[{"oa":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["EPTCS"],"day":"02","volume":169,"scopus_import":"1","publisher":"Open Publishing Association","conference":{"location":"Vienna, Austria","name":"HCVS: Horn Clauses for Verification and Synthesis","end_date":"2014-07-17","start_date":"2014-07-17"},"page":"31 - 38","citation":{"ieee":"A. Gupta, C. Popeea, and A. Rybalchenko, “Generalised interpolation by solving recursion free-horn clauses,” in <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, Vienna, Austria, 2014, vol. 169, pp. 31–38.","ama":"Gupta A, Popeea C, Rybalchenko A. Generalised interpolation by solving recursion free-horn clauses. In: <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>. Vol 169. Open Publishing Association; 2014:31-38. doi:<a href=\"https://doi.org/10.4204/EPTCS.169.5\">10.4204/EPTCS.169.5</a>","mla":"Gupta, Ashutosh, et al. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, vol. 169, Open Publishing Association, 2014, pp. 31–38, doi:<a href=\"https://doi.org/10.4204/EPTCS.169.5\">10.4204/EPTCS.169.5</a>.","apa":"Gupta, A., Popeea, C., &#38; Rybalchenko, A. (2014). Generalised interpolation by solving recursion free-horn clauses. In <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i> (Vol. 169, pp. 31–38). Vienna, Austria: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.169.5\">https://doi.org/10.4204/EPTCS.169.5</a>","chicago":"Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” In <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, 169:31–38. Open Publishing Association, 2014. <a href=\"https://doi.org/10.4204/EPTCS.169.5\">https://doi.org/10.4204/EPTCS.169.5</a>.","ista":"Gupta A, Popeea C, Rybalchenko A. 2014. Generalised interpolation by solving recursion free-horn clauses. Electronic Proceedings in Theoretical Computer Science, EPTCS. HCVS: Horn Clauses for Verification and Synthesis, EPTCS, vol. 169, 31–38.","short":"A. Gupta, C. Popeea, A. Rybalchenko, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing Association, 2014, pp. 31–38."},"publication":"Electronic Proceedings in Theoretical Computer Science, EPTCS","status":"public","year":"2014","author":[{"last_name":"Gupta","first_name":"Ashutosh","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Popeea, Corneliu","last_name":"Popeea","first_name":"Corneliu"},{"full_name":"Rybalchenko, Andrey","last_name":"Rybalchenko","first_name":"Andrey"}],"date_updated":"2025-06-11T08:03:28Z","external_id":{"arxiv":["1303.7378"]},"abstract":[{"lang":"eng","text":"In this paper we present INTERHORN, a solver for recursion-free Horn clauses. The main application domain of INTERHORN lies in solving interpolation problems arising in software verification. We show how a range of interpolation problems, including path, transition, nested, state/transition and well-founded interpolation can be handled directly by INTERHORN. By detailing these interpolation problems and their Horn clause representations, we hope to encourage the emergence of a common back-end interpolation interface useful for diverse verification tools."}],"arxiv":1,"type":"conference","month":"12","corr_author":"1","department":[{"_id":"ToHe"}],"article_processing_charge":"No","main_file_link":[{"url":"http://arxiv.org/abs/1303.7378","open_access":"1"}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:53:33Z","doi":"10.4204/EPTCS.169.5","title":"Generalised interpolation by solving recursion free-horn clauses","language":[{"iso":"eng"}],"publist_id":"5435","publication_status":"published","intvolume":"       169","_id":"1702","date_published":"2014-12-02T00:00:00Z"},{"status":"public","citation":{"ieee":"C. Savin and S. Denève, “Spatio-temporal representations of uncertainty in spiking neural networks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2014, vol. 27, no. January, pp. 2024–2032.","mla":"Savin, Cristina, and Sophie Denève. <i>Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks</i>. Vol. 27, no. January, Neural Information Processing Systems Foundation, 2014, pp. 2024–32.","apa":"Savin, C., &#38; Denève, S. (2014). Spatio-temporal representations of uncertainty in spiking neural networks (Vol. 27, pp. 2024–2032). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems Foundation.","ama":"Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking neural networks. In: Vol 27. Neural Information Processing Systems Foundation; 2014:2024-2032.","short":"C. Savin, S. Denève, in:, Neural Information Processing Systems Foundation, 2014, pp. 2024–2032.","chicago":"Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks,” 27:2024–32. Neural Information Processing Systems Foundation, 2014.","ista":"Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in spiking neural networks. NIPS: Neural Information Processing Systems vol. 27, 2024–2032."},"page":"2024 - 2032","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2014-12-08","end_date":"2014-12-13","location":"Montreal, Canada"},"publisher":"Neural Information Processing Systems Foundation","scopus_import":"1","date_updated":"2025-06-03T11:45:08Z","author":[{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"},{"full_name":"Denève, Sophie","first_name":"Sophie","last_name":"Denève"}],"year":"2014","quality_controlled":"1","oa":1,"volume":27,"issue":"January","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        27","publication_status":"published","publist_id":"5427","language":[{"iso":"eng"}],"date_published":"2014-01-01T00:00:00Z","_id":"1708","corr_author":"1","type":"conference","month":"01","abstract":[{"text":"It has been long argued that, because of inherent ambiguity and noise, the brain needs to represent uncertainty in the form of probability distributions. The neural encoding of such distributions remains however highly controversial. Here we present a novel circuit model for representing multidimensional real-valued distributions using a spike based spatio-temporal code. Our model combines the computational advantages of the currently competing models for probabilistic codes and exhibits realistic neural responses along a variety of classic measures. Furthermore, the model highlights the challenges associated with interpreting neural activity in relation to behavioral uncertainty and points to alternative population-level approaches for the experimental validation of distributed representations.","lang":"eng"}],"title":"Spatio-temporal representations of uncertainty in spiking neural networks","date_created":"2018-12-11T11:53:35Z","oa_version":"None","main_file_link":[{"url":"http://papers.nips.cc/paper/5343-spatio-temporal-representations-of-uncertainty-in-spiking-neural-networks.pdf","open_access":"1"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}]},{"volume":560,"issue":"3","day":"04","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","oa":1,"date_updated":"2025-09-29T13:14:25Z","author":[{"first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin","full_name":"Chmelik, Martin"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"}],"year":"2014","status":"public","publication":"Theoretical Computer Science","citation":{"ista":"Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. 2014. Interface simulation distances. Theoretical Computer Science. 560(3), 348–363.","chicago":"Cerny, Pavol, Martin Chmelik, Thomas A Henzinger, and Arjun Radhakrishna. “Interface Simulation Distances.” <i>Theoretical Computer Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tcs.2014.08.019\">https://doi.org/10.1016/j.tcs.2014.08.019</a>.","short":"P. Cerny, M. Chmelik, T.A. Henzinger, A. Radhakrishna, Theoretical Computer Science 560 (2014) 348–363.","ieee":"P. Cerny, M. Chmelik, T. A. Henzinger, and A. Radhakrishna, “Interface simulation distances,” <i>Theoretical Computer Science</i>, vol. 560, no. 3. Elsevier, pp. 348–363, 2014.","mla":"Cerny, Pavol, et al. “Interface Simulation Distances.” <i>Theoretical Computer Science</i>, vol. 560, no. 3, Elsevier, 2014, pp. 348–63, doi:<a href=\"https://doi.org/10.1016/j.tcs.2014.08.019\">10.1016/j.tcs.2014.08.019</a>.","apa":"Cerny, P., Chmelik, M., Henzinger, T. A., &#38; Radhakrishna, A. (2014). Interface simulation distances. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2014.08.019\">https://doi.org/10.1016/j.tcs.2014.08.019</a>","ama":"Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. Interface simulation distances. <i>Theoretical Computer Science</i>. 2014;560(3):348-363. doi:<a href=\"https://doi.org/10.1016/j.tcs.2014.08.019\">10.1016/j.tcs.2014.08.019</a>"},"page":"348 - 363","publisher":"Elsevier","scopus_import":"1","ec_funded":1,"title":"Interface simulation distances","doi":"10.1016/j.tcs.2014.08.019","date_created":"2018-12-11T11:53:43Z","oa_version":"Submitted Version","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1210.2450"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"corr_author":"1","month":"12","arxiv":1,"type":"journal_article","abstract":[{"lang":"eng","text":"The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a distance for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intuitively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces, and how to synthesize an interface from incompatible requirements. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies."}],"external_id":{"isi":["000347601300009"],"arxiv":["1210.2450"]},"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"date_published":"2014-12-04T00:00:00Z","related_material":{"record":[{"id":"2916","relation":"earlier_version","status":"public"}]},"_id":"1733","isi":1,"intvolume":"       560","publication_status":"published","publist_id":"5392","language":[{"iso":"eng"}]},{"publication_status":"published","intvolume":"         3","language":[{"iso":"eng"}],"date_published":"2014-08-01T00:00:00Z","_id":"8044","publication_identifier":{"isbn":["9788961058063"]},"corr_author":"1","abstract":[{"text":"Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system.","lang":"eng"}],"month":"08","type":"conference","title":"Structure of the excitation spectrum for many-body quantum systems","main_file_link":[{"open_access":"1","url":"http://www.icm2014.org/en/vod/proceedings.html"}],"article_processing_charge":"No","oa_version":"Published Version","date_created":"2020-06-29T07:59:35Z","department":[{"_id":"RoSe"}],"publication":"Proceeding of the International Congress of Mathematicans","status":"public","OA_type":"free access","page":"1175-1194","citation":{"ista":"Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum systems. Proceeding of the International Congress of Mathematicans. ICM: International Congress of Mathematicans vol. 3, 1175–1194.","chicago":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” In <i>Proceeding of the International Congress of Mathematicans</i>, 3:1175–94. International Congress of Mathematicians, 2014.","short":"R. Seiringer, in:, Proceeding of the International Congress of Mathematicans, International Congress of Mathematicians, 2014, pp. 1175–1194.","ieee":"R. Seiringer, “Structure of the excitation spectrum for many-body quantum systems,” in <i>Proceeding of the International Congress of Mathematicans</i>, Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.","mla":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” <i>Proceeding of the International Congress of Mathematicans</i>, vol. 3, International Congress of Mathematicians, 2014, pp. 1175–94.","apa":"Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum systems. In <i>Proceeding of the International Congress of Mathematicans</i> (Vol. 3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.","ama":"Seiringer R. Structure of the excitation spectrum for many-body quantum systems. In: <i>Proceeding of the International Congress of Mathematicans</i>. Vol 3. International Congress of Mathematicians; 2014:1175-1194."},"scopus_import":"1","publisher":"International Congress of Mathematicians","conference":{"end_date":"2014-08-21","start_date":"2014-08-13","name":"ICM: International Congress of Mathematicans","location":"Seoul, South Korea"},"date_updated":"2025-07-15T08:39:50Z","year":"2014","author":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"quality_controlled":"1","oa":1,"volume":3,"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher"},{"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"external_id":{"pmid":["24630728"]},"type":"journal_article","month":"03","abstract":[{"lang":"eng","text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints."}],"date_created":"2021-06-04T12:00:16Z","oa_version":"Published Version","doi":"10.1016/j.cell.2014.01.029","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"article_processing_charge":"No","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","department":[{"_id":"DaZi"}],"pmid":1,"intvolume":"       156","publication_status":"published","language":[{"iso":"eng"}],"date_published":"2014-03-13T00:00:00Z","_id":"9458","oa":1,"article_type":"original","quality_controlled":"1","issue":"6","volume":156,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"13","citation":{"short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014."},"page":"1286-1297","publication":"Cell","status":"public","publisher":"Elsevier","scopus_import":"1","extern":"1","date_updated":"2021-12-14T08:22:36Z","author":[{"full_name":"Huff, Jason T.","first_name":"Jason T.","last_name":"Huff"},{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"year":"2014"},{"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"external_id":{"pmid":["25344531"]},"type":"journal_article","month":"11","abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}],"date_created":"2021-06-07T07:23:43Z","oa_version":"Published Version","doi":"10.1073/pnas.1418564111","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"article_processing_charge":"No","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","department":[{"_id":"DaZi"}],"pmid":1,"intvolume":"       111","publication_status":"published","language":[{"iso":"eng"}],"date_published":"2014-11-11T00:00:00Z","_id":"9479","oa":1,"article_type":"original","quality_controlled":"1","issue":"45","volume":111,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"11","citation":{"chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>"},"page":"16166-16171","status":"public","publication":"Proceedings of the National Academy of Sciences","publisher":"National Academy of Sciences","scopus_import":"1","extern":"1","date_updated":"2021-12-14T08:23:26Z","author":[{"last_name":"Mérai","first_name":"Zsuzsanna","full_name":"Mérai, Zsuzsanna"},{"first_name":"Nina","last_name":"Chumak","full_name":"Chumak, Nina"},{"full_name":"García-Aguilar, Marcelina","last_name":"García-Aguilar","first_name":"Marcelina"},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"full_name":"Schoft, Vera K.","last_name":"Schoft","first_name":"Vera K."},{"first_name":"János","last_name":"Bindics","full_name":"Bindics, János"},{"full_name":"Ślusarz, Lucyna","last_name":"Ślusarz","first_name":"Lucyna"},{"full_name":"Arnoux, Stéphanie","first_name":"Stéphanie","last_name":"Arnoux"},{"first_name":"Susanne","last_name":"Opravil","full_name":"Opravil, Susanne"},{"last_name":"Mechtler","first_name":"Karl","full_name":"Mechtler, Karl"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Tamaru","first_name":"Hisashi","full_name":"Tamaru, Hisashi"}],"year":"2014"},{"language":[{"iso":"eng"}],"publication_status":"published","intvolume":"        19","pmid":1,"_id":"9519","date_published":"2014-05-04T00:00:00Z","abstract":[{"lang":"eng","text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression."}],"month":"05","type":"journal_article","external_id":{"pmid":["24618094 "]},"publication_identifier":{"eissn":["1878-4372"],"issn":["1360-1385"]},"department":[{"_id":"DaZi"}],"title":"DNA methylation as a system of plant genomic immunity","article_processing_charge":"No","date_created":"2021-06-07T14:38:09Z","oa_version":"None","doi":"10.1016/j.tplants.2014.01.014","scopus_import":"1","publisher":"Elsevier","status":"public","publication":"Trends in Plant Science","page":"320-326","citation":{"apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>.","ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326."},"year":"2014","author":[{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel"}],"date_updated":"2021-12-14T08:24:48Z","extern":"1","quality_controlled":"1","article_type":"review","day":"04","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":19,"issue":"5"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"JoCs"}],"day":"14","doi":"10.1371/journal.pone.0111430.s006","date_created":"2021-07-26T14:35:00Z","oa_version":"Published Version","article_processing_charge":"No","title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","month":"11","type":"research_data_reference","author":[{"full_name":"Lovrics, Anna","first_name":"Anna","last_name":"Lovrics"},{"full_name":"Gao, Yu","last_name":"Gao","first_name":"Yu"},{"full_name":"Juhász, Bianka","last_name":"Juhász","first_name":"Bianka"},{"full_name":"Bock, István","last_name":"Bock","first_name":"István"},{"last_name":"Byrne","first_name":"Helen M.","full_name":"Byrne, Helen M."},{"first_name":"András","last_name":"Dinnyés","full_name":"Dinnyés, András"},{"full_name":"Kovács, Krisztián","last_name":"Kovács","first_name":"Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87"}],"year":"2014","related_material":{"record":[{"id":"2004","relation":"used_in_publication","status":"public"}]},"_id":"9722","date_published":"2014-11-14T00:00:00Z","date_updated":"2025-09-29T12:02:47Z","publisher":"Public Library of Science","citation":{"chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>.","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","ieee":"A. Lovrics <i>et al.</i>, “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","mla":"Lovrics, Anna, et al. <i>Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &#38; Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>"},"status":"public"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"KrCh"}],"day":"11","article_processing_charge":"No","doi":"10.1371/journal.pcbi.1003818.s001","oa_version":"Published Version","date_created":"2021-07-28T08:13:57Z","title":"Detailed proofs for “The time scale of evolutionary innovation”","type":"research_data_reference","month":"09","year":"2014","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"last_name":"Adlam","first_name":"Ben","full_name":"Adlam, Ben"},{"full_name":"Novak, Martin","last_name":"Novak","first_name":"Martin"}],"related_material":{"record":[{"relation":"used_in_publication","id":"2039","status":"public"}]},"_id":"9739","date_published":"2014-09-11T00:00:00Z","date_updated":"2025-09-29T11:53:46Z","publisher":"Public Library of Science","citation":{"chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>","mla":"Chatterjee, Krishnendu, et al. <i>Detailed Proofs for “The Time Scale of Evolutionary Innovation.”</i> Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>"},"status":"public"},{"related_material":{"record":[{"id":"1993","relation":"used_in_publication","status":"public"}]},"_id":"9740","author":[{"full_name":"Konrad, Matthias","first_name":"Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon"},{"last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"year":"2014","date_updated":"2025-09-23T07:55:02Z","date_published":"2014-11-13T00:00:00Z","publisher":"Dryad","status":"public","citation":{"mla":"Konrad, Matthias, et al. <i>Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>.","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, <a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014)."},"day":"13","department":[{"_id":"SyCr"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","date_created":"2021-07-28T08:38:40Z","oa_version":"Published Version","doi":"10.5061/dryad.vm0vc","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.vm0vc"}],"month":"11","type":"research_data_reference","abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens."}],"oa":1,"corr_author":"1"},{"publisher":"Dryad","status":"public","citation":{"chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>.","ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, <a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","short":"M. Lagator, N. Colegrave, P. Neve, (2014).","apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>","ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.","mla":"Lagator, Mato, et al. <i>Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>."},"_id":"9741","related_material":{"record":[{"relation":"used_in_publication","id":"2036","status":"public"}]},"year":"2014","author":[{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"date_updated":"2025-09-29T11:54:45Z","date_published":"2014-08-21T00:00:00Z","abstract":[{"text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.","lang":"eng"}],"month":"08","type":"research_data_reference","oa":1,"day":"21","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"CaGu"}],"title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","main_file_link":[{"url":"https://doi.org/10.5061/dryad.85dn7","open_access":"1"}],"article_processing_charge":"No","doi":"10.5061/dryad.85dn7","date_created":"2021-07-28T08:48:06Z","oa_version":"Published Version"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"CaGu"}],"day":"17","date_created":"2021-07-28T15:32:55Z","doi":"10.5061/dryad.s42n1","oa_version":"Published Version","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.s42n1","open_access":"1"}],"title":"Data from: Role of sex and migration in adaptation to sink environments","oa":1,"month":"04","type":"research_data_reference","abstract":[{"text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.","lang":"eng"}],"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato"},{"full_name":"Morgan, Andrew","first_name":"Andrew","last_name":"Morgan"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"},{"full_name":"Colegrave, Nick","last_name":"Colegrave","first_name":"Nick"}],"year":"2014","related_material":{"record":[{"relation":"used_in_publication","id":"2083","status":"public"}]},"_id":"9747","date_published":"2014-04-17T00:00:00Z","date_updated":"2025-09-29T11:46:47Z","publisher":"Dryad","citation":{"ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, <a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>","mla":"Lagator, Mato, et al. <i>Data from: Role of Sex and Migration in Adaptation to Sink Environments</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>."},"status":"public"},{"date_published":"2014-11-07T00:00:00Z","date_updated":"2025-09-29T14:27:23Z","year":"2014","author":[{"full_name":"Simmons, Kristina","first_name":"Kristina","last_name":"Simmons"},{"full_name":"Prentice, Jason","last_name":"Prentice","first_name":"Jason"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Homann","first_name":"Jan","full_name":"Homann, Jan"},{"full_name":"Yee, Heather","first_name":"Heather","last_name":"Yee"},{"full_name":"Palmer, Stephanie","first_name":"Stephanie","last_name":"Palmer"},{"last_name":"Nelson","first_name":"Philip","full_name":"Nelson, Philip"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"}],"_id":"9752","related_material":{"record":[{"status":"public","id":"2277","relation":"used_in_publication"}]},"citation":{"ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>","mla":"Simmons, Kristina, et al. <i>Data from: Transformation of Stimulus Correlations by the Retina</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, <a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>."},"status":"public","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.246qg"}],"article_processing_charge":"No","doi":"10.5061/dryad.246qg","date_created":"2021-07-30T08:13:52Z","oa_version":"Published Version","title":"Data from: Transformation of stimulus correlations by the retina","department":[{"_id":"GaTk"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"07","oa":1,"abstract":[{"lang":"eng","text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible."}],"month":"11","type":"research_data_reference"},{"citation":{"short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies, Dryad, <a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>.","mla":"Tragust, Simon, et al. <i>Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies.” Dryad, 2014.","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2014). Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. Dryad. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>"},"status":"public","publisher":"Dryad","date_published":"2014-10-08T00:00:00Z","date_updated":"2025-09-29T14:24:12Z","author":[{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust","first_name":"Simon","full_name":"Tragust, Simon"},{"first_name":"Line V","last_name":"Ugelvig","full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883"},{"full_name":"Chapuisat, Michel","last_name":"Chapuisat","first_name":"Michel"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"},{"last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"year":"2014","related_material":{"record":[{"status":"public","id":"2284","relation":"used_in_publication"}]},"_id":"9753","oa":1,"month":"10","type":"research_data_reference","abstract":[{"text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.","lang":"eng"}],"oa_version":"Published Version","doi":"10.5061/dryad.nc0gc","date_created":"2021-07-30T08:24:11Z","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.nc0gc","open_access":"1"}],"title":"Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","department":[{"_id":"SyCr"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"08"},{"_id":"468","isi":1,"date_published":"2014-09-23T00:00:00Z","language":[{"iso":"eng"}],"publist_id":"7352","intvolume":"         9","publication_status":"published","department":[{"_id":"CampIT"}],"oa_version":"Published Version","doi":"10.1371/journal.pone.0107518","date_created":"2018-12-11T11:46:38Z","article_processing_charge":"No","title":"Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin's finches","external_id":{"isi":["000342351800025"]},"type":"journal_article","month":"09","file_date_updated":"2020-07-14T12:46:34Z","abstract":[{"lang":"eng","text":"Invasive alien parasites and pathogens are a growing threat to biodiversity worldwide, which can contribute to the extinction of endemic species. On the Galápagos Islands, the invasive parasitic fly Philornis downsi poses a major threat to the endemic avifauna. Here, we investigated the influence of this parasite on the breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea) and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island in 2010 and 2012. While the population of the small tree finch appeared to be stable, the warbler finch has experienced a dramatic decline in population size on Santa Cruz Island since 1997. We aimed to identify whether warbler finches are particularly vulnerable during different stages of the breeding cycle. Contrary to our prediction, breeding success was lower in the small tree finch than in the warbler finch. In both species P. downsi had a strong negative impact on breeding success and our data suggest that heavy rain events also lowered the fledging success. On the one hand parents might be less efficient in compensating their chicks' energy loss due to parasitism as they might be less efficient in foraging on days of heavy rain. On the other hand, intense rainfalls might lead to increased humidity and more rapid cooling of the nests. In the case of the warbler finch we found that the control of invasive plant species with herbicides had a significant additive negative impact on the breeding success. It is very likely that the availability of insects (i.e. food abundance) is lower in such controlled areas, as herbicide usage led to the removal of the entire understory. Predation seems to be a minor factor in brood loss."}],"acknowledgement":"The study was funded by the University of Vienna (Focus of Excellence grant), the Galápagos Conservation Trust, and the Ethologische Gesellschaft e.V.","pubrep_id":"954","author":[{"first_name":"Arno","last_name":"Cimadom","full_name":"Cimadom, Arno"},{"first_name":"Angel","last_name":"Ulloa","full_name":"Ulloa, Angel"},{"first_name":"Patrick","last_name":"Meidl","full_name":"Meidl, Patrick","id":"4709BCE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markus","last_name":"Zöttl","full_name":"Zöttl, Markus"},{"full_name":"Zöttl, Elisabet","first_name":"Elisabet","last_name":"Zöttl"},{"last_name":"Fessl","first_name":"Birgit","full_name":"Fessl, Birgit"},{"last_name":"Nemeth","first_name":"Erwin","full_name":"Nemeth, Erwin"},{"full_name":"Dvorak, Michael","first_name":"Michael","last_name":"Dvorak"},{"full_name":"Cunninghame, Francesca","first_name":"Francesca","last_name":"Cunninghame"},{"full_name":"Tebbich, Sabine","last_name":"Tebbich","first_name":"Sabine"}],"year":"2014","date_updated":"2025-09-29T13:19:35Z","file":[{"date_created":"2018-12-12T10:14:48Z","access_level":"open_access","date_updated":"2020-07-14T12:46:34Z","file_size":489387,"checksum":"b24e7518ccd41effed0d7d9e2498f67f","content_type":"application/pdf","file_id":"5103","relation":"main_file","file_name":"IST-2018-954-v1+1_2014_Meidl_Invasive_parasites.PDF","creator":"system"}],"publisher":"Public Library of Science","has_accepted_license":"1","scopus_import":"1","ddc":["576"],"citation":{"chicago":"Cimadom, Arno, Angel Ulloa, Patrick Meidl, Markus Zöttl, Elisabet Zöttl, Birgit Fessl, Erwin Nemeth, Michael Dvorak, Francesca Cunninghame, and Sabine Tebbich. “Invasive Parasites Habitat Change and Heavy Rainfall Reduce Breeding Success in Darwin’s Finches.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0107518\">https://doi.org/10.1371/journal.pone.0107518</a>.","short":"A. Cimadom, A. Ulloa, P. Meidl, M. Zöttl, E. Zöttl, B. Fessl, E. Nemeth, M. Dvorak, F. Cunninghame, S. Tebbich, PLoS One 9 (2014).","ista":"Cimadom A, Ulloa A, Meidl P, Zöttl M, Zöttl E, Fessl B, Nemeth E, Dvorak M, Cunninghame F, Tebbich S. 2014. Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches. PLoS One. 9(9), 0107518.","apa":"Cimadom, A., Ulloa, A., Meidl, P., Zöttl, M., Zöttl, E., Fessl, B., … Tebbich, S. (2014). Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0107518\">https://doi.org/10.1371/journal.pone.0107518</a>","mla":"Cimadom, Arno, et al. “Invasive Parasites Habitat Change and Heavy Rainfall Reduce Breeding Success in Darwin’s Finches.” <i>PLoS One</i>, vol. 9, no. 9, 0107518, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0107518\">10.1371/journal.pone.0107518</a>.","ama":"Cimadom A, Ulloa A, Meidl P, et al. Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches. <i>PLoS One</i>. 2014;9(9). doi:<a href=\"https://doi.org/10.1371/journal.pone.0107518\">10.1371/journal.pone.0107518</a>","ieee":"A. Cimadom <i>et al.</i>, “Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches,” <i>PLoS One</i>, vol. 9, no. 9. Public Library of Science, 2014."},"article_number":"0107518","publication":"PLoS One","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"23","issue":"9","volume":9,"oa":1,"quality_controlled":"1","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)"}},{"date_updated":"2025-04-14T13:51:05Z","year":"2014","author":[{"id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","full_name":"Aminof, Benjamin","first_name":"Benjamin","last_name":"Aminof"},{"id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin","first_name":"Sasha","full_name":"Rubin, Sasha"}],"ddc":["004"],"page":"83 - 90","citation":{"ista":"Aminof B, Rubin S. 2014. First cycle games. Electronic Proceedings in Theoretical Computer Science, EPTCS. SR: Strategic Reasoning, EPTCS, vol. 146, 83–90.","short":"B. Aminof, S. Rubin, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing Association, 2014, pp. 83–90.","chicago":"Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” In <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, 146:83–90. Open Publishing Association, 2014. <a href=\"https://doi.org/10.4204/EPTCS.146.11\">https://doi.org/10.4204/EPTCS.146.11</a>.","ama":"Aminof B, Rubin S. First cycle games. In: <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>. Vol 146. Open Publishing Association; 2014:83-90. doi:<a href=\"https://doi.org/10.4204/EPTCS.146.11\">10.4204/EPTCS.146.11</a>","mla":"Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, vol. 146, Open Publishing Association, 2014, pp. 83–90, doi:<a href=\"https://doi.org/10.4204/EPTCS.146.11\">10.4204/EPTCS.146.11</a>.","ieee":"B. Aminof and S. Rubin, “First cycle games,” in <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, Grenoble, France, 2014, vol. 146, pp. 83–90.","apa":"Aminof, B., &#38; Rubin, S. (2014). First cycle games. In <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i> (Vol. 146, pp. 83–90). Grenoble, France: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.146.11\">https://doi.org/10.4204/EPTCS.146.11</a>"},"publication":"Electronic Proceedings in Theoretical Computer Science, EPTCS","status":"public","ec_funded":1,"has_accepted_license":"1","scopus_import":"1","publisher":"Open Publishing Association","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:46:35Z","date_created":"2018-12-12T10:17:08Z","file_size":100115,"content_type":"application/pdf","checksum":"4d7b4ab82980cca2b96ac7703992a8c8","file_name":"IST-2018-952-v1+1_2014_Rubin_First_cycle.pdf","creator":"system","file_id":"5260","relation":"main_file"}],"conference":{"location":"Grenoble, France","end_date":"2014-04-06","start_date":"2014-04-05","name":"SR: Strategic Reasoning"},"volume":146,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["EPTCS"],"day":"01","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)"},"oa":1,"quality_controlled":"1","date_published":"2014-04-01T00:00:00Z","_id":"475","publist_id":"7345","publication_status":"published","intvolume":"       146","language":[{"iso":"eng"}],"article_processing_charge":"No","date_created":"2018-12-11T11:46:41Z","doi":"10.4204/EPTCS.146.11","oa_version":"Published Version","title":"First cycle games","department":[{"_id":"KrCh"}],"corr_author":"1","pubrep_id":"952","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"external_id":{"arxiv":["1404.0843"]},"abstract":[{"lang":"eng","text":"First cycle games (FCG) are played on a finite graph by two players who push a token along the edges until a vertex is repeated, and a simple cycle is formed. The winner is determined by some fixed property Y of the sequence of labels of the edges (or nodes) forming this cycle. These games are traditionally of interest because of their connection with infinite-duration games such as parity and mean-payoff games. We study the memory requirements for winning strategies of FCGs and certain associated infinite duration games. We exhibit a simple FCG that is not memoryless determined (this corrects a mistake in Memoryless determinacy of parity and mean payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims that FCGs for which Y is closed under cyclic permutations are memoryless determined). We show that θ (n)! memory (where n is the number of nodes in the graph), which is always sufficient, may be necessary to win some FCGs. On the other hand, we identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations, and both Y and its complement are closed under concatenation) that are sufficient to ensure that the corresponding FCGs and their associated infinite duration games are memoryless determined. We demonstrate that many games considered in the literature, such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE, solving some families of FCGs is PSPACE-hard. "}],"type":"conference","month":"04","file_date_updated":"2020-07-14T12:46:35Z","arxiv":1},{"publication_status":"published","intvolume":"        70","publist_id":"7282","language":[{"iso":"eng"}],"date_published":"2014-11-01T00:00:00Z","isi":1,"_id":"535","related_material":{"record":[{"relation":"earlier_version","id":"10905","status":"public"}]},"abstract":[{"text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help.","lang":"eng"}],"arxiv":1,"type":"journal_article","month":"11","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"external_id":{"arxiv":["1604.08234"],"isi":["000340552300005"]},"title":"Polynomial-time algorithms for energy games with special weight structures","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1604.08234","open_access":"1"}],"oa_version":"Preprint","doi":"10.1007/s00453-013-9843-7","date_created":"2018-12-11T11:47:01Z","department":[{"_id":"KrCh"}],"status":"public","publication":"Algorithmica","citation":{"short":"K. Chatterjee, M. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70 (2014) 457–492.","ista":"Chatterjee K, Henzinger M, Krinninger S, Nanongkai D. 2014. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 70(3), 457–492.","chicago":"Chatterjee, Krishnendu, Monika Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” <i>Algorithmica</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00453-013-9843-7\">https://doi.org/10.1007/s00453-013-9843-7</a>.","ieee":"K. Chatterjee, M. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” <i>Algorithmica</i>, vol. 70, no. 3. Springer, pp. 457–492, 2014.","mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” <i>Algorithmica</i>, vol. 70, no. 3, Springer, 2014, pp. 457–92, doi:<a href=\"https://doi.org/10.1007/s00453-013-9843-7\">10.1007/s00453-013-9843-7</a>.","ama":"Chatterjee K, Henzinger M, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. <i>Algorithmica</i>. 2014;70(3):457-492. doi:<a href=\"https://doi.org/10.1007/s00453-013-9843-7\">10.1007/s00453-013-9843-7</a>","apa":"Chatterjee, K., Henzinger, M., Krinninger, S., &#38; Nanongkai, D. (2014). Polynomial-time algorithms for energy games with special weight structures. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-013-9843-7\">https://doi.org/10.1007/s00453-013-9843-7</a>"},"page":"457 - 492","scopus_import":"1","ec_funded":1,"publisher":"Springer","date_updated":"2025-09-29T13:18:38Z","year":"2014","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"last_name":"Nanongkai","first_name":"Danupon","full_name":"Nanongkai, Danupon"}],"quality_controlled":"1","article_type":"original","oa":1,"volume":70,"issue":"3","day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"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)"},"oa":1,"volume":4,"issue":"15","day":"19","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Ecology and Evolution","status":"public","citation":{"short":"R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.","chicago":"Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/ece3.1150\">https://doi.org/10.1002/ece3.1150</a>.","ista":"Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.","ieee":"R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” <i>Ecology and Evolution</i>, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014.","mla":"Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” <i>Ecology and Evolution</i>, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:<a href=\"https://doi.org/10.1002/ece3.1150\">10.1002/ece3.1150</a>.","apa":"Prizak, R., Ezard, T., &#38; Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.1150\">https://doi.org/10.1002/ece3.1150</a>","ama":"Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. <i>Ecology and Evolution</i>. 2014;4(15):3139-3145. doi:<a href=\"https://doi.org/10.1002/ece3.1150\">10.1002/ece3.1150</a>"},"ddc":["530","571"],"page":"3139 - 3145","scopus_import":"1","has_accepted_license":"1","file":[{"checksum":"e32abf75a248e7a11811fd7f60858769","file_size":621582,"content_type":"application/pdf","date_created":"2018-12-12T10:11:31Z","access_level":"open_access","date_updated":"2020-07-14T12:46:38Z","relation":"main_file","file_id":"4886","creator":"system","file_name":"IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf"}],"publisher":"Wiley-Blackwell","date_updated":"2025-09-29T13:17:53Z","year":"2014","author":[{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan","full_name":"Prizak, Roshan"},{"last_name":"Ezard","first_name":"Thomas","full_name":"Ezard, Thomas"},{"last_name":"Hoyle","first_name":"Rebecca","full_name":"Hoyle, Rebecca"}],"pubrep_id":"934","abstract":[{"text":"Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:38Z","type":"journal_article","month":"07","external_id":{"isi":["000340575000015"]},"title":"Fitness consequences of maternal and grandmaternal effects","article_processing_charge":"No","oa_version":"Published Version","date_created":"2018-12-11T11:47:02Z","doi":"10.1002/ece3.1150","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publication_status":"published","intvolume":"         4","publist_id":"7280","language":[{"iso":"eng"}],"date_published":"2014-07-19T00:00:00Z","isi":1,"_id":"537"},{"abstract":[{"lang":"eng","text":"Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing.\r\nIn this paper, we study compositional properties of the IOCO-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the IOCO conformance relation, the resulting methodology can be applied to a broader class of systems."}],"type":"technical_report","file_date_updated":"2020-07-14T12:46:46Z","month":"01","oa":1,"publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"152","alternative_title":["IST Austria Technical Report"],"day":"28","department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Compositional specifications for IOCO testing","oa_version":"Published Version","date_created":"2018-12-12T11:39:11Z","doi":"10.15479/AT:IST-2014-148-v2-1","has_accepted_license":"1","file":[{"checksum":"0e03aba625cc334141a3148432aa5760","file_size":534732,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:46Z","access_level":"open_access","date_created":"2018-12-12T11:54:21Z","file_name":"IST-2014-148-v2+1_main_tr.pdf","creator":"system","file_id":"5543","relation":"main_file"}],"publisher":"IST Austria","language":[{"iso":"eng"}],"publication_status":"published","status":"public","citation":{"chicago":"Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic. <i>Compositional Specifications for IOCO Testing</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-148-v2-1\">https://doi.org/10.15479/AT:IST-2014-148-v2-1</a>.","short":"P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, Compositional Specifications for IOCO Testing, IST Austria, 2014.","ista":"Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications for IOCO testing, IST Austria, 20p.","apa":"Daca, P., Henzinger, T. A., Krenn, W., &#38; Nickovic, D. (2014). <i>Compositional specifications for IOCO testing</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-148-v2-1\">https://doi.org/10.15479/AT:IST-2014-148-v2-1</a>","ama":"Daca P, Henzinger TA, Krenn W, Nickovic D. <i>Compositional Specifications for IOCO Testing</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-148-v2-1\">10.15479/AT:IST-2014-148-v2-1</a>","ieee":"P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, <i>Compositional specifications for IOCO testing</i>. IST Austria, 2014.","mla":"Daca, Przemyslaw, et al. <i>Compositional Specifications for IOCO Testing</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-148-v2-1\">10.15479/AT:IST-2014-148-v2-1</a>."},"ddc":["000"],"page":"20","_id":"5411","related_material":{"record":[{"status":"public","relation":"later_version","id":"2167"}]},"year":"2014","author":[{"id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krenn","first_name":"Willibald","full_name":"Krenn, Willibald"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic"}],"date_updated":"2025-09-29T11:40:47Z","date_published":"2014-01-28T00:00:00Z"},{"oa":1,"month":"01","file_date_updated":"2020-07-14T12:46:47Z","type":"technical_report","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.\r\nWe introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.\r\nWe present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. "}],"pubrep_id":"153","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"day":"29","alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2014-153-v1-1","oa_version":"Published Version","date_created":"2018-12-12T11:39:11Z","title":"CEGAR for qualitative analysis of probabilistic systems","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","file_size":423322,"checksum":"4d6cda4bebed970926403ad6ad8c745f","date_created":"2018-12-12T11:53:39Z","date_updated":"2020-07-14T12:46:47Z","access_level":"open_access","relation":"main_file","file_id":"5500","creator":"system","file_name":"IST-2014-153-v1+1_main.pdf"}],"publisher":"IST Austria","has_accepted_license":"1","page":"31","ddc":["000"],"citation":{"chicago":"Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. <i>CEGAR for Qualitative Analysis of Probabilistic Systems</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-153-v1-1\">https://doi.org/10.15479/AT:IST-2014-153-v1-1</a>.","short":"K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic Systems, IST Austria, 2014.","ista":"Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic systems, IST Austria, 31p.","mla":"Chatterjee, Krishnendu, et al. <i>CEGAR for Qualitative Analysis of Probabilistic Systems</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-153-v1-1\">10.15479/AT:IST-2014-153-v1-1</a>.","apa":"Chatterjee, K., Daca, P., &#38; Chmelik, M. (2014). <i>CEGAR for qualitative analysis of probabilistic systems</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-153-v1-1\">https://doi.org/10.15479/AT:IST-2014-153-v1-1</a>","ieee":"K. Chatterjee, P. Daca, and M. Chmelik, <i>CEGAR for qualitative analysis of probabilistic systems</i>. IST Austria, 2014.","ama":"Chatterjee K, Daca P, Chmelik M. <i>CEGAR for Qualitative Analysis of Probabilistic Systems</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-153-v1-1\">10.15479/AT:IST-2014-153-v1-1</a>"},"status":"public","publication_status":"published","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"}],"year":"2014","_id":"5412","related_material":{"record":[{"status":"public","relation":"later_version","id":"5413"},{"status":"public","relation":"later_version","id":"5414"},{"id":"2063","relation":"later_version","status":"public"}]},"date_published":"2014-01-29T00:00:00Z","date_updated":"2025-04-15T07:56:48Z"}]