysis</i>, vol. 271, no. 3. Academic Press, pp. 672–719, 2016.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the Free Additive Convolution.” <i>Journal of Functional Analysis</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">https://doi.org/10.1016/j.jfa.2016.04.006</a>.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016) 672–719.","ista":"Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution. Journal of Functional Analysis. 271(3), 672–719."},"quality_controlled":"1","author":[{"first_name":"Zhigang","last_name":"Bao","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin","last_name":"Schnelli"}],"year":"2016","intvolume":"       271","publist_id":"5764","month":"08","date_created":"2018-12-11T11:52:00Z","status":"public","volume":271,"issue":"3","publisher":"Academic Press","ec_funded":1,"department":[{"_id":"LaEr"}],"doi":"10.1016/j.jfa.2016.04.006","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_updated":"2021-01-12T06:50:42Z","type":"journal_article","day":"01","scopus_import":1,"date_published":"2016-08-01T00:00:00Z","page":"672 - 719"},{"scopus_import":1,"date_published":"2016-01-01T00:00:00Z","file":[{"relation":"main_file","date_created":"2018-12-12T10:09:17Z","creator":"system","content_type":"application/pdf","file_size":1395180,"date_updated":"2020-07-14T12:44:54Z","file_id":"4740","checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da","file_name":"IST-2016-580-v1+1_1207393.pdf","access_level":"open_access"}],"doi":"10.1155/2016/1207393","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"has_accepted_license":"1","date_updated":"2021-01-12T06:50:43Z","type":"journal_article","oa_version":"Published Version","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:00Z","month":"01","article_number":"1207393","status":"public","intvolume":"      2016","publist_id":"5762","file_date_updated":"2020-07-14T12:44:54Z","publisher":"Hindawi Publishing Corporation","volume":2016,"pubrep_id":"580","publication_status":"published","abstract":[{"lang":"eng","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."}],"publication":"Neural Plasticity","title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction","ddc":["570"],"oa":1,"_id":"1435","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","citation":{"ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.","chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>. Hindawi Publishing Corporation, 2016. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>.","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,” <i>Neural Plasticity</i>, vol. 2016. Hindawi Publishing Corporation, 2016.","ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. 2016;2016. doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>","apa":"Guzmán, J., &#38; Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. Hindawi Publishing Corporation. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>","mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>."},"author":[{"full_name":"Guzmán, José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","last_name":"Guzmán"},{"last_name":"Gerevich","first_name":"Zoltan","full_name":"Gerevich, Zoltan"}],"quality_controlled":"1"},{"file":[{"file_size":658491,"creator":"system","content_type":"application/pdf","date_created":"2018-12-12T10:10:36Z","relation":"main_file","access_level":"open_access","file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf","checksum":"c5afe1f6935bc7f2b546adbde1d31a35","date_updated":"2020-07-14T12:44:54Z","file_id":"4825"}],"date_published":"2016-01-01T00:00:00Z","page":"1 - 30","scopus_import":1,"oa_version":"Published Version","type":"journal_article","date_updated":"2021-01-12T06:50:43Z","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"has_accepted_license":"1","department":[{"_id":"RoSe"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1016/j.matpur.2015.09.003","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:54Z","publisher":"Elsevier","pubrep_id":"581","volume":105,"issue":"1","month":"01","date_created":"2018-12-11T11:52:00Z","status":"public","intvolume":"       105","publist_id":"5763","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2016","citation":{"mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>.","apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., &#38; Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>","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,” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1. Elsevier, pp. 1–30, 2016.","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. <i>Journal de Mathématiques Pures et Appliquées</i>. 2016;105(1):1-30. doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>","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.","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.” <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>.","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30."},"quality_controlled":"1","author":[{"last_name":"Bach","first_name":"Volker","full_name":"Bach, Volker"},{"full_name":"Breteaux, Sébastien","last_name":"Breteaux","first_name":"Sébastien"},{"orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrat","first_name":"Sören P"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"},{"full_name":"Tzaneteas, Tim","first_name":"Tim","last_name":"Tzaneteas"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction","publication":"Journal de Mathématiques Pures et Appliquées","_id":"1436","ddc":["510","530"],"oa":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","oa_version":"Preprint","type":"conference","date_updated":"2024-03-25T23:30:18Z","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"doi":"10.1145/2837614.2837624","ec_funded":1,"page":"733 - 747","external_id":{"arxiv":["1510.07565"]},"date_published":"2016-01-11T00:00:00Z","scopus_import":1,"alternative_title":["POPL"],"arxiv":1,"quality_controlled":"1","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Goharshady","first_name":"Amir","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas"}],"main_file_link":[{"url":"http://arxiv.org/abs/1510.07565","open_access":"1"}],"citation":{"apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>","mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. Vol. 20–22, ACM, 2016, pp. 733–47, doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747."},"year":"2016","_id":"1437","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5441"},{"id":"5442","status":"public","relation":"earlier_version"},{"id":"821","relation":"dissertation_contains","status":"public"},{"id":"6009","relation":"later_version","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8934"}]},"oa":1,"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}],"publication_status":"published","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"volume":"20-22","publisher":"ACM","publist_id":"5761","status":"public","conference":{"start_date":"2016-01-20","location":"St. Petersburg, FL, USA","name":"POPL: Principles of Programming Languages","end_date":"2016-01-22"},"month":"01","date_created":"2018-12-11T11:52:01Z"},{"alternative_title":["POPL"],"scopus_import":1,"arxiv":1,"external_id":{"arxiv":["1510.08517"]},"date_published":"2016-01-11T00:00:00Z","page":"327 - 342","ec_funded":1,"department":[{"_id":"KrCh"}],"doi":"10.1145/2837614.2837639","language":[{"iso":"eng"}],"acknowledgement":"Supported by the Natural Science Foundation of China (NSFC) under Grant No. 61532019 ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_updated":"2023-09-19T14:38:41Z","type":"conference","day":"11","publist_id":"5760","conference":{"name":"POPL: Principles of Programming Languages","end_date":"2016-01-22","location":"St. Petersburg, FL, USA","start_date":"2016-01-20"},"month":"01","date_created":"2018-12-11T11:52:01Z","status":"public","volume":"20-22","publisher":"ACM","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","_id":"1438","oa":1,"related_material":{"record":[{"id":"5993","relation":"later_version","status":"public"}]},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"abstract":[{"text":"In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism.","lang":"eng"}],"publication_status":"published","citation":{"ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 327–342.","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. In: Vol 20-22. ACM; 2016:327-342. doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>.","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342.","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342.","mla":"Chatterjee, Krishnendu, et al. <i>Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs</i>. Vol. 20–22, ACM, 2016, pp. 327–42, doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>.","apa":"Chatterjee, K., Fu, H., Novotný, P., &#38; Hasheminezhad, R. (2016). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>"},"main_file_link":[{"url":"http://arxiv.org/abs/1510.08517","open_access":"1"}],"quality_controlled":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu"},{"first_name":"Petr","last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr"},{"first_name":"Rouzbeh","last_name":"Hasheminezhad","full_name":"Hasheminezhad, Rouzbeh"}],"year":"2016"},{"year":"2016","main_file_link":[{"url":"https://hal.inria.fr/hal-01251199/","open_access":"1"}],"citation":{"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.","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:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","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. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>.","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.","apa":"Dragoi, C., Henzinger, T. A., &#38; 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. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>","mla":"Dragoi, Cezara, et al. <i>PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms</i>. Vol. 20–22, ACM, 2016, pp. 400–15, doi:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>."},"author":[{"full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","last_name":"Dragoi"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","last_name":"Zufferey","first_name":"Damien"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"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."}],"publication_status":"published","title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","_id":"1439","oa":1,"publisher":"ACM","volume":"20-22","conference":{"start_date":"2016-01-20","location":"St. Petersburg, FL, USA","end_date":"2016-01-22","name":"POPL: Principles of Programming Languages"},"month":"01","date_created":"2018-12-11T11:52:01Z","status":"public","publist_id":"5759","oa_version":"Preprint","type":"conference","date_updated":"2021-01-12T06:50:45Z","day":"11","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","ec_funded":1,"department":[{"_id":"ToHe"}],"doi":"10.1145/2837614.2837650","language":[{"iso":"eng"}],"date_published":"2016-01-11T00:00:00Z","page":"400 - 415","alternative_title":["ACM SIGPLAN Notices"],"scopus_import":1},{"author":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"H.L. Janovjak, Structure 24 (2016) 213–215.","chicago":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” <i>Structure</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>.","ama":"Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. 2016;24(2):213-215. doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>","ieee":"H. L. Janovjak, “Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain,” <i>Structure</i>, 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.” <i>Structure</i>, vol. 24, no. 2, Cell Press, 2016, pp. 213–15, doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>.","apa":"Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>"},"day":"02","year":"2016","type":"journal_article","date_updated":"2021-01-12T06:50:46Z","oa_version":"None","doi":"10.1016/j.str.2016.01.002","language":[{"iso":"eng"}],"_id":"1440","department":[{"_id":"HaJa"}],"publication":"Structure","ec_funded":1,"title":"Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain","publication_status":"published","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).","project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"}],"issue":"2","volume":24,"page":"213 - 215","date_published":"2016-02-02T00:00:00Z","publisher":"Cell Press","publist_id":"5756","scopus_import":1,"intvolume":"        24","status":"public","date_created":"2018-12-11T11:52:02Z","month":"02"},{"quality_controlled":"1","author":[{"last_name":"Gschaider-Reichhart","first_name":"Eva","full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tichy","first_name":"Alexandra-Madelaine"},{"first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L"}],"citation":{"ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie - International Edition. 55(21), 6339–6342.","short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.","chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>.","ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016.","ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. 2016;55(21):6339-6342. doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>","apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &#38; Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>."},"year":"2016","_id":"1441","oa":1,"ddc":["571","576"],"related_material":{"record":[{"id":"418","status":"public","relation":"dissertation_contains"}]},"title":"A phytochrome sensory domain permits receptor activation by red light","publication":"Angewandte Chemie - International Edition","abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1."}],"publication_status":"published","project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"pubrep_id":"840","volume":55,"issue":"21","publisher":"Wiley","file_date_updated":"2020-07-14T12:44:55Z","publist_id":"5755","intvolume":"        55","status":"public","month":"05","date_created":"2018-12-11T11:52:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"17","oa_version":"Submitted Version","date_updated":"2023-09-07T12:49:08Z","type":"journal_article","has_accepted_license":"1","department":[{"_id":"HaJa"}],"doi":"10.1002/anie.201601736","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).","page":"6339 - 6342","file":[{"date_updated":"2020-07-14T12:44:55Z","file_id":"5255","checksum":"26da07960e57ac4750b54179197ce57f","file_name":"IST-2017-840-v1+1_reichhart.pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:03Z","creator":"system","content_type":"application/pdf","file_size":1268662}],"date_published":"2016-05-17T00:00:00Z","scopus_import":1},{"scopus_import":"1","page":"213 - 232","file":[{"relation":"main_file","date_created":"2018-12-12T10:10:56Z","content_type":"application/pdf","creator":"system","file_size":806035,"file_id":"4848","date_updated":"2020-07-14T12:44:55Z","checksum":"32d46268588b87d9b686492018e6a2b2","file_name":"IST-2016-530-v1+1_s11192-016-1842-4.pdf","access_level":"open_access"}],"date_published":"2016-04-01T00:00:00Z","has_accepted_license":"1","department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"doi":"10.1007/s11192-016-1842-4","day":"01","oa_version":"Published Version","type":"journal_article","date_updated":"2021-11-16T08:29:11Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","status":"public","month":"04","date_created":"2018-12-11T11:52:04Z","publist_id":"5750","intvolume":"       107","publisher":"Springer","file_date_updated":"2020-07-14T12:44:55Z","pubrep_id":"530","volume":107,"issue":"1","abstract":[{"lang":"eng","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."}],"publication_status":"published","_id":"1446","oa":1,"ddc":["000"],"related_material":{"link":[{"url":"https://doi.org/10.1007/s11192-016-1902-9","relation":"erratum"}]},"title":"On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data","publication":"Scientometrics","year":"2016","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","author":[{"last_name":"Calatrava Moreno","first_name":"Maria","full_name":"Calatrava Moreno, Maria"},{"first_name":"Thomas","last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Werthner, Hannes","first_name":"Hannes","last_name":"Werthner"}],"citation":{"ieee":"M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data,” <i>Scientometrics</i>, vol. 107, no. 1. Springer, pp. 213–232, 2016.","ama":"Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. <i>Scientometrics</i>. 2016;107(1):213-232. doi:<a href=\"https://doi.org/10.1007/s11192-016-1842-4\">10.1007/s11192-016-1842-4</a>","chicago":"Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” <i>Scientometrics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11192-016-1842-4\">https://doi.org/10.1007/s11192-016-1842-4</a>.","short":"M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016) 213–232.","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.","apa":"Calatrava Moreno, M., Auzinger, T., &#38; Werthner, H. (2016). On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. <i>Scientometrics</i>. Springer. <a href=\"https://doi.org/10.1007/s11192-016-1842-4\">https://doi.org/10.1007/s11192-016-1842-4</a>","mla":"Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” <i>Scientometrics</i>, vol. 107, no. 1, Springer, 2016, pp. 213–32, doi:<a href=\"https://doi.org/10.1007/s11192-016-1842-4\">10.1007/s11192-016-1842-4</a>."}},{"date_created":"2018-12-11T11:52:05Z","month":"06","status":"public","intvolume":"        26","publist_id":"5748","publisher":"Institute of Mathematical Statistics","issue":"3","volume":26,"publication_status":"published","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"}],"publication":"The Annals of Applied Probability","title":"Entropic Ricci curvature bounds for discrete interacting systems","oa":1,"_id":"1448","year":"2016","main_file_link":[{"url":"http://arxiv.org/abs/1501.00562","open_access":"1"}],"citation":{"short":"M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.","chicago":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/15-AAP1133\">https://doi.org/10.1214/15-AAP1133</a>.","ista":"Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 26(3), 1774–1806.","ama":"Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems. <i>The Annals of Applied Probability</i>. 2016;26(3):1774-1806. doi:<a href=\"https://doi.org/10.1214/15-AAP1133\">10.1214/15-AAP1133</a>","ieee":"M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting systems,” <i>The Annals of Applied Probability</i>, vol. 26, no. 3. Institute of Mathematical Statistics, pp. 1774–1806, 2016.","apa":"Fathi, M., &#38; Maas, J. (2016). Entropic Ricci curvature bounds for discrete interacting systems. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/15-AAP1133\">https://doi.org/10.1214/15-AAP1133</a>","mla":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” <i>The Annals of Applied Probability</i>, vol. 26, no. 3, Institute of Mathematical Statistics, 2016, pp. 1774–806, doi:<a href=\"https://doi.org/10.1214/15-AAP1133\">10.1214/15-AAP1133</a>."},"quality_controlled":"1","author":[{"last_name":"Fathi","first_name":"Max","full_name":"Fathi, Max"},{"first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"}],"scopus_import":1,"date_published":"2016-06-01T00:00:00Z","page":"1774 - 1806","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. ","language":[{"iso":"eng"}],"doi":"10.1214/15-AAP1133","department":[{"_id":"JaMa"}],"type":"journal_article","date_updated":"2021-01-12T06:50:49Z","oa_version":"Preprint","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"scopus_import":1,"file":[{"file_name":"IST-2016-529-v1+1_elife-10276-v1.pdf","checksum":"d1cc44870580756ba8badd8e41adfdb5","access_level":"open_access","date_updated":"2020-07-14T12:44:56Z","file_id":"4793","file_size":5198001,"content_type":"application/pdf","creator":"system","relation":"main_file","date_created":"2018-12-12T10:10:08Z"}],"date_published":"2016-02-25T00:00:00Z","has_accepted_license":"1","department":[{"_id":"DaSi"}],"language":[{"iso":"eng"}],"doi":"10.7554/eLife.10276","ec_funded":1,"day":"25","oa_version":"Published Version","date_updated":"2021-01-12T06:50:59Z","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"e10276","status":"public","month":"02","date_created":"2018-12-11T11:52:14Z","publist_id":"5721","intvolume":"         5","publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:44:56Z","pubrep_id":"529","issue":"February 2016","volume":5,"abstract":[{"lang":"eng","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."}],"publication_status":"published","project":[{"_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions"}],"_id":"1475","oa":1,"ddc":["570"],"title":"Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton","publication":"eLife","year":"2016","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Toshima, Junko","last_name":"Toshima","first_name":"Junko"},{"full_name":"Furuya, Eri","first_name":"Eri","last_name":"Furuya"},{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"last_name":"Kanno","first_name":"Chisa","full_name":"Kanno, Chisa"},{"full_name":"Sakamoto, Yuta","last_name":"Sakamoto","first_name":"Yuta"},{"full_name":"Ebihara, Masashi","last_name":"Ebihara","first_name":"Masashi"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"quality_controlled":"1","citation":{"ieee":"J. Toshima <i>et al.</i>, “Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton,” <i>eLife</i>, vol. 5, no. February 2016. eLife Sciences Publications, 2016.","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. <i>eLife</i>. 2016;5(February 2016). doi:<a href=\"https://doi.org/10.7554/eLife.10276\">10.7554/eLife.10276</a>","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.” <i>ELife</i>. eLife Sciences Publications, 2016. <a href=\"https://doi.org/10.7554/eLife.10276\">https://doi.org/10.7554/eLife.10276</a>.","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. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.10276\">https://doi.org/10.7554/eLife.10276</a>","mla":"Toshima, Junko, et al. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” <i>ELife</i>, vol. 5, no. February 2016, e10276, eLife Sciences Publications, 2016, doi:<a href=\"https://doi.org/10.7554/eLife.10276\">10.7554/eLife.10276</a>."}}]