[{"oa_version":"Published Version","status":"public","corr_author":"1","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 &quot;hygienic behaviour&quot;-is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.","lang":"eng"}],"publication":"BMC Evolutionary Biology","file":[{"file_name":"IST-2016-402-v1+1_1471-2148-13-225.pdf","file_id":"5026","date_updated":"2020-07-14T12:45:37Z","access_level":"open_access","file_size":281736,"creator":"system","content_type":"application/pdf","relation":"main_file","checksum":"c16ef36f2a10786a7885e19c4528d707","date_created":"2018-12-12T10:13:41Z"}],"issue":"1","pubrep_id":"402","file_date_updated":"2020-07-14T12:45:37Z","language":[{"iso":"eng"}],"date_published":"2013-10-14T00:00:00Z","doi":"10.1186/1471-2148-13-225","article_processing_charge":"No","volume":13,"date_updated":"2026-07-28T09:35:11Z","isi":1,"project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"},{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"},{"_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"302004","name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach"}],"day":"14","publisher":"BioMed Central","author":[{"last_name":"Tragust","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V","last_name":"Ugelvig","full_name":"Ugelvig, Line V"},{"first_name":"Michel","last_name":"Chapuisat","full_name":"Chapuisat, Michel"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"type":"journal_article","month":"10","ddc":["570"],"acknowledgement":"The study was funded by the European Research Council (Marie Curie ERG 036569) and Marie Curie IEF 302204 to LVU\r\nCC BY 2.0\r\n","publication_status":"published","oa":1,"scopus_import":"1","year":"2013","external_id":{"isi":["000326620500001"]},"das_tickbox":"1","intvolume":"        13","related_material":{"record":[{"id":"9753","relation":"research_data","status":"public"}]},"_id":"2284","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4647","article_number":"225","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","citation":{"ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. <i>BMC Evolutionary Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-13-225\">10.1186/1471-2148-13-225</a>","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2013). Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-225\">https://doi.org/10.1186/1471-2148-13-225</a>","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2013. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 13(1), 225.","short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, BMC Evolutionary Biology 13 (2013).","mla":"Tragust, Simon, et al. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, 225, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-225\">10.1186/1471-2148-13-225</a>.","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-225\">https://doi.org/10.1186/1471-2148-13-225</a>.","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, 2013."},"date_created":"2018-12-11T11:56:46Z","department":[{"_id":"SyCr"}],"quality_controlled":"1","title":"Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies"},{"_id":"1387","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"publist_id":"5823","citation":{"short":"U. Boker, D. Kuperberg, O. Kupferman, M. Skrzypczak, 7966 (2013) 89–100.","ista":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. 2013. Nondeterminism in the presence of a diverse or unknown future. 7966(PART 2), 89–100.","ama":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. Nondeterminism in the presence of a diverse or unknown future. 2013;7966(PART 2):89-100. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>","apa":"Boker, U., Kuperberg, D., Kupferman, O., &#38; Skrzypczak, M. (2013). Nondeterminism in the presence of a diverse or unknown future. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>","ieee":"U. Boker, D. Kuperberg, O. Kupferman, and M. Skrzypczak, “Nondeterminism in the presence of a diverse or unknown future,” vol. 7966, no. PART 2. Springer, pp. 89–100, 2013.","chicago":"Boker, Udi, Denis Kuperberg, Orna Kupferman, and Michał Skrzypczak. “Nondeterminism in the Presence of a Diverse or Unknown Future.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>.","mla":"Boker, Udi, et al. <i>Nondeterminism in the Presence of a Diverse or Unknown Future</i>. Vol. 7966, no. PART 2, Springer, 2013, pp. 89–100, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>."},"has_accepted_license":"1","date_created":"2018-12-11T11:51:44Z","title":"Nondeterminism in the presence of a diverse or unknown future","department":[{"_id":"ToHe"}],"quality_controlled":"1","month":"07","acknowledgement":"This work was supported in part by the Polish Ministry of Science grant no. N206 567840, Poland’s NCN grant no. DEC-2012/05/N/ST6/03254, Austrian Science Fund NFN RiSE (Rigorous Systems Engineering), ERC Advanced Grant QUAREM (Quantitative Reactive Modeling), and ERC Grant QUALITY. The full version is available at the authors’ URLs.","publication_status":"published","ddc":["000"],"alternative_title":["LNCS"],"scopus_import":"1","oa":1,"year":"2013","intvolume":"      7966","das_tickbox":"1","date_updated":"2026-07-28T09:26:19Z","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"01","publisher":"Springer","author":[{"first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi","last_name":"Boker"},{"full_name":"Kuperberg, Denis","last_name":"Kuperberg","first_name":"Denis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"},{"first_name":"Michał","full_name":"Skrzypczak, Michał","last_name":"Skrzypczak"}],"type":"conference","conference":{"end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming","location":"Riga, Latvia","start_date":"2013-07-08"},"oa_version":"Submitted Version","series_title":"Lecture Notes in Computer Science","abstract":[{"text":"Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata.","lang":"eng"}],"status":"public","issue":"PART 2","file":[{"date_created":"2020-05-15T11:05:50Z","checksum":"98bc02e3793072e279ec8d364b381ff3","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_size":276982,"access_level":"open_access","file_name":"2013_ICALP_Boker.pdf","date_updated":"2020-07-14T12:44:48Z","file_id":"7857"}],"language":[{"iso":"eng"}],"date_published":"2013-07-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:48Z","page":"89 - 100","article_processing_charge":"No","doi":"10.1007/978-3-642-39212-2_11","volume":7966},{"conference":{"end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming","start_date":"2013-07-08","location":"Riga, Latvia"},"oa_version":"Submitted Version","status":"public","series_title":"Lecture Notes in Computer Science","abstract":[{"text":"Traditional formal methods are based on a Boolean satisfaction notion: a reactive system satisfies, or not, a given specification. We generalize formal methods to also address the quality of systems. As an adequate specification formalism we introduce the linear temporal logic LTL[F]. The satisfaction value of an LTL[F] formula is a number between 0 and 1, describing the quality of the satisfaction. The logic generalizes traditional LTL by augmenting it with a (parameterized) set F of arbitrary functions over the interval [0,1]. For example, F may contain the maximum or minimum between the satisfaction values of subformulas, their product, and their average. The classical decision problems in formal methods, such as satisfiability, model checking, and synthesis, are generalized to search and optimization problems in the quantitative setting. For example, model checking asks for the quality in which a specification is satisfied, and synthesis returns a system satisfying the specification with the highest quality. Reasoning about quality gives rise to other natural questions, like the distance between specifications. We formalize these basic questions and study them for LTL[F]. By extending the automata-theoretic approach for LTL to a setting that takes quality into an account, we are able to solve the above problems and show that reasoning about LTL[F] has roughly the same complexity as reasoning about traditional LTL.","lang":"eng"}],"file":[{"content_type":"application/pdf","file_name":"2013_ICALP_Almagor.pdf","date_updated":"2020-07-14T12:45:42Z","file_id":"7860","access_level":"open_access","file_size":363031,"creator":"dernst","relation":"main_file","date_created":"2020-05-15T11:16:12Z","checksum":"85afbf6c18a2c7e377c52c9410e2d824"}],"issue":"Part 2","file_date_updated":"2020-07-14T12:45:42Z","date_published":"2013-07-01T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","doi":"10.1007/978-3-642-39212-2_3","page":"15 - 27","volume":7966,"date_updated":"2026-07-28T09:28:40Z","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"day":"01","publisher":"Springer","author":[{"full_name":"Almagor, Shaull","last_name":"Almagor","first_name":"Shaull"},{"first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker","full_name":"Boker, Udi"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"type":"conference","month":"07","publication_status":"published","ddc":["000"],"acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering), by the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling), and the ERC Grant QUALITY. The full version is available at the authors’ URLs.","oa":1,"scopus_import":"1","alternative_title":["LNCS"],"year":"2013","das_tickbox":"1","intvolume":"      7966","_id":"2517","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"publist_id":"4384","has_accepted_license":"1","citation":{"apa":"Almagor, S., Boker, U., &#38; Kupferman, O. (2013). Formalizing and reasoning about quality. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>","ama":"Almagor S, Boker U, Kupferman O. Formalizing and reasoning about quality. 2013;7966(Part 2):15-27. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>","short":"S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27.","ista":"Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality. 7966(Part 2), 15–27.","mla":"Almagor, Shaull, et al. <i>Formalizing and Reasoning about Quality</i>. Vol. 7966, no. Part 2, Springer, 2013, pp. 15–27, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>.","ieee":"S. Almagor, U. Boker, and O. Kupferman, “Formalizing and reasoning about quality,” vol. 7966, no. Part 2. Springer, pp. 15–27, 2013.","chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “Formalizing and Reasoning about Quality.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>."},"date_created":"2018-12-11T11:58:08Z","quality_controlled":"1","department":[{"_id":"ToHe"}],"title":"Formalizing and reasoning about quality"},{"intvolume":"       200","das_tickbox":"1","external_id":{"isi":["000330955300012"]},"year":"2013","oa":1,"article_type":"original","scopus_import":"1","ddc":["580"],"acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","publication_status":"published","month":"12","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","department":[{"_id":"JiFr"}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1111/nph.12437","open_access":"1"}],"date_created":"2018-12-11T11:57:41Z","citation":{"ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>."},"ec_funded":1,"publist_id":"4460","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2443","volume":200,"page":"1034 - 1048","doi":"10.1111/nph.12437","article_processing_charge":"No","OA_type":"free access","date_published":"2013-12-01T00:00:00Z","language":[{"iso":"eng"}],"issue":"4","publication":"New Phytologist","abstract":[{"text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.","lang":"eng"}],"status":"public","oa_version":"Published Version","type":"journal_article","author":[{"orcid":"0000-0002-1998-6741","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu","last_name":"Simon"},{"first_name":"Martin","last_name":"Kubeš","full_name":"Kubeš, Martin"},{"first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","full_name":"Baster, Pawel"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"first_name":"Petre","full_name":"Dobrev, Petre","last_name":"Dobrev"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"}],"publisher":"Wiley","day":"01","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"isi":1,"date_updated":"2026-07-28T09:29:45Z"},{"month":"01","ddc":["000","004"],"acknowledgement":"This work has been supported by the European Research Council\r\nadvanced grant QUAREM, the National Research Network RiSE\r\non Rigorous Systems Engineering (Austrian Science Fund S11404-\r\nN23), and an Elise Richter Fellowship (Austrian Science Fund\r\nV00125). We thank the anonymous referees for their constructive\r\nand inspiring comments and suggestions. Ana Sokolova wishes to\r\nthank Dexter Kozen and in particular Joel Ouaknine: had they not\r\nsaved her life, she would have missed a lot of the fun involved in\r\nworking on this paper and seeing it finished.","publication_status":"published","oa":1,"scopus_import":"1","year":"2013","related_material":{"record":[{"status":"deleted","relation":"later_version","id":"10901"}]},"_id":"2181","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-1-4503-1832-7"]},"ec_funded":1,"publist_id":"4801","has_accepted_license":"1","citation":{"ista":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. 2013. Quantitative relaxation of concurrent data structures. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 317–328.","short":"T.A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, A. Sokolova, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 317–328.","apa":"Henzinger, T. A., Kirsch, C., Payer, H., Sezgin, A., &#38; Sokolova, A. (2013). Quantitative relaxation of concurrent data structures. In <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i> (pp. 317–328). Rome, Italy: ACM. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>","ama":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. Quantitative relaxation of concurrent data structures. In: <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>. ACM; 2013:317-328. doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>","chicago":"Henzinger, Thomas A, Christoph Kirsch, Hannes Payer, Ali Sezgin, and Ana Sokolova. “Quantitative Relaxation of Concurrent Data Structures.” In <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, 317–28. ACM, 2013. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>.","ieee":"T. A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, and A. Sokolova, “Quantitative relaxation of concurrent data structures,” in <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i>, Rome, Italy, 2013, pp. 317–328.","mla":"Henzinger, Thomas A., et al. “Quantitative Relaxation of Concurrent Data Structures.” <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, ACM, 2013, pp. 317–28, doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>."},"date_created":"2018-12-11T11:56:11Z","department":[{"_id":"ToHe"}],"quality_controlled":"1","title":"Quantitative relaxation of concurrent data structures","conference":{"name":"POPL: Principles of Programming Languages","start_date":"2013-01-23","location":"Rome, Italy","end_date":"2013-01-25"},"oa_version":"Submitted Version","status":"public","abstract":[{"lang":"eng","text":"There is a trade-off between performance and correctness in implementing concurrent data structures. Better performance may be achieved at the expense of relaxing correctness, by redefining the semantics of data structures. We address such a redefinition of data structure semantics and present a systematic and formal framework for obtaining new data structures by quantitatively relaxing existing ones. We view a data structure as a sequential specification S containing all &quot;legal&quot; sequences over an alphabet of method calls. Relaxing the data structure corresponds to defining a distance from any sequence over the alphabet to the sequential specification: the k-relaxed sequential specification contains all sequences over the alphabet within distance k from the original specification. In contrast to other existing work, our relaxations are semantic (distance in terms of data structure states). As an instantiation of our framework, we present two simple yet generic relaxation schemes, called out-of-order and stuttering relaxation, along with several ways of computing distances. We show that the out-of-order relaxation, when further instantiated to stacks, queues, and priority queues, amounts to tolerating bounded out-of-order behavior, which cannot be captured by a purely syntactic relaxation (distance in terms of sequence manipulation, e.g. edit distance). We give concurrent implementations of relaxed data structures and demonstrate that bounded relaxations provide the means for trading correctness for performance in a controlled way. The relaxations are monotonic which further highlights the trade-off: increasing k increases the number of permitted sequences, which as we demonstrate can lead to better performance. Finally, since a relaxed stack or queue also implements a pool, we actually have new concurrent pool implementations that outperform the state-of-the-art ones."}],"corr_author":"1","file":[{"checksum":"adf465e70948f4e80e48057524516456","date_created":"2018-12-12T10:14:33Z","relation":"main_file","creator":"system","file_size":294689,"access_level":"open_access","file_name":"IST-2014-198-v1+1_popl128-henzinger-clean.pdf","date_updated":"2020-07-14T12:45:31Z","file_id":"5086","content_type":"application/pdf"}],"publication":"Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language","file_date_updated":"2020-07-14T12:45:31Z","pubrep_id":"198","date_published":"2013-01-01T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","doi":"10.1145/2429069.2429109","page":"317 - 328","date_updated":"2026-07-28T11:18:47Z","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"day":"01","author":[{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Kirsch, Christoph","last_name":"Kirsch","first_name":"Christoph"},{"first_name":"Hannes","last_name":"Payer","full_name":"Payer, Hannes"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","full_name":"Sezgin, Ali","last_name":"Sezgin"},{"first_name":"Ana","last_name":"Sokolova","full_name":"Sokolova, Ana"}],"publisher":"ACM","type":"conference"},{"quality_controlled":"1","department":[{"_id":"ToHe"}],"title":"Synthesizing multiple boolean functions using interpolation on a single proof","date_created":"2018-12-11T11:51:43Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1308.4767"}],"citation":{"ista":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. 2013. Synthesizing multiple boolean functions using interpolation on a single proof. 2013 Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 77–84.","short":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, R. Bloem, in:, 2013 Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 77–84.","apa":"Hofferek, G., Gupta, A., Könighofer, B., Jiang, J., &#38; Bloem, R. (2013). Synthesizing multiple boolean functions using interpolation on a single proof. In <i>2013 Formal Methods in Computer-Aided Design</i> (pp. 77–84). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>","ama":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. Synthesizing multiple boolean functions using interpolation on a single proof. In: <i>2013 Formal Methods in Computer-Aided Design</i>. IEEE; 2013:77-84. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>","chicago":"Hofferek, Georg, Ashutosh Gupta, Bettina Könighofer, Jie Jiang, and Roderick Bloem. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” In <i>2013 Formal Methods in Computer-Aided Design</i>, 77–84. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>.","ieee":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, and R. Bloem, “Synthesizing multiple boolean functions using interpolation on a single proof,” in <i>2013 Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 77–84.","mla":"Hofferek, Georg, et al. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” <i>2013 Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 77–84, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>."},"publist_id":"5825","ec_funded":1,"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1385","das_tickbox":"1","year":"2013","external_id":{"arxiv":["1308.4767"]},"arxiv":1,"oa":1,"scopus_import":"1","acknowledgement":"This research was supported by the European Commission through project\r\nDIAMOND (FP7-2009-IST-4-248613), the Austrian Science Fund (FWF)\r\nthrough projects RiSE (S11406-N23) and QUAINT (I774-N23), and ERC\r\nAdvanced Grant QUAREM (Quantitative Reactive Modeling)","publication_status":"published","month":"12","type":"conference","author":[{"last_name":"Hofferek","full_name":"Hofferek, Georg","first_name":"Georg"},{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"full_name":"Könighofer, Bettina","last_name":"Könighofer","first_name":"Bettina"},{"first_name":"Jie","full_name":"Jiang, Jie","last_name":"Jiang"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"}],"publisher":"IEEE","day":"11","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"date_updated":"2026-07-28T11:20:30Z","article_processing_charge":"No","doi":"10.1109/FMCAD.2013.6679394","page":"77 - 84","OA_type":"green","language":[{"iso":"eng"}],"date_published":"2013-12-11T00:00:00Z","publication":"2013 Formal Methods in Computer-Aided Design","status":"public","abstract":[{"text":"It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results.","lang":"eng"}],"oa_version":"Preprint","conference":{"end_date":"2013-10-23","start_date":"2013-10-20","location":"Portland, OR, United States","name":"FMCAD: Formal Methods in Computer-Aided Design"}},{"volume":154,"article_processing_charge":"No","doi":"10.1016/j.cell.2013.07.037","page":"971-982","date_published":"2013-08-29T00:00:00Z","language":[{"iso":"eng"}],"OA_type":"free access","publication":"Cell","issue":"5","status":"public","abstract":[{"lang":"eng","text":"Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process."}],"oa_version":"Published Version","type":"journal_article","author":[{"first_name":"Brandon H.","full_name":"Toyama, Brandon H.","last_name":"Toyama"},{"last_name":"Savas","full_name":"Savas, Jeffrey N.","first_name":"Jeffrey N."},{"last_name":"Park","full_name":"Park, Sung Kyu","first_name":"Sung Kyu"},{"last_name":"Harris","full_name":"Harris, Michael S.","first_name":"Michael S."},{"first_name":"Nicholas T.","last_name":"Ingolia","full_name":"Ingolia, Nicholas T."},{"last_name":"Yates","full_name":"Yates, John R.","first_name":"John R."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","full_name":"HETZER, Martin W"}],"publisher":"Elsevier","day":"29","date_updated":"2026-07-28T10:15:26Z","keyword":["General Biochemistry","Genetics and Molecular Biology"],"das_tickbox":"1","intvolume":"       154","year":"2013","external_id":{"pmid":["23993091"]},"article_type":"original","scopus_import":"1","oa":1,"publication_status":"published","month":"08","quality_controlled":"1","department":[{"_id":"MaHe"}],"title":"Identification of long-lived proteins reveals exceptional stability of essential cellular structures","extern":"1","date_created":"2022-04-07T07:51:08Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.07.037"}],"citation":{"mla":"Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>, vol. 154, no. 5, Elsevier, 2013, pp. 971–82, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>.","ieee":"B. H. Toyama <i>et al.</i>, “Identification of long-lived proteins reveals exceptional stability of essential cellular structures,” <i>Cell</i>, vol. 154, no. 5. Elsevier, pp. 971–982, 2013.","chicago":"Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris, Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>.","ama":"Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. 2013;154(5):971-982. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>","apa":"Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., &#38; Hetzer, M. (2013). Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>","short":"B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates, M. Hetzer, Cell 154 (2013) 971–982.","ista":"Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 154(5), 971–982."},"pmid":1,"publication_identifier":{"issn":["0092-8674"]},"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11087"},{"has_accepted_license":"1","citation":{"mla":"Blanc, Régis, et al. <i>Tree Interpolation in Vampire</i>. Vol. 8312, Springer, 2013, pp. 173–81, doi:<a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">10.1007/978-3-642-45221-5_13</a>.","chicago":"Blanc, Régis, Ashutosh Gupta, Laura Kovács, and Bernhard Kragl. “Tree Interpolation in Vampire.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">https://doi.org/10.1007/978-3-642-45221-5_13</a>.","ieee":"R. Blanc, A. Gupta, L. Kovács, and B. Kragl, “Tree interpolation in Vampire,” vol. 8312. Springer, pp. 173–181, 2013.","ama":"Blanc R, Gupta A, Kovács L, Kragl B. Tree interpolation in Vampire. 2013;8312:173-181. doi:<a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">10.1007/978-3-642-45221-5_13</a>","apa":"Blanc, R., Gupta, A., Kovács, L., &#38; Kragl, B. (2013). Tree interpolation in Vampire. Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Stellenbosch, South Africa: Springer. <a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">https://doi.org/10.1007/978-3-642-45221-5_13</a>","ista":"Blanc R, Gupta A, Kovács L, Kragl B. 2013. Tree interpolation in Vampire. 8312, 173–181.","short":"R. Blanc, A. Gupta, L. Kovács, B. Kragl, 8312 (2013) 173–181."},"department":[{"_id":"ToHe"}],"quality_controlled":"1","title":"Tree interpolation in Vampire","date_created":"2018-12-11T11:56:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2237","publist_id":"4724","year":"2013","das_tickbox":"1","intvolume":"      8312","month":"01","scopus_import":"1","oa":1,"alternative_title":["LNCS"],"acknowledgement":"This research was partly supported by the Austrian National Research Network RiSE (FWF grants S11402-N23 and S11410-N23) and the WWTF PROSEED grant (ICT C-050).","publication_status":"published","ddc":["000"],"author":[{"first_name":"Régis","last_name":"Blanc","full_name":"Blanc, Régis"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laura","last_name":"Kovács","full_name":"Kovács, Laura"},{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl","full_name":"Kragl, Bernhard"}],"publisher":"Springer","type":"conference","date_updated":"2026-07-28T10:10:38Z","day":"14","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"file_date_updated":"2020-07-14T12:45:34Z","language":[{"iso":"eng"}],"date_published":"2013-01-14T00:00:00Z","volume":8312,"doi":"10.1007/978-3-642-45221-5_13","article_processing_charge":"No","page":"173 - 181","oa_version":"Submitted Version","conference":{"name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning","start_date":"2013-12-14","location":"Stellenbosch, South Africa","end_date":"2013-12-19"},"file":[{"content_type":"application/pdf","creator":"dernst","file_size":279206,"access_level":"open_access","file_id":"7858","date_updated":"2020-07-14T12:45:34Z","file_name":"2013_LPAR_Blanc.pdf","checksum":"9cebaafca032e6769d273f393305c705","date_created":"2020-05-15T11:10:40Z","relation":"main_file"}],"status":"public","abstract":[{"lang":"eng","text":"We describe new extensions of the Vampire theorem prover for computing tree interpolants. These extensions generalize Craig interpolation in Vampire, and can also be used to derive sequence interpolants. We evaluated our implementation on a large number of examples over the theory of linear integer arithmetic and integer-indexed arrays, with and without quantifiers. When compared to other methods, our experiments show that some examples could only be solved by our implementation."}],"series_title":"Lecture Notes in Computer Science"},{"type":"dissertation","date_created":"2018-12-11T11:51:50Z","degree_awarded":"PhD","title":"Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"doi_confirm":"1","supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"citation":{"apa":"Campinho, P. (2013). <i>Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading</i>. Institute of Science and Technology Austria.","ama":"Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.","short":"P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013.","ista":"Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.","mla":"Campinho, Pedro. <i>Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading</i>. Institute of Science and Technology Austria, 2013.","ieee":"P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013.","chicago":"Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013."},"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro","last_name":"Campinho"}],"OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"publist_id":"5801","day":"01","date_updated":"2026-07-29T10:00:09Z","_id":"1406","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"123","article_processing_charge":"No","year":"2013","language":[{"iso":"eng"}],"date_published":"2013-10-01T00:00:00Z","corr_author":"1","abstract":[{"lang":"eng","text":"Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading."}],"status":"public","publication_status":"published","alternative_title":["ISTA Thesis"],"month":"10","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa_version":"None"},{"publication":"Nature Cell Biology","corr_author":"1","abstract":[{"text":"Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly.","lang":"eng"}],"status":"public","oa_version":"Submitted Version","volume":15,"page":"1405 - 1414","article_processing_charge":"No","doi":"10.1038/ncb2869","language":[{"iso":"eng"}],"date_published":"2013-11-10T00:00:00Z","day":"10","isi":1,"project":[{"grant_number":"I930-B20","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_updated":"2026-07-29T10:07:18Z","type":"journal_article","author":[{"full_name":"Campinho, Pedro","last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","first_name":"Pedro","orcid":"0000-0002-8526-5416"},{"last_name":"Behrndt","full_name":"Behrndt, Martin","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ranft","full_name":"Ranft, Jonas","first_name":"Jonas"},{"first_name":"Thomas","last_name":"Risler","full_name":"Risler, Thomas"},{"last_name":"Minc","full_name":"Minc, Nicolas","first_name":"Nicolas"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"Nature Publishing Group","oa":1,"scopus_import":"1","publication_status":"published","acknowledgement":"This work was supported by the IST Austria and MPI-CBG ","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"month":"11","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1403"}]},"intvolume":"        15","external_id":{"isi":["000327944200005"]},"year":"2013","publist_id":"4652","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2282","title":"Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly","quality_controlled":"1","department":[{"_id":"CaHe"}],"main_file_link":[{"open_access":"1","url":"http://hal.upmc.fr/hal-00983313/"}],"date_created":"2018-12-11T11:56:45Z","citation":{"chicago":"Campinho, Pedro, Martin Behrndt, Jonas Ranft, Thomas Risler, Nicolas Minc, and Carl-Philipp J Heisenberg. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/ncb2869\">https://doi.org/10.1038/ncb2869</a>.","ieee":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, and C.-P. J. Heisenberg, “Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly,” <i>Nature Cell Biology</i>, vol. 15. Nature Publishing Group, pp. 1405–1414, 2013.","mla":"Campinho, Pedro, et al. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” <i>Nature Cell Biology</i>, vol. 15, Nature Publishing Group, 2013, pp. 1405–14, doi:<a href=\"https://doi.org/10.1038/ncb2869\">10.1038/ncb2869</a>.","ista":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. 2013. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 15, 1405–1414.","short":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, C.-P.J. Heisenberg, Nature Cell Biology 15 (2013) 1405–1414.","ama":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. <i>Nature Cell Biology</i>. 2013;15:1405-1414. doi:<a href=\"https://doi.org/10.1038/ncb2869\">10.1038/ncb2869</a>","apa":"Campinho, P., Behrndt, M., Ranft, J., Risler, T., Minc, N., &#38; Heisenberg, C.-P. J. (2013). Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2869\">https://doi.org/10.1038/ncb2869</a>"}},{"month":"12","oa":1,"scopus_import":"1","ddc":["000"],"publication_status":"published","external_id":{"isi":["000328731800009"]},"year":"2013","related_material":{"record":[{"status":"public","relation":"research_data","id":"9749"},{"relation":"dissertation_contains","status":"public","id":"1400"}]},"intvolume":"         8","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2247","article_number":"e80814","ec_funded":1,"publist_id":"4702","citation":{"ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . <i>PLoS One</i>. 2013;8(12). doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814\">10.1371/journal.pone.0080814</a>","apa":"Zagorsky, B., Reiter, J., Chatterjee, K., &#38; Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0080814\">https://doi.org/10.1371/journal.pone.0080814</a>","short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, PLoS One 8 (2013).","ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma . PLoS One. 8(12), e80814.","mla":"Zagorsky, Benjamin, et al. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” <i>PLoS One</i>, vol. 8, no. 12, e80814, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814\">10.1371/journal.pone.0080814</a>.","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma ,” <i>PLoS One</i>, vol. 8, no. 12. Public Library of Science, 2013.","chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0080814\">https://doi.org/10.1371/journal.pone.0080814</a>."},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"title":"Forgiver triumphs in alternating prisoner's dilemma ","department":[{"_id":"KrCh"}],"quality_controlled":"1","date_created":"2018-12-11T11:56:33Z","oa_version":"Published Version","issue":"12","file":[{"content_type":"application/pdf","file_id":"4868","date_updated":"2020-07-14T12:45:34Z","file_name":"IST-2016-409-v1+1_journal.pone.0080814.pdf","access_level":"open_access","creator":"system","file_size":1050042,"relation":"main_file","date_created":"2018-12-12T10:11:15Z","checksum":"808e8b9e6e89658bee4ffbbfac1bd19d"}],"publication":"PLoS One","abstract":[{"text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise.","lang":"eng"}],"status":"public","date_published":"2013-12-12T00:00:00Z","language":[{"iso":"eng"}],"pubrep_id":"409","file_date_updated":"2020-07-14T12:45:34Z","volume":8,"article_processing_charge":"No","doi":"10.1371/journal.pone.0080814","date_updated":"2026-07-29T10:15:25Z","day":"12","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"isi":1,"publisher":"Public Library of Science","author":[{"full_name":"Zagorsky, Benjamin","last_name":"Zagorsky","first_name":"Benjamin"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"type":"journal_article"},{"language":[{"iso":"eng"}],"date_published":"2013-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:51Z","pubrep_id":"415","volume":6,"page":"34 - 45","article_processing_charge":"No","doi":"10.1111/eva.12020","oa_version":"Published Version","issue":"1","publication":"Evolutionary Applications","file":[{"file_name":"IST-2016-415-v1+1_Reiter_et_al-2013-Evolutionary_Applications.pdf","date_updated":"2020-07-14T12:45:51Z","file_id":"5173","access_level":"open_access","file_size":1172037,"creator":"system","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:15:50Z","checksum":"e2955b3889f8a823c3d5a72cb16f8957"}],"corr_author":"1","abstract":[{"text":"Tumor growth is caused by the acquisition of driver mutations, which enhance the net reproductive rate of cells. Driver mutations may increase cell division, reduce cell death, or allow cells to overcome density-limiting effects. We study the dynamics of tumor growth as one additional driver mutation is acquired. Our models are based on two-type branching processes that terminate in either tumor disappearance or tumor detection. In our first model, both cell types grow exponentially, with a faster rate for cells carrying the additional driver. We find that the additional driver mutation does not affect the survival probability of the lesion, but can substantially reduce the time to reach the detectable size if the lesion is slow growing. In our second model, cells lacking the additional driver cannot exceed a fixed carrying capacity, due to density limitations. In this case, the time to detection depends strongly on this carrying capacity. Our model provides a quantitative framework for studying tumor dynamics during different stages of progression. We observe that early, small lesions need additional drivers, while late stage metastases are only marginally affected by them. These results help to explain why additional driver mutations are typically not detected in fast-growing metastases.","lang":"eng"}],"status":"public","publisher":"Wiley-Blackwell","author":[{"orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Reiter, Johannes","last_name":"Reiter"},{"first_name":"Ivana","full_name":"Božić, Ivana","last_name":"Božić"},{"full_name":"Allen, Benjamin","last_name":"Allen","first_name":"Benjamin","id":"135B5B70-E9D2-11E9-BD74-BB415DA2B523"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"type":"journal_article","date_updated":"2026-07-29T10:15:25Z","day":"01","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"}],"isi":1,"external_id":{"isi":["000313878800004"]},"year":"2013","related_material":{"record":[{"id":"1400","status":"public","relation":"dissertation_contains"}]},"intvolume":"         6","month":"01","oa":1,"scopus_import":"1","publication_status":"published","ddc":["570"],"citation":{"ieee":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, and M. Nowak, “The effect of one additional driver mutation on tumor progression,” <i>Evolutionary Applications</i>, vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013.","chicago":"Reiter, Johannes, Ivana Božić, Benjamin Allen, Krishnendu Chatterjee, and Martin Nowak. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>.","mla":"Reiter, Johannes, et al. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>, vol. 6, no. 1, Wiley-Blackwell, 2013, pp. 34–45, doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>.","short":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, M. Nowak, Evolutionary Applications 6 (2013) 34–45.","ista":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. 2013. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 6(1), 34–45.","apa":"Reiter, J., Božić, I., Allen, B., Chatterjee, K., &#38; Nowak, M. (2013). The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>","ama":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. 2013;6(1):34-45. doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>"},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"title":"The effect of one additional driver mutation on tumor progression","quality_controlled":"1","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:59:58Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2858","ec_funded":1,"publist_id":"3931"},{"department":[{"_id":"KrCh"}],"quality_controlled":"1","title":"Evolutionary dynamics of cancer in response to targeted combination therapy","date_created":"2018-12-11T11:59:45Z","has_accepted_license":"1","citation":{"ista":"Božić I, Reiter J, Allen B, Antal T, Chatterjee K, Shah P, Moon Y, Yaqubie A, Kelly N, Le D, Lipson E, Chapman P, Diaz L, Vogelstein B, Nowak M. 2013. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife. 2, e00747.","short":"I. Božić, J. Reiter, B. Allen, T. Antal, K. Chatterjee, P. Shah, Y. Moon, A. Yaqubie, N. Kelly, D. Le, E. Lipson, P. Chapman, L. Diaz, B. Vogelstein, M. Nowak, ELife 2 (2013).","ama":"Božić I, Reiter J, Allen B, et al. Evolutionary dynamics of cancer in response to targeted combination therapy. <i>eLife</i>. 2013;2. doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>","apa":"Božić, I., Reiter, J., Allen, B., Antal, T., Chatterjee, K., Shah, P., … Nowak, M. (2013). Evolutionary dynamics of cancer in response to targeted combination therapy. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>","chicago":"Božić, Ivana, Johannes Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee, Preya Shah, Yo Moon, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>. eLife Sciences Publications, 2013. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>.","ieee":"I. Božić <i>et al.</i>, “Evolutionary dynamics of cancer in response to targeted combination therapy,” <i>eLife</i>, vol. 2. eLife Sciences Publications, 2013.","mla":"Božić, Ivana, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>, vol. 2, e00747, eLife Sciences Publications, 2013, doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publist_id":"3985","article_number":"e00747","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2816","related_material":{"record":[{"id":"1400","status":"public","relation":"dissertation_contains"}]},"intvolume":"         2","year":"2013","external_id":{"isi":["000328619300005"]},"oa":1,"scopus_import":"1","publication_status":"published","ddc":["570","610"],"month":"06","type":"journal_article","publisher":"eLife Sciences Publications","author":[{"first_name":"Ivana","full_name":"Božić, Ivana","last_name":"Božić"},{"last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","last_name":"Allen","full_name":"Allen, Benjamin"},{"first_name":"Tibor","full_name":"Antal, Tibor","last_name":"Antal"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Preya","full_name":"Shah, Preya","last_name":"Shah"},{"last_name":"Moon","full_name":"Moon, Yo","first_name":"Yo"},{"first_name":"Amin","full_name":"Yaqubie, Amin","last_name":"Yaqubie"},{"full_name":"Kelly, Nicole","last_name":"Kelly","first_name":"Nicole"},{"full_name":"Le, Dung","last_name":"Le","first_name":"Dung"},{"last_name":"Lipson","full_name":"Lipson, Evan","first_name":"Evan"},{"first_name":"Paul","full_name":"Chapman, Paul","last_name":"Chapman"},{"first_name":"Luis","last_name":"Diaz","full_name":"Diaz, Luis"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"day":"25","isi":1,"date_updated":"2026-07-29T10:15:25Z","volume":2,"article_processing_charge":"No","doi":"10.7554/eLife.00747","pubrep_id":"134","file_date_updated":"2020-07-14T12:45:49Z","language":[{"iso":"eng"}],"date_published":"2013-06-25T00:00:00Z","file":[{"relation":"main_file","checksum":"2c38c47815eacd8fa66cb8b404cf7c61","date_created":"2018-12-12T10:12:48Z","content_type":"application/pdf","file_name":"IST-2013-134-v1+1_e00747.full.pdf","file_id":"4967","date_updated":"2020-07-14T12:45:49Z","access_level":"open_access","creator":"system","file_size":3358321}],"publication":"eLife","status":"public","abstract":[{"lang":"eng","text":"In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics."}],"oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2000","ec_funded":1,"publist_id":"5077","citation":{"mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, vol. 8044, Springer, 2013, pp. 101–06, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>.","ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.","chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>.","ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>","apa":"Reiter, J., Božić, I., Chatterjee, K., &#38; Nowak, M. (2013). TTP: Tool for tumor progression. In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i> (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>","short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106."},"title":"TTP: Tool for tumor progression","department":[{"_id":"KrCh"}],"quality_controlled":"1","date_created":"2018-12-11T11:55:08Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1303.5251"}],"month":"01","alternative_title":["LNCS"],"scopus_import":1,"oa":1,"publication_status":"published","external_id":{"arxiv":["1303.5251"]},"arxiv":1,"year":"2013","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5399"},{"relation":"dissertation_contains","status":"public","id":"1400"}]},"intvolume":"      8044","date_updated":"2026-07-29T10:15:25Z","day":"01","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"publisher":"Springer","type":"conference","oa_version":"Preprint","conference":{"name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia","start_date":"2013-07-13","end_date":"2013-07-19"},"publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","abstract":[{"lang":"eng","text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics."}],"series_title":"Lecture Notes in Computer Science","status":"public","language":[{"iso":"eng"}],"date_published":"2013-01-01T00:00:00Z","volume":8044,"page":"101 - 106","doi":"10.1007/978-3-642-39799-8_6"},{"intvolume":"       280","year":"2013","external_id":{"pmid":["23173202"],"isi":["000311943100012"]},"publication_status":"published","oa":1,"month":"01","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/"}],"date_created":"2018-12-11T11:46:32Z","quality_controlled":"1","department":[{"_id":"NiBa"}],"title":"Source population characteristics affect heterosis following genetic rescue of fragmented plant populations","pmid":1,"citation":{"apa":"Pickup, M., Field, D., Rowell, D., &#38; Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>","ama":"Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2013;280(1750). doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>","ista":"Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","mla":"Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750, 2058, Royal Society, 2013, doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>.","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2013. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>.","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750. Royal Society, 2013."},"article_number":"2058","publist_id":"7372","_id":"450","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1098/rspb.2012.2058","article_processing_charge":"No","volume":280,"date_published":"2013-01-07T00:00:00Z","language":[{"iso":"eng"}],"status":"public","corr_author":"1","abstract":[{"text":"Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations.","lang":"eng"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","issue":"1750","oa_version":"Submitted Version","type":"journal_article","publisher":"Royal Society","author":[{"full_name":"Pickup, Melinda","last_name":"Pickup","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Rowell","full_name":"Rowell, David","first_name":"David"},{"first_name":"Andrew","full_name":"Young, Andrew","last_name":"Young"}],"isi":1,"day":"07","date_updated":"2026-08-12T06:25:53Z"},{"department":[{"_id":"BjHo"}],"quality_controlled":"1","title":"Nature of laminar-turbulence intermittency in shear flows","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1306.5890"}],"date_created":"2018-12-11T11:59:43Z","citation":{"apa":"Avila, M., &#38; Hof, B. (2013). Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>","ama":"Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. 2013;87(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>","ista":"Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 063012.","short":"M. Avila, B. Hof, Physical Review E 87 (2013).","mla":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>, vol. 87, no. 6, 063012, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>.","chicago":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>.","ieee":"M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear flows,” <i>Physical Review E</i>, vol. 87, no. 6. American Physical Society, 2013."},"publist_id":"4074","ec_funded":1,"article_number":"063012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2811","intvolume":"        87","year":"2013","arxiv":1,"external_id":{"arxiv":["1306.5890"],"isi":["000320645700009"]},"scopus_import":"1","oa":1,"publication_status":"published","month":"06","type":"journal_article","author":[{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"publisher":"American Physical Society","day":"18","isi":1,"project":[{"grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_updated":"2026-08-12T14:29:19Z","volume":87,"article_processing_charge":"No","doi":"10.1103/PhysRevE.87.063012","date_published":"2013-06-18T00:00:00Z","language":[{"iso":"eng"}],"publication":"Physical Review E","issue":"6","status":"public","abstract":[{"text":"In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers.","lang":"eng"}],"oa_version":"Preprint"},{"place":"New York","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-06-21T11:51:58Z","_id":"10896","day":"23","edition":"1","publication_identifier":{"eisbn":["9781461439035"],"isbn":["9781461439028"]},"author":[{"id":"3C77F464-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","full_name":"zur Nedden, Stephanie","last_name":"zur Nedden"},{"first_name":"Alexander S.","last_name":"Doney","full_name":"Doney, Alexander S."},{"last_name":"Frenguelli","full_name":"Frenguelli, Bruno G.","first_name":"Bruno G."}],"publisher":"Springer","citation":{"ama":"zur Nedden S, Doney AS, Frenguelli BG. The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Masino S, Boison D, eds. <i>Adenosine</i>. 1st ed. New York: Springer; 2012:109-129. doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>","apa":"zur Nedden, S., Doney, A. S., &#38; Frenguelli, B. G. (2012). The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In S. Masino &#38; D. Boison (Eds.), <i>Adenosine</i> (1st ed., pp. 109–129). New York: Springer. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>","ista":"zur Nedden S, Doney AS, Frenguelli BG. 2012.The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Adenosine. , 109–129.","short":"S. zur Nedden, A.S. Doney, B.G. Frenguelli, in:, S. Masino, D. Boison (Eds.), Adenosine, 1st ed., Springer, New York, 2012, pp. 109–129.","mla":"zur Nedden, Stephanie, et al. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., Springer, 2012, pp. 109–29, doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>.","chicago":"Nedden, Stephanie zur, Alexander S. Doney, and Bruno G. Frenguelli. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” In <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., 109–29. New York: Springer, 2012. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>.","ieee":"S. zur Nedden, A. S. Doney, and B. G. Frenguelli, “The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books,” in <i>Adenosine</i>, 1st ed., S. Masino and D. Boison, Eds. New York: Springer, 2012, pp. 109–129."},"editor":[{"full_name":"Masino, Susan","last_name":"Masino","first_name":"Susan"},{"last_name":"Boison","full_name":"Boison, Detlev","first_name":"Detlev"}],"department":[{"_id":"HaJa"}],"quality_controlled":"1","title":"The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books","type":"book_chapter","date_created":"2022-03-21T07:16:12Z","oa_version":"None","month":"07","publication":"Adenosine","scopus_import":"1","status":"public","publication_status":"published","acknowledgement":"We are grateful to Research into Ageing/Ageing UK and The Dunhill Trust for funding SzN’s graduate studies, and to Prof Nicholas Dale for his valuable input.","abstract":[{"lang":"eng","text":"Under physiological conditions the brain, via the purine salvage pathway, reuses the preformed purine bases hypoxanthine, derived from ATP degradation, and adenine (Ade), derived from polyamine synthesis, to restore its ATP pool. However, the massive degradation of ATP during ischemia, although providing valuable neuroprotective adenosine, results in the accumulation and loss of diffusible purine metabolites and thereby leads to a protracted reduction in the post-ischemic ATP pool size. In vivo, this may both limit the ability to deploy ATP-dependent reparative mechanisms and reduce the subsequent availability of adenosine, whilst in brain slices results in tissue with substantially lower levels of ATP than in vivo. In the present review, we describe the mechanisms by which brain tissue replenishes its ATP, how this can be improved with the clinically tolerated chemicals D-ribose and adenine, and the functional, and potential therapeutic, implications of doing so."}],"date_published":"2012-07-23T00:00:00Z","language":[{"iso":"eng"}],"year":"2012","doi":"10.1007/978-1-4614-3903-5_6","article_processing_charge":"No","page":"109-129"},{"conference":{"start_date":"2012-10-03","location":"Thiruvananthapuram, India","name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2012-10-06"},"oa_version":"None","status":"public","abstract":[{"lang":"eng","text":"We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas."}],"series_title":"LNCS","corr_author":"1","publication":"Automated Technology for Verification and Analysis","language":[{"iso":"eng"}],"date_published":"2012-10-15T00:00:00Z","doi":"10.1007/978-3-642-33386-6_14","article_processing_charge":"No","page":"167-182","volume":7561,"date_updated":"2024-10-09T21:02:34Z","place":"Berlin, Heidelberg","day":"15","author":[{"first_name":"Ahmed","last_name":"Bouajjani","full_name":"Bouajjani, Ahmed"},{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","full_name":"Dragoi, Cezara","last_name":"Dragoi"},{"first_name":"Constantin","last_name":"Enea","full_name":"Enea, Constantin"},{"first_name":"Mihaela","full_name":"Sighireanu, Mihaela","last_name":"Sighireanu"}],"publisher":"Springer","type":"conference","month":"10","acknowledgement":"This work has been partially supported by the French ANR project Veridyc","publication_status":"published","scopus_import":"1","alternative_title":["LNCS"],"year":"2012","intvolume":"      7561","_id":"10903","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642333859"],"eisbn":["9783642333866"],"issn":["0302-9743"]},"citation":{"ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>","apa":"Bouajjani, A., Dragoi, C., Enea, C., &#38; Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>","short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182.","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182.","mla":"Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer, 2012, pp. 167–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>.","ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in <i>Automated Technology for Verification and Analysis</i>, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182.","chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In <i>Automated Technology for Verification and Analysis</i>, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>."},"date_created":"2022-03-21T07:58:39Z","quality_controlled":"1","department":[{"_id":"ToHe"}],"title":"Accurate invariant checking for programs manipulating lists and arrays with infinite data"},{"department":[{"_id":"MaHe"}],"quality_controlled":"1","title":"Extremely long-lived nuclear pore proteins in the rat brain","extern":"1","date_created":"2022-04-07T07:52:01Z","citation":{"short":"J.N. Savas, B.H. Toyama, T. Xu, J.R. Yates, M. Hetzer, Science 335 (2012) 942–942.","ista":"Savas JN, Toyama BH, Xu T, Yates JR, Hetzer M. 2012. Extremely long-lived nuclear pore proteins in the rat brain. Science. 335(6071), 942–942.","ama":"Savas JN, Toyama BH, Xu T, Yates JR, Hetzer M. Extremely long-lived nuclear pore proteins in the rat brain. <i>Science</i>. 2012;335(6071):942-942. doi:<a href=\"https://doi.org/10.1126/science.1217421\">10.1126/science.1217421</a>","apa":"Savas, J. N., Toyama, B. H., Xu, T., Yates, J. R., &#38; Hetzer, M. (2012). Extremely long-lived nuclear pore proteins in the rat brain. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1217421\">https://doi.org/10.1126/science.1217421</a>","ieee":"J. N. Savas, B. H. Toyama, T. Xu, J. R. Yates, and M. Hetzer, “Extremely long-lived nuclear pore proteins in the rat brain,” <i>Science</i>, vol. 335, no. 6071. American Association for the Advancement of Science, pp. 942–942, 2012.","chicago":"Savas, Jeffrey N., Brandon H. Toyama, Tao Xu, John R. Yates, and Martin Hetzer. “Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1217421\">https://doi.org/10.1126/science.1217421</a>.","mla":"Savas, Jeffrey N., et al. “Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain.” <i>Science</i>, vol. 335, no. 6071, American Association for the Advancement of Science, 2012, pp. 942–942, doi:<a href=\"https://doi.org/10.1126/science.1217421\">10.1126/science.1217421</a>."},"pmid":1,"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11092","intvolume":"       335","year":"2012","external_id":{"pmid":["22300851"]},"scopus_import":"1","article_type":"letter_note","publication_status":"published","month":"02","type":"journal_article","author":[{"full_name":"Savas, Jeffrey N.","last_name":"Savas","first_name":"Jeffrey N."},{"first_name":"Brandon H.","full_name":"Toyama, Brandon H.","last_name":"Toyama"},{"last_name":"Xu","full_name":"Xu, Tao","first_name":"Tao"},{"last_name":"Yates","full_name":"Yates, John R.","first_name":"John R."},{"orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","last_name":"HETZER"}],"publisher":"American Association for the Advancement of Science","day":"02","date_updated":"2025-12-15T10:03:06Z","volume":335,"doi":"10.1126/science.1217421","article_processing_charge":"No","page":"942-942","date_published":"2012-02-02T00:00:00Z","language":[{"iso":"eng"}],"publication":"Science","issue":"6071","status":"public","abstract":[{"lang":"eng","text":"To combat the functional decline of the proteome, cells use the process of protein turnover to replace potentially impaired polypeptides with new functional copies. We found that extremely long-lived proteins (ELLPs) did not turn over in postmitotic cells of the rat central nervous system. These ELLPs were associated with chromatin and the nuclear pore complex, the central transport channels that mediate all molecular trafficking in and out of the nucleus. The longevity of these proteins would be expected to expose them to potentially harmful metabolites, putting them at risk of accumulating damage over extended periods of time. Thus, it is possible that failure to maintain proper levels and functional integrity of ELLPs in nonproliferative cells might contribute to age-related deterioration in cell and tissue function."}],"oa_version":"None"},{"type":"journal_article","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Mateescu","full_name":"Mateescu, Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"publisher":"IEEE","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"isi":1,"day":"03","date_updated":"2025-09-29T14:17:43Z","page":"310 - 322","article_processing_charge":"No","doi":"10.1109/TCBB.2012.91","volume":10,"language":[{"iso":"eng"}],"date_published":"2012-07-03T00:00:00Z","corr_author":"1","abstract":[{"text":"We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only &quot;significant&quot; mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.","lang":"eng"}],"status":"public","issue":"2","publication":"IEEE ACM Transactions on Computational Biology and Bioinformatics","oa_version":"None","date_created":"2018-12-11T11:56:52Z","title":"The propagation approach for computing biochemical reaction networks","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"quality_controlled":"1","citation":{"apa":"Henzinger, T. A., &#38; Mateescu, M. (2012). The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>","ama":"Henzinger TA, Mateescu M. The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. 2012;10(2):310-322. doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>","ista":"Henzinger TA, Mateescu M. 2012. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 10(2), 310–322.","short":"T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology and Bioinformatics 10 (2012) 310–322.","mla":"Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>.","chicago":"Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE, 2012. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>.","ieee":"T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical reaction networks,” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2. IEEE, pp. 310–322, 2012."},"pmid":1,"ec_funded":1,"publist_id":"4625","_id":"2302","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        10","external_id":{"pmid":["22778152"],"isi":["000323504100006"]},"year":"2012","publication_status":"published","scopus_import":"1","month":"07"}]