[{"article_processing_charge":"No","title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes","related_material":{"record":[{"id":"323","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-25T23:30:09Z","_id":"1321","has_accepted_license":"1","year":"2016","project":[{"call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"acknowledgement":"This work was supported by the German Research Foundation (DFG) Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria for excellent technical support.","oa":1,"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"author":[{"last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"last_name":"Eichner","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","full_name":"Eichner, Alexander"},{"first_name":"Jan","full_name":"Müller, Jan","last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D"},{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","first_name":"Anne","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928"},{"last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus","first_name":"Markus"},{"full_name":"Schwarz, Jan","first_name":"Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Merrin, Jack","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"last_name":"De Gorter","first_name":"David","full_name":"De Gorter, David"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian","first_name":"Florian","orcid":"0000-0003-4790-8078"},{"first_name":"Jonathan","full_name":"Bayerl, Jonathan","last_name":"Bayerl"},{"full_name":"De Vries, Ingrid","first_name":"Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217","first_name":"Stefan","full_name":"Wieser, Stefan"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lai, Frank","first_name":"Frank","last_name":"Lai"},{"first_name":"Markus","full_name":"Moser, Markus","last_name":"Moser"},{"first_name":"Dontscho","full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"},{"last_name":"Small","full_name":"Small, Victor","first_name":"Victor"},{"last_name":"Stradal","first_name":"Theresia","full_name":"Stradal, Theresia"},{"first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"status":"public","oa_version":"Submitted Version","date_created":"2018-12-11T11:51:21Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":18,"doi":"10.1038/ncb3426","date_published":"2016-10-24T00:00:00Z","day":"24","ddc":["570"],"type":"journal_article","month":"10","intvolume":"        18","acknowledged_ssus":[{"_id":"SSU"}],"page":"1253 - 1259","ec_funded":1,"quality_controlled":"1","citation":{"short":"A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz, J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild, F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt, Nature Cell Biology 18 (2016) 1253–1259.","mla":"Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>.","ieee":"A. F. Leithner <i>et al.</i>, “Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes,” <i>Nature Cell Biology</i>, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016.","ista":"Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J, De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 18, 1253–1259.","apa":"Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz, J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>","chicago":"Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>.","ama":"Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. 2016;18:1253-1259. doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>"},"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"publist_id":"5949","abstract":[{"text":"Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:43Z","publication":"Nature Cell Biology","scopus_import":1,"file":[{"relation":"main_file","date_updated":"2020-07-14T12:44:43Z","file_name":"2018_NatureCell_Leithner.pdf","file_size":4433280,"date_created":"2020-05-14T16:33:46Z","access_level":"open_access","creator":"dernst","checksum":"e1411cb7c99a2d9089c178a6abef25e7","content_type":"application/pdf","file_id":"7844"}],"publisher":"Nature Publishing Group"},{"issue":"10","month":"10","pubrep_id":"716","intvolume":"        11","article_number":"e0163867","ddc":["004","006"],"type":"journal_article","file_date_updated":"2020-07-14T12:44:44Z","publication":"PLoS One","scopus_import":1,"file":[{"relation":"main_file","file_name":"IST-2016-716-v1+1_journal.pone.0163867.PDF","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:08:08Z","file_size":2077905,"creator":"system","access_level":"open_access","checksum":"6b33e394003dfe8b4ca6be1858aaa8e3","content_type":"application/pdf","file_id":"4668"}],"publisher":"Public Library of Science","language":[{"iso":"eng"}],"publist_id":"5948","department":[{"_id":"KrCh"}],"abstract":[{"text":"Direct reciprocity is a major mechanism for the evolution of cooperation. Several classical studies have suggested that humans should quickly learn to adopt reciprocal strategies to establish mutual cooperation in repeated interactions. On the other hand, the recently discovered theory of ZD strategies has found that subjects who use extortionate strategies are able to exploit and subdue cooperators. Although such extortioners have been predicted to succeed in any population of adaptive opponents, theoretical follow-up studies questioned whether extortion can evolve in reality. However, most of these studies presumed that individuals have similar strategic possibilities and comparable outside options, whereas asymmetries are ubiquitous in real world applications. Here we show with a model and an economic experiment that extortionate strategies readily emerge once subjects differ in their strategic power. Our experiment combines a repeated social dilemma with asymmetric partner choice. In our main treatment there is one randomly chosen group member who is unilaterally allowed to exchange one of the other group members after every ten rounds of the social dilemma. We find that this asymmetric replacement opportunity generally promotes cooperation, but often the resulting payoff distribution reflects the underlying power structure. Almost half of the subjects in a better strategic position turn into extortioners, who quickly proceed to exploit their peers. By adapting their cooperation probabilities consistent with ZD theory, extortioners force their co-players to cooperate without being similarly cooperative themselves. Comparison to non-extortionate players under the same conditions indicates a substantial net gain to extortion. Our results thus highlight how power asymmetries can endanger mutually beneficial interactions, and transform them into exploitative relationships. In particular, our results indicate that the extortionate strategies predicted from ZD theory could play a more prominent role in our daily interactions than previously thought.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","citation":{"ista":"Hilbe C, Hagel K, Milinski M. 2016. Asymmetric power boosts extortion in an economic experiment. PLoS One. 11(10), e0163867.","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Asymmetric power boosts extortion in an economic experiment,” <i>PLoS One</i>, vol. 11, no. 10. Public Library of Science, 2016.","short":"C. Hilbe, K. Hagel, M. Milinski, PLoS One 11 (2016).","mla":"Hilbe, Christian, et al. “Asymmetric Power Boosts Extortion in an Economic Experiment.” <i>PLoS One</i>, vol. 11, no. 10, e0163867, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867\">10.1371/journal.pone.0163867</a>.","ama":"Hilbe C, Hagel K, Milinski M. Asymmetric power boosts extortion in an economic experiment. <i>PLoS One</i>. 2016;11(10). doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867\">10.1371/journal.pone.0163867</a>","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Asymmetric power boosts extortion in an economic experiment. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867\">https://doi.org/10.1371/journal.pone.0163867</a>","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Asymmetric Power Boosts Extortion in an Economic Experiment.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867\">https://doi.org/10.1371/journal.pone.0163867</a>."},"oa":1,"has_accepted_license":"1","acknowledgement":"CH was funded by the Schrödinger program of the Austrian Science Fund (FWF) J3475. ","year":"2016","related_material":{"record":[{"id":"9867","status":"public","relation":"research_data"},{"id":"9868","status":"public","relation":"research_data"}]},"date_updated":"2023-02-23T14:11:27Z","_id":"1322","title":"Asymmetric power boosts extortion in an economic experiment","date_published":"2016-10-04T00:00:00Z","day":"04","date_created":"2018-12-11T11:51:22Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":11,"doi":"10.1371/journal.pone.0163867","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hagel","full_name":"Hagel, Kristin","first_name":"Kristin"},{"last_name":"Milinski","full_name":"Milinski, Manfred","first_name":"Manfred"}],"oa_version":"Published Version"},{"file":[{"relation":"main_file","date_created":"2018-12-12T10:17:05Z","file_size":1477891,"date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-715-v1+1_e17977-download.pdf","content_type":"application/pdf","checksum":"a7201280c571bed88ebd459ce5ce6a47","access_level":"open_access","creator":"system","file_id":"5257"}],"publication":"eLife","scopus_import":1,"file_date_updated":"2020-07-14T12:44:44Z","publisher":"eLife Sciences Publications","department":[{"_id":"PeJo"}],"publist_id":"5947","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Mossy fiber synapses on CA3 pyramidal cells are 'conditional detonators' that reliably discharge postsynaptic targets. The 'conditional' nature implies that burst activity in dentate gyrus granule cells is required for detonation. Whether single unitary excitatory postsynaptic potentials (EPSPs) trigger spikes in CA3 neurons remains unknown. Mossy fiber synapses exhibit both pronounced short-term facilitation and uniquely large post-tetanic potentiation (PTP). We tested whether PTP could convert mossy fiber synapses from subdetonator into detonator mode, using a recently developed method to selectively and noninvasively stimulate individual presynaptic terminals in rat brain slices. Unitary EPSPs failed to initiate a spike in CA3 neurons under control conditions, but reliably discharged them after induction of presynaptic short-term plasticity. Remarkably, PTP switched mossy fiber synapses into full detonators for tens of seconds. Plasticity-dependent detonation may be critical for efficient coding, storage, and recall of information in the granule cell–CA3 cell network."}],"publication_status":"published","quality_controlled":"1","citation":{"short":"N. Vyleta, C. Borges Merjane, P.M. Jonas, ELife 5 (2016).","mla":"Vyleta, Nicholas, et al. “Plasticity-Dependent, Full Detonation at Hippocampal Mossy Fiber–CA3 Pyramidal Neuron Synapses.” <i>ELife</i>, vol. 5, e17977, eLife Sciences Publications, 2016, doi:<a href=\"https://doi.org/10.7554/eLife.17977\">10.7554/eLife.17977</a>.","ista":"Vyleta N, Borges Merjane C, Jonas PM. 2016. Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. eLife. 5, e17977.","ieee":"N. Vyleta, C. Borges Merjane, and P. M. Jonas, “Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses,” <i>eLife</i>, vol. 5. eLife Sciences Publications, 2016.","chicago":"Vyleta, Nicholas, Carolina Borges Merjane, and Peter M Jonas. “Plasticity-Dependent, Full Detonation at Hippocampal Mossy Fiber–CA3 Pyramidal Neuron Synapses.” <i>ELife</i>. eLife Sciences Publications, 2016. <a href=\"https://doi.org/10.7554/eLife.17977\">https://doi.org/10.7554/eLife.17977</a>.","apa":"Vyleta, N., Borges Merjane, C., &#38; Jonas, P. M. (2016). Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.17977\">https://doi.org/10.7554/eLife.17977</a>","ama":"Vyleta N, Borges Merjane C, Jonas PM. Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. <i>eLife</i>. 2016;5. doi:<a href=\"https://doi.org/10.7554/eLife.17977\">10.7554/eLife.17977</a>"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"ec_funded":1,"month":"10","intvolume":"         5","pubrep_id":"715","article_number":"e17977","ddc":["571","572"],"type":"journal_article","date_published":"2016-10-25T00:00:00Z","day":"25","date_created":"2018-12-11T11:51:22Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":5,"doi":"10.7554/eLife.17977","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Vyleta, Nicholas","first_name":"Nicholas","last_name":"Vyleta","id":"36C4978E-F248-11E8-B48F-1D18A9856A87"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M"}],"status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","project":[{"grant_number":"268548","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","grant_number":"692692"}],"year":"2016","date_updated":"2023-02-21T10:34:24Z","_id":"1323","title":"Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses"},{"publisher":"AAAI Press","day":"01","date_published":"2016-01-01T00:00:00Z","publication":"Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling","scopus_import":1,"abstract":[{"text":"DEC-POMDPs extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. DEC-POMDPs have been studied with finite-horizon and infinite-horizon discounted-sum objectives, and there exist solvers both for exact and approximate solutions. In this work we consider Goal-DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the RTDP-Bel approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. Copyright ","lang":"eng"}],"department":[{"_id":"KrCh"}],"publist_id":"5946","language":[{"iso":"eng"}],"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:22Z","volume":"2016-January","oa_version":"None","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"}],"quality_controlled":"1","status":"public","citation":{"short":"K. Chatterjee, M. Chmelik, in:, Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, AAAI Press, 2016, pp. 88–96.","mla":"Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability in Goal-DEC-POMDPs.” <i>Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling</i>, vol. 2016–January, AAAI Press, 2016, pp. 88–96.","ieee":"K. Chatterjee and M. Chmelik, “Indefinite-horizon reachability in Goal-DEC-POMDPs,” in <i>Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling</i>, London, United Kingdom, 2016, vol. 2016–January, pp. 88–96.","ista":"Chatterjee K, Chmelik M. 2016. Indefinite-horizon reachability in Goal-DEC-POMDPs. Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 2016–January, 88–96.","chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability in Goal-DEC-POMDPs.” In <i>Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling</i>, 2016–January:88–96. AAAI Press, 2016.","apa":"Chatterjee, K., &#38; Chmelik, M. (2016). Indefinite-horizon reachability in Goal-DEC-POMDPs. In <i>Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling</i> (Vol. 2016–January, pp. 88–96). London, United Kingdom: AAAI Press.","ama":"Chatterjee K, Chmelik M. Indefinite-horizon reachability in Goal-DEC-POMDPs. In: <i>Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling</i>. Vol 2016-January. AAAI Press; 2016:88-96."},"page":"88 - 96","ec_funded":1,"year":"2016","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"month":"01","date_updated":"2021-01-12T06:49:53Z","_id":"1324","type":"conference","conference":{"start_date":"2016-06-12","end_date":"2016-06-17","name":"ICAPS: International Conference on Automated Planning and Scheduling","location":"London, United Kingdom"},"main_file_link":[{"url":"http://www.aaai.org/ocs/index.php/ICAPS/ICAPS16/paper/view/12999"}],"title":"Indefinite-horizon reachability in Goal-DEC-POMDPs"},{"oa":1,"has_accepted_license":"1","year":"2016","acknowledgement":"The work has been supported by the Czech Science Foundation, grant No. 15-17564S, by EPSRC grant\r\nEP/M023656/1, and by the People Programme (Marie Curie Actions) of the European Union’s Seventh\r\nFramework Programme (FP7/2007-2013) under REA grant agreement no [291734]","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"conference":{"location":"Quebec City, Canada","name":"CONCUR: Concurrency Theory","start_date":"2016-08-23","end_date":"2016-08-26"},"date_updated":"2021-01-12T06:49:53Z","_id":"1325","title":"Stability in graphs and games","date_published":"2016-08-01T00:00:00Z","day":"01","date_created":"2018-12-11T11:51:23Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":59,"doi":"10.4230/LIPIcs.CONCUR.2016.10","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"last_name":"Forejt","full_name":"Forejt, Vojtěch","first_name":"Vojtěch"},{"full_name":"Kučera, Antonín","first_name":"Antonín","last_name":"Kučera"},{"last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Novotny, Petr"}],"status":"public","oa_version":"Published Version","ec_funded":1,"month":"08","pubrep_id":"665","intvolume":"        59","article_number":"10","ddc":["004"],"type":"conference","file":[{"access_level":"open_access","creator":"system","content_type":"application/pdf","checksum":"3c2dc6ab0358f8aa8f7aa7d6c1293159","file_id":"5229","relation":"main_file","date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-665-v1+1_Forejt_et_al__Stability_in_graphs_and_games.pdf","date_created":"2018-12-12T10:16:40Z","file_size":553648}],"file_date_updated":"2020-07-14T12:44:44Z","scopus_import":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publist_id":"5944","abstract":[{"lang":"eng","text":"We study graphs and two-player games in which rewards are assigned to states, and the goal of the players is to satisfy or dissatisfy certain property of the generated outcome, given as a mean payoff property. Since the notion of mean-payoff does not reflect possible fluctuations from the mean-payoff along a run, we propose definitions and algorithms for capturing the stability of the system, and give algorithms for deciding if a given mean payoff and stability objective can be ensured in the system."}],"publication_status":"published","alternative_title":["LIPIcs"],"quality_controlled":"1","citation":{"ista":"Brázdil T, Forejt V, Kučera A, Novotný P. 2016. Stability in graphs and games. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 10.","ieee":"T. Brázdil, V. Forejt, A. Kučera, and P. Novotný, “Stability in graphs and games,” presented at the CONCUR: Concurrency Theory, Quebec City, Canada, 2016, vol. 59.","short":"T. Brázdil, V. Forejt, A. Kučera, P. Novotný, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Brázdil, Tomáš, et al. <i>Stability in Graphs and Games</i>. Vol. 59, 10, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.10\">10.4230/LIPIcs.CONCUR.2016.10</a>.","ama":"Brázdil T, Forejt V, Kučera A, Novotný P. Stability in graphs and games. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.10\">10.4230/LIPIcs.CONCUR.2016.10</a>","apa":"Brázdil, T., Forejt, V., Kučera, A., &#38; Novotný, P. (2016). Stability in graphs and games (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.10\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.10</a>","chicago":"Brázdil, Tomáš, Vojtěch Forejt, Antonín Kučera, and Petr Novotný. “Stability in Graphs and Games,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.10\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.10</a>."}},{"alternative_title":["LNCS"],"quality_controlled":"1","citation":{"ieee":"T. Brázdil, A. Kučera, and P. Novotný, “Optimizing the expected mean payoff in Energy Markov Decision Processes,” presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan, 2016, vol. 9938, pp. 32–49.","ista":"Brázdil T, Kučera A, Novotný P. 2016. Optimizing the expected mean payoff in Energy Markov Decision Processes. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 9938, 32–49.","short":"T. Brázdil, A. Kučera, P. Novotný, in:, Springer, 2016, pp. 32–49.","mla":"Brázdil, Tomáš, et al. <i>Optimizing the Expected Mean Payoff in Energy Markov Decision Processes</i>. Vol. 9938, Springer, 2016, pp. 32–49, doi:<a href=\"https://doi.org/10.1007/978-3-319-46520-3_3\">10.1007/978-3-319-46520-3_3</a>.","ama":"Brázdil T, Kučera A, Novotný P. Optimizing the expected mean payoff in Energy Markov Decision Processes. In: Vol 9938. Springer; 2016:32-49. doi:<a href=\"https://doi.org/10.1007/978-3-319-46520-3_3\">10.1007/978-3-319-46520-3_3</a>","apa":"Brázdil, T., Kučera, A., &#38; Novotný, P. (2016). Optimizing the expected mean payoff in Energy Markov Decision Processes (Vol. 9938, pp. 32–49). Presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan: Springer. <a href=\"https://doi.org/10.1007/978-3-319-46520-3_3\">https://doi.org/10.1007/978-3-319-46520-3_3</a>","chicago":"Brázdil, Tomáš, Antonín Kučera, and Petr Novotný. “Optimizing the Expected Mean Payoff in Energy Markov Decision Processes,” 9938:32–49. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-46520-3_3\">https://doi.org/10.1007/978-3-319-46520-3_3</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"Energy Markov Decision Processes (EMDPs) are finite-state Markov decision processes where each transition is assigned an integer counter update and a rational payoff. An EMDP configuration is a pair s(n), where s is a control state and n is the current counter value. The configurations are changed by performing transitions in the standard way. We consider the problem of computing a safe strategy (i.e., a strategy that keeps the counter non-negative) which maximizes the expected mean payoff. "}],"publist_id":"5943","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00678"}],"type":"conference","intvolume":"      9938","month":"09","page":"32 - 49","ec_funded":1,"oa_version":"Preprint","author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"},{"full_name":"Novotny, Petr","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny"}],"status":"public","doi":"10.1007/978-3-319-46520-3_3","date_created":"2018-12-11T11:51:23Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":9938,"day":"22","date_published":"2016-09-22T00:00:00Z","title":"Optimizing the expected mean payoff in Energy Markov Decision Processes","date_updated":"2021-01-12T06:49:53Z","_id":"1326","conference":{"end_date":"2016-10-20","start_date":"2016-10-17","name":"ATVA: Automated Technology for Verification and Analysis","location":"Chiba, Japan"},"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"year":"2016","acknowledgement":"The research was funded by the Czech Science Foundation Grant No. P202/12/G061 and by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].","oa":1},{"publication":"Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems","scopus_import":1,"date_published":"2016-01-01T00:00:00Z","day":"01","publisher":"ACM","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publist_id":"5942","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize the expected total cost until the target set is reached. We extend the traditional framework of POMDPs to model energy consumption, which represents a hard constraint. The energy levels may increase and decrease with transitions, and the hard constraint requires that the energy level must remain positive in all steps till the target is reached. First, we present a novel algorithm for solving POMDPs with energy levels, developing on existing POMDP solvers and using RTDP as its main method. Our second contribution is related to policy representation. For larger POMDP instances the policies computed by existing solvers are too large to be understandable. We present an automated procedure based on machine learning techniques that automatically extracts important decisions of the policy allowing us to compute succinct human readable policies. Finally, we show experimentally that our algorithm performs well and computes succinct policies on a number of POMDP instances from the literature that were naturally enhanced with energy levels. "}],"publication_status":"published","date_created":"2018-12-11T11:51:23Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, P. Novotný, in:, Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–1466.","mla":"Brázdil, Tomáš, et al. “Stochastic Shortest Path with Energy Constraints in POMDPs.” <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i>, ACM, 2016, pp. 1465–66.","ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, and P. Novotný, “Stochastic shortest path with energy constraints in POMDPs,” in <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i>, Singapore, 2016, pp. 1465–1466.","ista":"Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. 2016. Stochastic shortest path with energy constraints in POMDPs. Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. AAMAS: Autonomous Agents &#38; Multiagent Systems, 1465–1466.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Anchit Gupta, and Petr Novotný. “Stochastic Shortest Path with Energy Constraints in POMDPs.” In <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i>, 1465–66. ACM, 2016.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Gupta, A., &#38; Novotný, P. (2016). Stochastic shortest path with energy constraints in POMDPs. In <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i> (pp. 1465–1466). Singapore: ACM.","ama":"Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. Stochastic shortest path with energy constraints in POMDPs. In: <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i>. ACM; 2016:1465-1466."},"quality_controlled":"1","status":"public","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin"},{"last_name":"Gupta","first_name":"Anchit","full_name":"Gupta, Anchit"},{"last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr","first_name":"Petr"}],"oa_version":"Preprint","ec_funded":1,"oa":1,"page":"1465 - 1466","month":"01","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"}],"year":"2016","conference":{"start_date":"2016-05-09","end_date":"2016-05-13","location":"Singapore","name":"AAMAS: Autonomous Agents & Multiagent Systems"},"type":"conference","_id":"1327","date_updated":"2021-01-12T06:49:54Z","title":"Stochastic shortest path with energy constraints in POMDPs","main_file_link":[{"url":"https://arxiv.org/abs/1602.07565","open_access":"1"}]},{"oa":1,"has_accepted_license":"1","year":"2016","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7","grant_number":"335497"}],"acknowledgement":"The work was supported by the EC FP7 ICT project SiSPIN no. 323841, the EC FP7 ICT project PAMS no. 610446, the ERC Starting Grant no. 335497, the FWF-I-1190-N20 project, and the Swiss NSF. We acknowledge F. Schäffler for fruitful discussions related to the hut wire growth and for giving us access to the molecular beam epitaxy system, M. Schatzl for her support in electron beam lithography, and V. Jadris ̌ko for helping us with the COMSOL simulations. Finally, we thank G. Bauer for his continuous support. ","related_material":{"record":[{"status":"for_moderation","id":"7977","relation":"popular_science"},{"id":"7996","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-09-07T13:15:02Z","_id":"1328","title":"Heavy-hole states in germanium hut wires","date_published":"2016-09-22T00:00:00Z","day":"22","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:24Z","volume":16,"doi":"10.1021/acs.nanolett.6b02715","author":[{"last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes","first_name":"Hannes"},{"full_name":"Kloeffel, Christoph","first_name":"Christoph","last_name":"Kloeffel"},{"last_name":"Vukusic","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","full_name":"Vukusic, Lada","first_name":"Lada"},{"first_name":"Marta","full_name":"Rossell, Marta","last_name":"Rossell"},{"full_name":"Sessi, Violetta","first_name":"Violetta","last_name":"Sessi"},{"first_name":"Josip","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka"},{"last_name":"Kirchschlager","full_name":"Kirchschlager, Raimund","first_name":"Raimund"},{"first_name":"Elisabeth","full_name":"Lausecker, Elisabeth","id":"33662F76-F248-11E8-B48F-1D18A9856A87","last_name":"Lausecker"},{"id":"49CBC780-F248-11E8-B48F-1D18A9856A87","last_name":"Truhlar","full_name":"Truhlar, Alisha","first_name":"Alisha"},{"last_name":"Glaser","first_name":"Martin","full_name":"Glaser, Martin"},{"first_name":"Armando","full_name":"Rastelli, Armando","last_name":"Rastelli"},{"last_name":"Fuhrer","first_name":"Andreas","full_name":"Fuhrer, Andreas"},{"first_name":"Daniel","full_name":"Loss, Daniel","last_name":"Loss"},{"first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","issue":"11","page":"6879 - 6885","ec_funded":1,"month":"09","pubrep_id":"664","intvolume":"        16","ddc":["539"],"type":"journal_article","scopus_import":1,"publication":"Nano Letters","file":[{"file_id":"5053","creator":"system","access_level":"open_access","checksum":"b63feece90d7b620ece49ca632e34ff3","content_type":"application/pdf","file_name":"IST-2016-664-v1+1_acs.nanolett.6b02715.pdf","date_updated":"2020-07-14T12:44:44Z","file_size":535121,"date_created":"2018-12-12T10:14:04Z","relation":"main_file"}],"file_date_updated":"2020-07-14T12:44:44Z","publisher":"American Chemical Society","publist_id":"5941","department":[{"_id":"GeKa"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Hole spins have gained considerable interest in the past few years due to their potential for fast electrically controlled qubits. Here, we study holes confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature magnetotransport measurements reveal a large anisotropy between the in-plane and out-of-plane g-factors of up to 18. Numerical simulations verify that this large anisotropy originates from a confined wave function of heavy-hole character. A light-hole admixture of less than 1% is estimated for the states of lowest energy, leading to a surprisingly large reduction of the out-of-plane g-factors compared with those for pure heavy holes. Given this tiny light-hole contribution, the spin lifetimes are expected to be very long, even in isotopically nonpurified samples.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","citation":{"mla":"Watzinger, Hannes, et al. “Heavy-Hole States in Germanium Hut Wires.” <i>Nano Letters</i>, vol. 16, no. 11, American Chemical Society, 2016, pp. 6879–85, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">10.1021/acs.nanolett.6b02715</a>.","short":"H. Watzinger, C. Kloeffel, L. Vukušić, M. Rossell, V. Sessi, J. Kukucka, R. Kirchschlager, E. Lausecker, A. Truhlar, M. Glaser, A. Rastelli, A. Fuhrer, D. Loss, G. Katsaros, Nano Letters 16 (2016) 6879–6885.","ieee":"H. Watzinger <i>et al.</i>, “Heavy-hole states in germanium hut wires,” <i>Nano Letters</i>, vol. 16, no. 11. American Chemical Society, pp. 6879–6885, 2016.","ista":"Watzinger H, Kloeffel C, Vukušić L, Rossell M, Sessi V, Kukucka J, Kirchschlager R, Lausecker E, Truhlar A, Glaser M, Rastelli A, Fuhrer A, Loss D, Katsaros G. 2016. Heavy-hole states in germanium hut wires. Nano Letters. 16(11), 6879–6885.","apa":"Watzinger, H., Kloeffel, C., Vukušić, L., Rossell, M., Sessi, V., Kukucka, J., … Katsaros, G. (2016). Heavy-hole states in germanium hut wires. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">https://doi.org/10.1021/acs.nanolett.6b02715</a>","chicago":"Watzinger, Hannes, Christoph Kloeffel, Lada Vukušić, Marta Rossell, Violetta Sessi, Josip Kukucka, Raimund Kirchschlager, et al. “Heavy-Hole States in Germanium Hut Wires.” <i>Nano Letters</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">https://doi.org/10.1021/acs.nanolett.6b02715</a>.","ama":"Watzinger H, Kloeffel C, Vukušić L, et al. Heavy-hole states in germanium hut wires. <i>Nano Letters</i>. 2016;16(11):6879-6885. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">10.1021/acs.nanolett.6b02715</a>"}},{"day":"01","date_published":"2016-10-01T00:00:00Z","doi":"10.1093/gbe/evw221","volume":8,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:24Z","oa_version":"Published Version","status":"public","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961"},{"first_name":"Alberto","full_name":"López Ezquerra, Alberto","last_name":"López Ezquerra"},{"last_name":"Parsch","first_name":"John","full_name":"Parsch, John"},{"last_name":"Cordellier","full_name":"Cordellier, Mathilde","first_name":"Mathilde"}],"oa":1,"year":"2016","acknowledgement":"This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). The authors would like to thank I. Schrank, L. Theodosiou, M. Kredler, C. Laforsch, J. Wolinska, J. Griebel, R. Jaenichen, and K. Otte for providing the necessary resources and help for maintaining Daphnia cultures in the laboratory. H. Lainer supported us for the molecular laboratory work. D. Gilbert and J. K. Colbourne contributed ideas for the bioinformatics analysis, and L. Hardulak did the orthology mapping including more insect species. This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). This work benefits from and contributes to the Daphnia Genomics Consortium.","has_accepted_license":"1","_id":"1329","date_updated":"2021-01-12T06:49:55Z","title":"De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata","publisher":"Oxford University Press","publication":"Genome Biology and Evolution","file":[{"file_id":"4924","checksum":"25c7adcb452d39d3b6343ff4b57a652d","content_type":"application/pdf","creator":"system","access_level":"open_access","date_created":"2018-12-12T10:12:06Z","file_size":1406265,"file_name":"IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf","date_updated":"2020-07-14T12:44:44Z","relation":"main_file"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:44Z","abstract":[{"lang":"eng","text":"Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species."}],"language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"publist_id":"5940","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","citation":{"apa":"Huylmans, A. K., López Ezquerra, A., Parsch, J., &#38; Cordellier, M. (2016). De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evw221\">https://doi.org/10.1093/gbe/evw221</a>","chicago":"Huylmans, Ann K, Alberto López Ezquerra, John Parsch, and Mathilde Cordellier. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/gbe/evw221\">https://doi.org/10.1093/gbe/evw221</a>.","ama":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. <i>Genome Biology and Evolution</i>. 2016;8(10):3120-3139. doi:<a href=\"https://doi.org/10.1093/gbe/evw221\">10.1093/gbe/evw221</a>","mla":"Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” <i>Genome Biology and Evolution</i>, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39, doi:<a href=\"https://doi.org/10.1093/gbe/evw221\">10.1093/gbe/evw221</a>.","short":"A.K. Huylmans, A. López Ezquerra, J. Parsch, M. Cordellier, Genome Biology and Evolution 8 (2016) 3120–3139.","ista":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. 2016. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 8(10), 3120–3139.","ieee":"A. K. Huylmans, A. López Ezquerra, J. Parsch, and M. Cordellier, “De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata,” <i>Genome Biology and Evolution</i>, vol. 8, no. 10. Oxford University Press, pp. 3120–3139, 2016."},"quality_controlled":"1","page":"3120 - 3139","issue":"10","pubrep_id":"663","intvolume":"         8","month":"10","type":"journal_article","ddc":["576"]},{"oa_version":"Preprint","author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan"},{"last_name":"Balitskiy","first_name":"Alexey","full_name":"Balitskiy, Alexey"}],"status":"public","doi":"10.1007/s11856-016-1429-z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:24Z","volume":216,"day":"15","date_published":"2016-10-15T00:00:00Z","title":"Billiards in convex bodies with acute angles","date_updated":"2021-01-12T06:49:56Z","_id":"1330","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"acknowledgement":"Supported by People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n°[291734]. Supported by the Russian Foundation for Basic Research grant 15-31-20403 (mol a ved), by the Russian Foundation for Basic Research grant 15-01-99563 A, in part by the Moebius Contest Foundation for Young Scientists, and in part by the Simons Foundation.","year":"2016","oa":1,"quality_controlled":"1","citation":{"apa":"Akopyan, A., &#38; Balitskiy, A. (2016). Billiards in convex bodies with acute angles. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-016-1429-z\">https://doi.org/10.1007/s11856-016-1429-z</a>","chicago":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” <i>Israel Journal of Mathematics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11856-016-1429-z\">https://doi.org/10.1007/s11856-016-1429-z</a>.","ama":"Akopyan A, Balitskiy A. Billiards in convex bodies with acute angles. <i>Israel Journal of Mathematics</i>. 2016;216(2):833-845. doi:<a href=\"https://doi.org/10.1007/s11856-016-1429-z\">10.1007/s11856-016-1429-z</a>","mla":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2, Springer, 2016, pp. 833–45, doi:<a href=\"https://doi.org/10.1007/s11856-016-1429-z\">10.1007/s11856-016-1429-z</a>.","short":"A. Akopyan, A. Balitskiy, Israel Journal of Mathematics 216 (2016) 833–845.","ista":"Akopyan A, Balitskiy A. 2016. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 216(2), 833–845.","ieee":"A. Akopyan and A. Balitskiy, “Billiards in convex bodies with acute angles,” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2. Springer, pp. 833–845, 2016."},"publication_status":"published","abstract":[{"text":"In this paper we investigate the existence of closed billiard trajectories in not necessarily smooth convex bodies. In particular, we show that if a body K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K is acute (in a certain sense), then there is a closed billiard trajectory in K.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"5938","department":[{"_id":"HeEd"}],"publisher":"Springer","publication":"Israel Journal of Mathematics","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1506.06014","open_access":"1"}],"type":"journal_article","intvolume":"       216","month":"10","page":"833 - 845","ec_funded":1,"issue":"2"},{"title":"Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress","article_processing_charge":"No","date_updated":"2022-05-24T09:26:03Z","_id":"1331","acknowledgement":"This work was financially supported by the following: The Alabama Agricultural Experiment Station HATCH grants 370222-310010-2055 and 370225-310006-2055 for funding to P.J.Z., E.A.K, A.M.P., and A.M.R. P.J.Z. and E.A.K were supported by an Auburn University Cellular and Molecular Biosciences Research Fellowship. I.D.C. is a postdoctoral fellow of the Research Foundation Flanders (FWO) (FWO/PDO14/043) and is also supported by FWO travel\r\ngrant 12N2415N. F.V.B. was supported by grants from the Interuniversity Attraction Poles Programme (IUAP P7/29 MARS) initiated by the Belgian Science Policy Office and Ghent University (Multidisciplinary Research Partnership Biotechnology for a Sustainable Economy, grant 01MRB510W).","year":"2016","oa":1,"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"oa_version":"Published Version","status":"public","author":[{"first_name":"Paul","full_name":"Zwack, Paul","last_name":"Zwack"},{"last_name":"De Clercq","first_name":"Inge","full_name":"De Clercq, Inge"},{"first_name":"Timothy","full_name":"Howton, Timothy","last_name":"Howton"},{"last_name":"Hallmark","first_name":"H Tucker","full_name":"Hallmark, H Tucker"},{"full_name":"Hurny, Andrej","first_name":"Andrej","last_name":"Hurny","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Keshishian","full_name":"Keshishian, Erika","first_name":"Erika"},{"last_name":"Parish","full_name":"Parish, Alyssa","first_name":"Alyssa"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mukhtar, M Shahid","first_name":"M Shahid","last_name":"Mukhtar"},{"first_name":"Frank","full_name":"Van Breusegem, Frank","last_name":"Van Breusegem"},{"last_name":"Rashotte","full_name":"Rashotte, Aaron","first_name":"Aaron"}],"doi":"10.1104/pp.16.00415","date_created":"2018-12-11T11:51:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":172,"day":"02","date_published":"2016-10-02T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.16.00415"}],"type":"journal_article","intvolume":"       172","month":"10","page":"1249 - 1258","issue":"2","quality_controlled":"1","citation":{"ama":"Zwack P, De Clercq I, Howton T, et al. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. <i>Plant Physiology</i>. 2016;172(2):1249-1258. doi:<a href=\"https://doi.org/10.1104/pp.16.00415\">10.1104/pp.16.00415</a>","apa":"Zwack, P., De Clercq, I., Howton, T., Hallmark, H. T., Hurny, A., Keshishian, E., … Rashotte, A. (2016). Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.16.00415\">https://doi.org/10.1104/pp.16.00415</a>","chicago":"Zwack, Paul, Inge De Clercq, Timothy Howton, H Tucker Hallmark, Andrej Hurny, Erika Keshishian, Alyssa Parish, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1104/pp.16.00415\">https://doi.org/10.1104/pp.16.00415</a>.","ista":"Zwack P, De Clercq I, Howton T, Hallmark HT, Hurny A, Keshishian E, Parish A, Benková E, Mukhtar MS, Van Breusegem F, Rashotte A. 2016. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 172(2), 1249–1258.","ieee":"P. Zwack <i>et al.</i>, “Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress,” <i>Plant Physiology</i>, vol. 172, no. 2. American Society of Plant Biologists, pp. 1249–1258, 2016.","mla":"Zwack, Paul, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” <i>Plant Physiology</i>, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1249–58, doi:<a href=\"https://doi.org/10.1104/pp.16.00415\">10.1104/pp.16.00415</a>.","short":"P. Zwack, I. De Clercq, T. Howton, H.T. Hallmark, A. Hurny, E. Keshishian, A. Parish, E. Benková, M.S. Mukhtar, F. Van Breusegem, A. Rashotte, Plant Physiology 172 (2016) 1249–1258."},"article_type":"original","publication_status":"published","abstract":[{"text":"Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6- dependent genes and establishes a novel connection between cytokinin and oxidative stress response.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"publist_id":"5937","publisher":"American Society of Plant Biologists","publication":"Plant Physiology","scopus_import":"1"},{"publist_id":"5936","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance."}],"file_date_updated":"2020-07-14T12:44:44Z","scopus_import":1,"file":[{"file_name":"IST-2016-662-v1+1_ncomms10333.pdf","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:13:52Z","file_size":1844107,"relation":"main_file","file_id":"5039","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"ef147bcbb8bd37e9079cf3ce06f5815d"}],"publication":"Nature Communications","publisher":"Nature Publishing Group","quality_controlled":"1","citation":{"ista":"Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333.","ieee":"R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","short":"R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).","mla":"Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” <i>Nature Communications</i>, vol. 7, 10333, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms10333\">10.1038/ncomms10333</a>.","ama":"Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms10333\">10.1038/ncomms10333</a>","chicago":"Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms10333\">https://doi.org/10.1038/ncomms10333</a>.","apa":"Chait, R. P., Palmer, A., Yelin, I., &#38; Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms10333\">https://doi.org/10.1038/ncomms10333</a>"},"publication_status":"published","month":"01","pubrep_id":"662","intvolume":"         7","article_number":"10333","ddc":["570","579"],"type":"journal_article","date_published":"2016-01-20T00:00:00Z","day":"20","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Chait, Remy P","first_name":"Remy P","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait"},{"last_name":"Palmer","first_name":"Adam","full_name":"Palmer, Adam"},{"last_name":"Yelin","full_name":"Yelin, Idan","first_name":"Idan"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}],"status":"public","oa_version":"Published Version","date_created":"2018-12-11T11:51:25Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":7,"doi":"10.1038/ncomms10333","has_accepted_license":"1","year":"2016","acknowledgement":"This work was partially supported by US National Institutes of Health grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant No. 152/11, and the European Research Council FP7 ERC Grant 281891.","oa":1,"title":"Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments","date_updated":"2021-01-12T06:49:57Z","_id":"1332"},{"citation":{"apa":"Milinski, M., Hilbe, C., Semmann, D., Sommerfeld, R., &#38; Marotzke, J. (2016). Humans choose representatives who enforce cooperation in social dilemmas through extortion. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms10915\">https://doi.org/10.1038/ncomms10915</a>","chicago":"Milinski, Manfred, Christian Hilbe, Dirk Semmann, Ralf Sommerfeld, and Jochem Marotzke. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms10915\">https://doi.org/10.1038/ncomms10915</a>.","ama":"Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. Humans choose representatives who enforce cooperation in social dilemmas through extortion. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms10915\">10.1038/ncomms10915</a>","mla":"Milinski, Manfred, et al. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” <i>Nature Communications</i>, vol. 7, 10915, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms10915\">10.1038/ncomms10915</a>.","short":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, J. Marotzke, Nature Communications 7 (2016).","ista":"Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. 2016. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 7, 10915.","ieee":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, and J. Marotzke, “Humans choose representatives who enforce cooperation in social dilemmas through extortion,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016."},"quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the &quot;representatives&quot; treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most."}],"publist_id":"5935","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","publication":"Nature Communications","file_date_updated":"2020-07-14T12:44:44Z","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-661-v1+1_ncomms10915.pdf","date_created":"2018-12-12T10:10:44Z","file_size":1432577,"relation":"main_file","file_id":"4834","access_level":"open_access","creator":"system","content_type":"application/pdf","checksum":"9ea0d7ce59a555a1cb8353d5559407cb"}],"type":"journal_article","ddc":["519","530","599"],"article_number":"10915","pubrep_id":"661","intvolume":"         7","month":"03","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Manfred","full_name":"Milinski, Manfred","last_name":"Milinski"},{"first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe"},{"first_name":"Dirk","full_name":"Semmann, Dirk","last_name":"Semmann"},{"first_name":"Ralf","full_name":"Sommerfeld, Ralf","last_name":"Sommerfeld"},{"last_name":"Marotzke","first_name":"Jochem","full_name":"Marotzke, Jochem"}],"doi":"10.1038/ncomms10915","volume":7,"date_created":"2018-12-11T11:51:25Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"07","date_published":"2016-03-07T00:00:00Z","title":"Humans choose representatives who enforce cooperation in social dilemmas through extortion","_id":"1333","date_updated":"2021-01-12T06:49:57Z","year":"2016","acknowledgement":"We thank the students for participation; H.-J. Krambeck for writing the software for the game; H. Arndt, T. Bakker, L. Becks, H. Brendelberger, S. Dobler and T. Reusch for support; and the Max Planck Society for the Advancement of Science for funding.","has_accepted_license":"1","oa":1},{"publication_status":"published","quality_controlled":"1","citation":{"apa":"Schönenberger, P., O’Neill, J., &#38; Csicsvari, J. L. (2016). Activity dependent plasticity of hippocampal place maps. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11824\">https://doi.org/10.1038/ncomms11824</a>","chicago":"Schönenberger, Philipp, Joseph O’Neill, and Jozsef L Csicsvari. “Activity Dependent Plasticity of Hippocampal Place Maps.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11824\">https://doi.org/10.1038/ncomms11824</a>.","ama":"Schönenberger P, O’Neill J, Csicsvari JL. Activity dependent plasticity of hippocampal place maps. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11824\">10.1038/ncomms11824</a>","short":"P. Schönenberger, J. O’Neill, J.L. Csicsvari, Nature Communications 7 (2016).","mla":"Schönenberger, Philipp, et al. “Activity Dependent Plasticity of Hippocampal Place Maps.” <i>Nature Communications</i>, vol. 7, 11824, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11824\">10.1038/ncomms11824</a>.","ieee":"P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Activity dependent plasticity of hippocampal place maps,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ista":"Schönenberger P, O’Neill J, Csicsvari JL. 2016. Activity dependent plasticity of hippocampal place maps. Nature Communications. 7, 11824."},"publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:44:44Z","scopus_import":1,"file":[{"file_size":1793846,"date_created":"2018-12-12T10:16:10Z","date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-660-v1+1_ncomms11824.pdf","relation":"main_file","file_id":"5196","checksum":"e43307754abe65b840a21939fe163618","content_type":"application/pdf","access_level":"open_access","creator":"system"}],"publication":"Nature Communications","abstract":[{"lang":"eng","text":"Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping."}],"department":[{"_id":"JoCs"}],"language":[{"iso":"eng"}],"publist_id":"5934","ddc":["570"],"type":"journal_article","ec_funded":1,"pubrep_id":"660","intvolume":"         7","article_number":"11824","month":"06","doi":"10.1038/ncomms11824","date_created":"2018-12-11T11:51:26Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":7,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","last_name":"Schönenberger","full_name":"Schönenberger, Philipp","first_name":"Philipp"},{"full_name":"O'Neill, Joseph","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","last_name":"O'Neill"},{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"day":"10","date_published":"2016-06-10T00:00:00Z","date_updated":"2021-01-12T06:49:57Z","_id":"1334","title":"Activity dependent plasticity of hippocampal place maps","oa":1,"project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","call_identifier":"FP7"},{"grant_number":"I2072-B27","call_identifier":"FWF","name":"Interneuron plasticity during spatial learning","_id":"257D4372-B435-11E9-9278-68D0E5697425"}],"year":"2016","has_accepted_license":"1"},{"ec_funded":1,"page":"23 - 38","intvolume":"      9837","month":"08","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1604.06764","open_access":"1"}],"publisher":"Springer","scopus_import":1,"abstract":[{"text":"In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties.","lang":"eng"}],"publist_id":"5932","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative monitor automata. In: Vol 9837. Springer; 2016:23-38. doi:<a href=\"https://doi.org/10.1007/978-3-662-53413-7_2\">10.1007/978-3-662-53413-7_2</a>","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Quantitative monitor automata (Vol. 9837, pp. 23–38). Presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53413-7_2\">https://doi.org/10.1007/978-3-662-53413-7_2</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Monitor Automata,” 9837:23–38. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53413-7_2\">https://doi.org/10.1007/978-3-662-53413-7_2</a>.","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative monitor automata. SAS: Static Analysis Symposium, LNCS, vol. 9837, 23–38.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative monitor automata,” presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom, 2016, vol. 9837, pp. 23–38.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Springer, 2016, pp. 23–38.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Monitor Automata</i>. Vol. 9837, Springer, 2016, pp. 23–38, doi:<a href=\"https://doi.org/10.1007/978-3-662-53413-7_2\">10.1007/978-3-662-53413-7_2</a>."},"alternative_title":["LNCS"],"quality_controlled":"1","oa":1,"year":"2016","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"_id":"1335","date_updated":"2021-01-12T06:49:58Z","conference":{"start_date":"2016-09-08","end_date":"2016-09-10","name":"SAS: Static Analysis Symposium","location":"Edinburgh, United Kingdom"},"title":"Quantitative monitor automata","day":"31","date_published":"2016-08-31T00:00:00Z","doi":"10.1007/978-3-662-53413-7_2","volume":9837,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:26Z","oa_version":"Preprint","status":"public","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan"}]},{"publication":"OncoImmunology","publisher":"Taylor & Francis","language":[{"iso":"eng"}],"abstract":[{"text":"Background: Anticancer vaccines could represent a valuable complementary strategy to established therapies, especially in settings of early stage and minimal residual disease. HER-2 is an important target for immunotherapy and addressed by the monoclonal antibody trastuzumab. We have previously generated HER-2 mimotope peptides from phage display libraries. The synthesized peptides were coupled to carriers and applied for epitope-specific induction of trastuzumab-like IgG. For simplification and to avoid methodological limitations of synthesis and coupling chemistry, we herewith present a novel and optimized approach by using adeno-associated viruses (AAV) as effective and high-density mimotope-display system, which can be directly used for vaccination. Methods: An AAV capsid display library was constructed by genetically incorporating random peptides in a plasmid encoding the wild-type AAV2 capsid protein. AAV clones, expressing peptides specifically reactive to trastuzumab, were employed to immunize BALB/c mice. Antibody titers against human HER-2 were determined, and the isotype composition and functional properties of these were tested. Finally, prophylactically immunized mice were challenged with human HER-2 transfected mouse D2F2/E2 cells. Results: HER-2 mimotope AAV-vaccines induced antibodies specific to human HER-2. Two clones were selected for immunization of mice, which were subsequently grafted D2F2/E2 cells. Both mimotope AAV clones delayed the growth of tumors significantly, as compared to controls. Conclusion: In this study, a novel mimotope AAV-based platform was created allowing the isolation of mimotopes, which can be directly used as anticancer vaccines. The example of trastuzumab AAV-mimotopes demonstrates that this vaccine strategy could help to establish active immunotherapy for breast-cancer patients.","lang":"eng"}],"publication_status":"published","article_type":"original","quality_controlled":"1","citation":{"chicago":"Singer, Josef, Krisztina Manzano-Szalai, Judit Singer, Kathrin Thell, Anna Bentley-Lukschal, Caroline Stremnitzer, Franziska Roth-Walter, et al. “Proof of Concept Study with an HER-2 Mimotope Anticancer Vaccine Deduced from a Novel AAV-Mimotope Library Platform.” <i>OncoImmunology</i>. Taylor &#38; Francis, 2016. <a href=\"https://doi.org/10.1080/2162402x.2016.1171446\">https://doi.org/10.1080/2162402x.2016.1171446</a>.","apa":"Singer, J., Manzano-Szalai, K., Singer, J., Thell, K., Bentley-Lukschal, A., Stremnitzer, C., … Jensen-Jarolim, E. (2016). Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform. <i>OncoImmunology</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/2162402x.2016.1171446\">https://doi.org/10.1080/2162402x.2016.1171446</a>","ama":"Singer J, Manzano-Szalai K, Singer J, et al. Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform. <i>OncoImmunology</i>. 2016;5(7). doi:<a href=\"https://doi.org/10.1080/2162402x.2016.1171446\">10.1080/2162402x.2016.1171446</a>","short":"J. Singer, K. Manzano-Szalai, J. Singer, K. Thell, A. Bentley-Lukschal, C. Stremnitzer, F. Roth-Walter, M. Weghofer, M. Ritter, K. Pino Tossi, M. Hörer, U. Michaelis, E. Jensen-Jarolim, OncoImmunology 5 (2016).","mla":"Singer, Josef, et al. “Proof of Concept Study with an HER-2 Mimotope Anticancer Vaccine Deduced from a Novel AAV-Mimotope Library Platform.” <i>OncoImmunology</i>, vol. 5, no. 7, e1171446, Taylor &#38; Francis, 2016, doi:<a href=\"https://doi.org/10.1080/2162402x.2016.1171446\">10.1080/2162402x.2016.1171446</a>.","ista":"Singer J, Manzano-Szalai K, Singer J, Thell K, Bentley-Lukschal A, Stremnitzer C, Roth-Walter F, Weghofer M, Ritter M, Pino Tossi K, Hörer M, Michaelis U, Jensen-Jarolim E. 2016. Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform. OncoImmunology. 5(7), e1171446.","ieee":"J. Singer <i>et al.</i>, “Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform,” <i>OncoImmunology</i>, vol. 5, no. 7. Taylor &#38; Francis, 2016."},"issue":"7","month":"06","intvolume":"         5","article_number":"e1171446","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/2162402X.2016.1171446"}],"date_published":"2016-06-30T00:00:00Z","day":"30","date_created":"2020-08-10T11:54:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":5,"doi":"10.1080/2162402x.2016.1171446","author":[{"first_name":"Josef","full_name":"Singer, Josef","last_name":"Singer"},{"last_name":"Manzano-Szalai","full_name":"Manzano-Szalai, Krisztina","first_name":"Krisztina"},{"last_name":"Fazekas","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","first_name":"Judit","full_name":"Fazekas, Judit"},{"full_name":"Thell, Kathrin","first_name":"Kathrin","last_name":"Thell"},{"first_name":"Anna","full_name":"Bentley-Lukschal, Anna","last_name":"Bentley-Lukschal"},{"full_name":"Stremnitzer, Caroline","first_name":"Caroline","last_name":"Stremnitzer"},{"last_name":"Roth-Walter","full_name":"Roth-Walter, Franziska","first_name":"Franziska"},{"full_name":"Weghofer, Margit","first_name":"Margit","last_name":"Weghofer"},{"first_name":"Mirko","full_name":"Ritter, Mirko","last_name":"Ritter"},{"last_name":"Pino Tossi","first_name":"Kerstin","full_name":"Pino Tossi, Kerstin"},{"last_name":"Hörer","full_name":"Hörer, Markus","first_name":"Markus"},{"last_name":"Michaelis","first_name":"Uwe","full_name":"Michaelis, Uwe"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"}],"status":"public","extern":"1","oa_version":"Published Version","publication_identifier":{"issn":["2162-402X"]},"oa":1,"year":"2016","date_updated":"2021-01-12T08:17:41Z","_id":"8241","title":"Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform","article_processing_charge":"No"},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-26T11:48:54Z","doi":"10.1109/etfa.2016.7733612","extern":"1","citation":{"ista":"Kokoris Kogias E, Voutyras O, Varvarigou T. 2016. TRM-SIoT: A scalable hybrid trust &#38; reputation model for the social Internet of Things. 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation. ETFA: Conference on Emerging Technologies and Factory Automation, 7733612.","ieee":"E. Kokoris Kogias, O. Voutyras, and T. Varvarigou, “TRM-SIoT: A scalable hybrid trust &#38; reputation model for the social Internet of Things,” in <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>, Berlin, Germany, 2016.","mla":"Kokoris Kogias, Eleftherios, et al. “TRM-SIoT: A Scalable Hybrid Trust &#38; Reputation Model for the Social Internet of Things.” <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>, 7733612, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/etfa.2016.7733612\">10.1109/etfa.2016.7733612</a>.","short":"E. Kokoris Kogias, O. Voutyras, T. Varvarigou, in:, 2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation, IEEE, 2016.","ama":"Kokoris Kogias E, Voutyras O, Varvarigou T. TRM-SIoT: A scalable hybrid trust &#38; reputation model for the social Internet of Things. In: <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>. IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/etfa.2016.7733612\">10.1109/etfa.2016.7733612</a>","apa":"Kokoris Kogias, E., Voutyras, O., &#38; Varvarigou, T. (2016). TRM-SIoT: A scalable hybrid trust &#38; reputation model for the social Internet of Things. In <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>. Berlin, Germany: IEEE. <a href=\"https://doi.org/10.1109/etfa.2016.7733612\">https://doi.org/10.1109/etfa.2016.7733612</a>","chicago":"Kokoris Kogias, Eleftherios, Orfefs Voutyras, and Theodora Varvarigou. “TRM-SIoT: A Scalable Hybrid Trust &#38; Reputation Model for the Social Internet of Things.” In <i>2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation</i>. IEEE, 2016. <a href=\"https://doi.org/10.1109/etfa.2016.7733612\">https://doi.org/10.1109/etfa.2016.7733612</a>."},"quality_controlled":"1","author":[{"full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"last_name":"Voutyras","full_name":"Voutyras, Orfefs","first_name":"Orfefs"},{"first_name":"Theodora","full_name":"Varvarigou, Theodora","last_name":"Varvarigou"}],"status":"public","oa_version":"None","publication":"2016 IEEE 21st International Conference on Emerging Technologies and Factory Automation","date_published":"2016-09-09T00:00:00Z","publisher":"IEEE","day":"09","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The integration of social networking concepts into Internet of Things systems is a burgeoning topic of research that promises to support novel and more powerful applications. In this paper we focus on the design and implementation of a highly scalable Trust and Reputation Model for the Internet of Things based on the social approach that the COSMOS project introduces, as part of its final results. We create our model by combining popular solutions proposed for Peer-to-Peer and mobile ad-hoc networks and adapting them on the Internet of Things concept. Each Thing can compute the Trust index of another Thing based on its own experiences, while it has the capability of determining its Reputation Index either by consulting its other “friends” (Followees) or referring to the Platform, a management system used in COSMOS. The model is tested through simulations of the proposed social system, demonstrating the ability of TRM-SIoT to achieve the Social Exclusion of malicious nodes and collectives from the network, with low computational overhead and high scalability. Furthermore, due to the adaptive nature of the system, Social Reintegration of these nodes is also possible."}],"conference":{"location":"Berlin, Germany","name":"ETFA: Conference on Emerging Technologies and Factory Automation","end_date":"2016-09-09","start_date":"2016-09-06"},"_id":"8300","type":"conference","date_updated":"2021-01-12T08:17:59Z","title":"TRM-SIoT: A scalable hybrid trust & reputation model for the social Internet of Things","article_processing_charge":"No","publication_identifier":{"isbn":["9781509013142"]},"month":"09","article_number":"7733612","year":"2016"},{"publisher":"USENIX Association","day":"01","publication":"Proceedings of the 25th USENIX Conference on Security Symposium","date_published":"2016-09-01T00:00:00Z","abstract":[{"text":"While showing great promise, Bitcoin requires users to wait tens of minutes for transactions to commit, and even then, offering only probabilistic guarantees. This paper introduces ByzCoin, a novel Byzantine consensus protocol that leverages scalable collective signing to commit Bitcoin transactions irreversibly within seconds. ByzCoin achieves Byzantine consensus while preserving Bitcoin’s open membership by dynamically forming hash power-proportionate consensus groups that represent recently-successful block miners. ByzCoin employs communication trees to optimize transaction commitment and verification under normal operation while guaranteeing safety and liveness under Byzantine faults, up to a near-optimal tolerance of f faulty group members among 3f + 2 total. ByzCoin mitigates double spending and selfish mining attacks by producing collectively signed transaction blocks within one minute of transaction submission. Tree-structured communication further reduces this latency to less than 30 seconds. Due to these optimizations, ByzCoin achieves a throughput higher than Paypal currently handles, with a confirmation latency of 15-20 seconds.","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["1602.06997"]},"publication_status":"published","date_created":"2020-08-26T12:08:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","citation":{"ista":"Kokoris Kogias E, Jovanovic P, Gailly N, Khoffi I, Gasser L, Ford B. 2016. Enhancing bitcoin security and performance with strong consistency via collective signing. Proceedings of the 25th USENIX Conference on Security Symposium. SEC: Security Symposium, 279–296.","ieee":"E. Kokoris Kogias, P. Jovanovic, N. Gailly, I. Khoffi, L. Gasser, and B. Ford, “Enhancing bitcoin security and performance with strong consistency via collective signing,” in <i>Proceedings of the 25th USENIX Conference on Security Symposium</i>, Austin, TX, United States, 2016, pp. 279–296.","short":"E. Kokoris Kogias, P. Jovanovic, N. Gailly, I. Khoffi, L. Gasser, B. Ford, in:, Proceedings of the 25th USENIX Conference on Security Symposium, USENIX Association, 2016, pp. 279–296.","mla":"Kokoris Kogias, Eleftherios, et al. “Enhancing Bitcoin Security and Performance with Strong Consistency via Collective Signing.” <i>Proceedings of the 25th USENIX Conference on Security Symposium</i>, USENIX Association, 2016, pp. 279–296.","ama":"Kokoris Kogias E, Jovanovic P, Gailly N, Khoffi I, Gasser L, Ford B. Enhancing bitcoin security and performance with strong consistency via collective signing. In: <i>Proceedings of the 25th USENIX Conference on Security Symposium</i>. USENIX Association; 2016:279–296.","chicago":"Kokoris Kogias, Eleftherios, Philipp Jovanovic, Nicolas Gailly, Ismail Khoffi, Linus Gasser, and Bryan Ford. “Enhancing Bitcoin Security and Performance with Strong Consistency via Collective Signing.” In <i>Proceedings of the 25th USENIX Conference on Security Symposium</i>, 279–296. USENIX Association, 2016.","apa":"Kokoris Kogias, E., Jovanovic, P., Gailly, N., Khoffi, I., Gasser, L., &#38; Ford, B. (2016). Enhancing bitcoin security and performance with strong consistency via collective signing. In <i>Proceedings of the 25th USENIX Conference on Security Symposium</i> (pp. 279–296). Austin, TX, United States: USENIX Association."},"extern":"1","status":"public","author":[{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Jovanovic","first_name":"Philipp","full_name":"Jovanovic, Philipp"},{"full_name":"Gailly, Nicolas","first_name":"Nicolas","last_name":"Gailly"},{"full_name":"Khoffi, Ismail","first_name":"Ismail","last_name":"Khoffi"},{"full_name":"Gasser, Linus","first_name":"Linus","last_name":"Gasser"},{"first_name":"Bryan","full_name":"Ford, Bryan","last_name":"Ford"}],"quality_controlled":"1","oa":1,"page":"279–296","publication_identifier":{"isbn":["9781931971324"]},"year":"2016","month":"09","_id":"8302","type":"conference","date_updated":"2021-01-12T08:18:00Z","conference":{"name":"SEC: Security Symposium","location":"Austin, TX, United States","end_date":"2016-08-12","start_date":"2016-08-10"},"arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1602.06997","open_access":"1"}],"article_processing_charge":"No","title":"Enhancing bitcoin security and performance with strong consistency via collective signing"},{"intvolume":"       113","year":"2016","month":"09","page":"11585-11590","issue":"41","publication_identifier":{"issn":["0027-8424","1091-6490"]},"article_processing_charge":"No","title":"A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis","type":"journal_article","_id":"8452","date_updated":"2021-01-12T08:19:22Z","abstract":[{"text":"During spore formation in Bacillus subtilis a transenvelope complex is assembled across the double membrane that separates the mother cell and forespore. This complex (called the “A–Q complex”) is required to maintain forespore development and is composed of proteins with remote homology to components of type II, III, and IV secretion systems found in Gram-negative bacteria. Here, we show that one of these proteins, SpoIIIAG, which has remote homology to ring-forming proteins found in type III secretion systems, assembles into an oligomeric ring in the periplasmic-like space between the two membranes. Three-dimensional reconstruction of images generated by cryo-electron microscopy indicates that the SpoIIIAG ring has a cup-and-saucer architecture with a 6-nm central pore. Structural modeling of SpoIIIAG generated a 24-member ring with dimensions similar to those of the EM-derived saucer. Point mutations in the predicted oligomeric interface disrupted ring formation in vitro and impaired forespore gene expression and efficient spore formation in vivo. Taken together, our data provide strong support for the model in which the A–Q transenvelope complex contains a conduit that connects the mother cell and forespore. We propose that a set of stacked rings spans the intermembrane space, as has been found for type III secretion systems.","lang":"eng"}],"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","day":"28","publication":"Proceedings of the National Academy of Sciences","date_published":"2016-09-28T00:00:00Z","oa_version":"None","citation":{"ama":"Rodrigues CDA, Henry X, Neumann E, et al. A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(41):11585-11590. doi:<a href=\"https://doi.org/10.1073/pnas.1609604113\">10.1073/pnas.1609604113</a>","apa":"Rodrigues, C. D. A., Henry, X., Neumann, E., Kurauskas, V., Bellard, L., Fichou, Y., … Morlot, C. (2016). A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1609604113\">https://doi.org/10.1073/pnas.1609604113</a>","chicago":"Rodrigues, Christopher D. A., Xavier Henry, Emmanuelle Neumann, Vilius Kurauskas, Laure Bellard, Yann Fichou, Paul Schanda, Guy Schoehn, David Z. Rudner, and Cecile Morlot. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore during Sporulation in Bacillus Subtilis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1609604113\">https://doi.org/10.1073/pnas.1609604113</a>.","ista":"Rodrigues CDA, Henry X, Neumann E, Kurauskas V, Bellard L, Fichou Y, Schanda P, Schoehn G, Rudner DZ, Morlot C. 2016. A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences. 113(41), 11585–11590.","ieee":"C. D. A. Rodrigues <i>et al.</i>, “A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 41. National Academy of Sciences, pp. 11585–11590, 2016.","short":"C.D.A. Rodrigues, X. Henry, E. Neumann, V. Kurauskas, L. Bellard, Y. Fichou, P. Schanda, G. Schoehn, D.Z. Rudner, C. Morlot, Proceedings of the National Academy of Sciences 113 (2016) 11585–11590.","mla":"Rodrigues, Christopher D. A., et al. “A Ring-Shaped Conduit Connects the Mother Cell and Forespore during Sporulation in Bacillus Subtilis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 41, National Academy of Sciences, 2016, pp. 11585–90, doi:<a href=\"https://doi.org/10.1073/pnas.1609604113\">10.1073/pnas.1609604113</a>."},"extern":"1","quality_controlled":"1","status":"public","author":[{"full_name":"Rodrigues, Christopher D. A.","first_name":"Christopher D. A.","last_name":"Rodrigues"},{"first_name":"Xavier","full_name":"Henry, Xavier","last_name":"Henry"},{"first_name":"Emmanuelle","full_name":"Neumann, Emmanuelle","last_name":"Neumann"},{"first_name":"Vilius","full_name":"Kurauskas, Vilius","last_name":"Kurauskas"},{"last_name":"Bellard","first_name":"Laure","full_name":"Bellard, Laure"},{"full_name":"Fichou, Yann","first_name":"Yann","last_name":"Fichou"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606"},{"full_name":"Schoehn, Guy","first_name":"Guy","last_name":"Schoehn"},{"first_name":"David Z.","full_name":"Rudner, David Z.","last_name":"Rudner"},{"full_name":"Morlot, Cecile","first_name":"Cecile","last_name":"Morlot"}],"article_type":"original","doi":"10.1073/pnas.1609604113","volume":113,"date_created":"2020-09-18T10:06:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"day":"08","publisher":"American Chemical Society","publication":"The Journal of Physical Chemistry B","date_published":"2016-08-08T00:00:00Z","abstract":[{"lang":"eng","text":"Transverse relaxation rate measurements in magic-angle spinning solid-state nuclear magnetic resonance provide information about molecular motions occurring on nanosecond-to-millisecond (ns–ms) time scales. The measurement of heteronuclear (13C, 15N) relaxation rate constants in the presence of a spin-lock radiofrequency field (R1ρ relaxation) provides access to such motions, and an increasing number of studies involving R1ρ relaxation in proteins have been reported. However, two factors that influence the observed relaxation rate constants have so far been neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR) and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that the CCR rate constant depends on ns–ms motions; it can thus provide insight into dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling effect on the doublet components. For measurements of dynamics, the use of R1ρ rate constants has practical advantages over the use of CCR rates, and this article reveals factors that have so far been disregarded and which are important for accurate measurements and interpretation."}],"language":[{"iso":"eng"}],"article_type":"original","doi":"10.1021/acs.jpcb.6b06129","volume":120,"publication_status":"published","date_created":"2020-09-18T10:07:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","keyword":["Physical and Theoretical Chemistry","Materials Chemistry","Surfaces","Coatings and Films"],"citation":{"ieee":"V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, and P. Schanda, “Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements,” <i>The Journal of Physical Chemistry B</i>, vol. 120, no. 34. American Chemical Society, pp. 8905–8913, 2016.","ista":"Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. 2016. Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements. The Journal of Physical Chemistry B. 120(34), 8905–8913.","short":"V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, P. Schanda, The Journal of Physical Chemistry B 120 (2016) 8905–8913.","mla":"Kurauskas, Vilius, et al. “Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application to Protein Backbone Dynamics Measurements.” <i>The Journal of Physical Chemistry B</i>, vol. 120, no. 34, American Chemical Society, 2016, pp. 8905–13, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.6b06129\">10.1021/acs.jpcb.6b06129</a>.","ama":"Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements. <i>The Journal of Physical Chemistry B</i>. 2016;120(34):8905-8913. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.6b06129\">10.1021/acs.jpcb.6b06129</a>","apa":"Kurauskas, V., Weber, E., Hessel, A., Ayala, I., Marion, D., &#38; Schanda, P. (2016). Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.6b06129\">https://doi.org/10.1021/acs.jpcb.6b06129</a>","chicago":"Kurauskas, Vilius, Emmanuelle Weber, Audrey Hessel, Isabel Ayala, Dominique Marion, and Paul Schanda. “Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application to Protein Backbone Dynamics Measurements.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acs.jpcb.6b06129\">https://doi.org/10.1021/acs.jpcb.6b06129</a>."},"extern":"1","status":"public","author":[{"last_name":"Kurauskas","full_name":"Kurauskas, Vilius","first_name":"Vilius"},{"last_name":"Weber","full_name":"Weber, Emmanuelle","first_name":"Emmanuelle"},{"first_name":"Audrey","full_name":"Hessel, Audrey","last_name":"Hessel"},{"last_name":"Ayala","full_name":"Ayala, Isabel","first_name":"Isabel"},{"first_name":"Dominique","full_name":"Marion, Dominique","last_name":"Marion"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"quality_controlled":"1","page":"8905-8913","issue":"34","publication_identifier":{"issn":["1520-6106","1520-5207"]},"year":"2016","intvolume":"       120","month":"08","_id":"8453","type":"journal_article","date_updated":"2021-01-12T08:19:22Z","article_processing_charge":"No","title":"Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements"}]