[{"scopus_import":1,"file":[{"date_updated":"2020-07-14T12:46:00Z","content_type":"application/pdf","file_name":"IST-2014-303-v1+1_Survey_Partial-Observation_Stochastic_Parity_Games.pdf","access_level":"open_access","file_size":163983,"file_id":"4882","creator":"system","date_created":"2018-12-12T10:11:27Z","checksum":"dd3d590f383bb2ac6cfda1489ac1c42a","relation":"main_file"}],"publisher":"Springer","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T12:01:33Z","date_published":"2012-10-01T00:00:00Z","abstract":[{"text":"We consider two-player zero-sum stochastic games on graphs with ω-regular winning conditions specified as parity objectives. These games have applications in the design and control of reactive systems. We survey the complexity results for the problem of deciding the winner in such games, and in classes of interest obtained as special cases, based on the information and the power of randomization available to the players, on the class of objectives and on the winning mode. On the basis of information, these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have complete view of the game). The one-sided partial-observation games have two important subclasses: the one-player games, known as partial-observation Markov decision processes (POMDPs), and the blind one-player games, known as probabilistic automata. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. Finally, various classes of games are obtained by restricting the parity objective to a reachability, safety, Büchi, or coBüchi condition. We also consider several winning modes, such as sure-winning (i.e., all outcomes of a strategy have to satisfy the winning condition), almost-sure winning (i.e., winning with probability 1), limit-sure winning (i.e., winning with probability arbitrarily close to 1), and value-threshold winning (i.e., winning with probability at least ν, where ν is a given rational). ","lang":"eng"}],"volume":43,"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"}],"issue":"2","file_date_updated":"2020-07-14T12:46:00Z","ec_funded":1,"year":"2012","language":[{"iso":"eng"}],"day":"01","publication":"Formal Methods in System Design","pubrep_id":"303","status":"public","type":"journal_article","title":"A survey of partial-observation stochastic parity games","citation":{"ista":"Chatterjee K, Doyen L, Henzinger TA. 2012. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 43(2), 268–284.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of partial-observation stochastic parity games,” <i>Formal Methods in System Design</i>, vol. 43, no. 2. Springer, pp. 268–284, 2012.","mla":"Chatterjee, Krishnendu, et al. “A Survey of Partial-Observation Stochastic Parity Games.” <i>Formal Methods in System Design</i>, vol. 43, no. 2, Springer, 2012, pp. 268–84, doi:<a href=\"https://doi.org/10.1007/s10703-012-0164-2\">10.1007/s10703-012-0164-2</a>.","apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2012). A survey of partial-observation stochastic parity games. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-012-0164-2\">https://doi.org/10.1007/s10703-012-0164-2</a>","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Partial-Observation Stochastic Parity Games.” <i>Formal Methods in System Design</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s10703-012-0164-2\">https://doi.org/10.1007/s10703-012-0164-2</a>.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design 43 (2012) 268–284.","ama":"Chatterjee K, Doyen L, Henzinger TA. A survey of partial-observation stochastic parity games. <i>Formal Methods in System Design</i>. 2012;43(2):268-284. doi:<a href=\"https://doi.org/10.1007/s10703-012-0164-2\">10.1007/s10703-012-0164-2</a>"},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"quality_controlled":"1","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, FWF NFN Grant No. S11407-N23(RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, ERC Advanced grant QUAREM, and FWF Grant No. S11403-N23 (RiSE).","intvolume":"        43","_id":"3128","page":"268 - 284","doi":"10.1007/s10703-012-0164-2","has_accepted_license":"1","date_updated":"2021-01-12T07:41:15Z","ddc":["005"],"publication_status":"published","oa":1,"publist_id":"3570","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"10","oa_version":"Submitted Version"},{"day":"19","year":"2012","language":[{"iso":"eng"}],"author":[{"full_name":"Busaryev, Oleksiy","last_name":"Busaryev","first_name":"Oleksiy"},{"full_name":"Cabello, Sergio","first_name":"Sergio","last_name":"Cabello"},{"last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dey","first_name":"Tamal","full_name":"Dey, Tamal"},{"full_name":"Wang, Yusu","first_name":"Yusu","last_name":"Wang"}],"volume":7357,"abstract":[{"lang":"eng","text":"Let K be a simplicial complex and g the rank of its p-th homology group Hp(K) defined with ℤ2 coefficients. We show that we can compute a basis H of Hp(K) and annotate each p-simplex of K with a binary vector of length g with the following property: the annotations, summed over all p-simplices in any p-cycle z, provide the coordinate vector of the homology class [z] in the basis H. The basis and the annotations for all simplices can be computed in O(n ω ) time, where n is the size of K and ω &lt; 2.376 is a quantity so that two n×n matrices can be multiplied in O(n ω ) time. The precomputed annotations permit answering queries about the independence or the triviality of p-cycles efficiently.\r\n\r\nUsing annotations of edges in 2-complexes, we derive better algorithms for computing optimal basis and optimal homologous cycles in 1 - dimensional homology. Specifically, for computing an optimal basis of H1(K) , we improve the previously known time complexity from O(n 4) to O(n ω  + n 2 g ω − 1). Here n denotes the size of the 2-skeleton of K and g the rank of H1(K) . Computing an optimal cycle homologous to a given 1-cycle is NP-hard even for surfaces and an algorithm taking 2 O(g) nlogn time is known for surfaces. We extend this algorithm to work with arbitrary 2-complexes in O(n ω ) + 2 O(g) n 2logn time using annotations.\r\n"}],"date_published":"2012-06-19T00:00:00Z","date_created":"2018-12-11T12:01:33Z","scopus_import":1,"publisher":"Springer","main_file_link":[{"url":"http://arxiv.org/abs/1107.3793","open_access":"1"}],"oa":1,"publication_status":"published","conference":{"end_date":"2012-07-06","start_date":"2012-07-04","name":"SWAT: Symposium and Workshops on Algorithm Theory","location":"Helsinki, Finland"},"date_updated":"2021-01-12T07:41:15Z","oa_version":"Preprint","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3569","arxiv":1,"alternative_title":["LNCS"],"quality_controlled":"1","department":[{"_id":"HeEd"}],"doi":"10.1007/978-3-642-31155-0_17","external_id":{"arxiv":["1107.3793"]},"page":"189 - 200","_id":"3129","intvolume":"      7357","title":"Annotating simplices with a homology basis and its applications","type":"conference","status":"public","citation":{"mla":"Busaryev, Oleksiy, et al. <i>Annotating Simplices with a Homology Basis and Its Applications</i>. Vol. 7357, Springer, 2012, pp. 189–200, doi:<a href=\"https://doi.org/10.1007/978-3-642-31155-0_17\">10.1007/978-3-642-31155-0_17</a>.","apa":"Busaryev, O., Cabello, S., Chen, C., Dey, T., &#38; Wang, Y. (2012). Annotating simplices with a homology basis and its applications (Vol. 7357, pp. 189–200). Presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland: Springer. <a href=\"https://doi.org/10.1007/978-3-642-31155-0_17\">https://doi.org/10.1007/978-3-642-31155-0_17</a>","short":"O. Busaryev, S. Cabello, C. Chen, T. Dey, Y. Wang, in:, Springer, 2012, pp. 189–200.","ama":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. Annotating simplices with a homology basis and its applications. In: Vol 7357. Springer; 2012:189-200. doi:<a href=\"https://doi.org/10.1007/978-3-642-31155-0_17\">10.1007/978-3-642-31155-0_17</a>","chicago":"Busaryev, Oleksiy, Sergio Cabello, Chao Chen, Tamal Dey, and Yusu Wang. “Annotating Simplices with a Homology Basis and Its Applications,” 7357:189–200. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-31155-0_17\">https://doi.org/10.1007/978-3-642-31155-0_17</a>.","ista":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. 2012. Annotating simplices with a homology basis and its applications. SWAT: Symposium and Workshops on Algorithm Theory, LNCS, vol. 7357, 189–200.","ieee":"O. Busaryev, S. Cabello, C. Chen, T. Dey, and Y. Wang, “Annotating simplices with a homology basis and its applications,” presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland, 2012, vol. 7357, pp. 189–200."}},{"year":"2012","language":[{"iso":"eng"}],"day":"28","publication":"PLoS Genetics","issue":"6","file_date_updated":"2020-07-14T12:46:01Z","date_published":"2012-06-28T00:00:00Z","abstract":[{"text":"Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.","lang":"eng"}],"volume":8,"author":[{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"},{"last_name":"Silander","first_name":"Olin","full_name":"Silander, Olin"}],"date_created":"2018-12-11T12:01:34Z","publisher":"Public Library of Science","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:46:01Z","file_size":2674138,"access_level":"open_access","file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf","file_id":"4973","checksum":"f8506fb579eda6fc5613ba9bf421b86a","relation":"main_file","creator":"system","date_created":"2018-12-12T10:12:52Z"}],"scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3567","oa_version":"Published Version","month":"06","date_updated":"2021-01-12T07:41:16Z","ddc":["576"],"publication_status":"published","oa":1,"has_accepted_license":"1","article_number":"e1002803","intvolume":"         8","license":"https://creativecommons.org/licenses/by/4.0/","_id":"3130","doi":"10.1371/journal.pgen.1002803","department":[{"_id":"CaGu"}],"quality_controlled":"1","acknowledgement":"We thank Alex Boehm for discussions and comments.","citation":{"mla":"Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” <i>PLoS Genetics</i>, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002803\">10.1371/journal.pgen.1002803</a>.","apa":"Bergmiller, T., Ackermann, M., &#38; Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002803\">https://doi.org/10.1371/journal.pgen.1002803</a>","short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).","chicago":"Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002803\">https://doi.org/10.1371/journal.pgen.1002803</a>.","ama":"Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. <i>PLoS Genetics</i>. 2012;8(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002803\">10.1371/journal.pgen.1002803</a>","ieee":"T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” <i>PLoS Genetics</i>, vol. 8, no. 6. Public Library of Science, 2012.","ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803."},"pubrep_id":"386","status":"public","type":"journal_article","title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"author":[{"first_name":"Daniel","last_name":"Weissman","full_name":"Weissman, Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"volume":8,"abstract":[{"lang":"eng","text":"In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection."}],"date_published":"2012-06-07T00:00:00Z","file_date_updated":"2020-07-14T12:46:01Z","issue":"6","ec_funded":1,"publication":"PLoS Genetics","day":"07","language":[{"iso":"eng"}],"year":"2012","scopus_import":1,"file":[{"date_created":"2018-12-12T10:08:00Z","creator":"system","checksum":"729a4becda7d786c4c3db8f9a1f77953","relation":"main_file","file_id":"4659","file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf","access_level":"open_access","file_size":1284801,"date_updated":"2020-07-14T12:46:01Z","content_type":"application/pdf"}],"publisher":"Public Library of Science","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"}],"date_created":"2018-12-11T12:01:34Z","article_number":"e1002740","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["570","576"],"date_updated":"2021-01-12T07:41:17Z","oa_version":"Published Version","month":"06","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3566","title":"Limits to the rate of adaptive substitution in sexual populations","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","status":"public","pubrep_id":"114","citation":{"ieee":"D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” <i>PLoS Genetics</i>, vol. 8, no. 6. Public Library of Science, 2012.","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740.","mla":"Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” <i>PLoS Genetics</i>, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002740\">10.1371/journal.pgen.1002740</a>.","apa":"Weissman, D., &#38; Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002740\">https://doi.org/10.1371/journal.pgen.1002740</a>","ama":"Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. <i>PLoS Genetics</i>. 2012;8(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002740\">10.1371/journal.pgen.1002740</a>","short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).","chicago":"Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002740\">https://doi.org/10.1371/journal.pgen.1002740</a>."},"acknowledgement":"The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions.","quality_controlled":"1","department":[{"_id":"NiBa"}],"doi":"10.1371/journal.pgen.1002740","_id":"3131","intvolume":"         8"},{"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","month":"06","oa_version":"Preprint","language":[{"iso":"eng"}],"year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3564","day":"20","conference":{"name":"SCG: Symposium on Computational Geometry","end_date":"2012-06-20","start_date":"2012-06-17","location":"Chapel Hill, NC, USA"},"oa":1,"publication_status":"published","date_updated":"2021-01-12T07:41:17Z","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kerber","first_name":"Michael","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2012-06-20T00:00:00Z","abstract":[{"text":"This note contributes to the point calculus of persistent homology by extending Alexander duality from spaces to real-valued functions. Given a perfect Morse function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds with common boundary M, we prove elementary relationships between the persistence diagrams of f restricted to U, to V, and to M. ","lang":"eng"}],"doi":"10.1145/2261250.2261287","date_created":"2018-12-11T12:01:35Z","page":"249 - 258","_id":"3133","quality_controlled":"1","acknowledgement":"his research is partially supported by the National Science Foundation (NSF) under grant DBI-0820624, the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.\r\nThe authors thank an anonymous referee for suggesting the simplified proof of the Contravariant PE Theorem given in this paper. They also thank Frederick Cohen, Yuriy Mileyko and Amit Patel for helpful discussions.","department":[{"_id":"HeEd"}],"citation":{"short":"H. Edelsbrunner, M. Kerber, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–258.","chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” In <i>Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry </i>, 249–58. ACM, 2012. <a href=\"https://doi.org/10.1145/2261250.2261287\">https://doi.org/10.1145/2261250.2261287</a>.","ama":"Edelsbrunner H, Kerber M. Alexander duality for functions: The persistent behavior of land and water and shore. In: <i>Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry </i>. ACM; 2012:249-258. doi:<a href=\"https://doi.org/10.1145/2261250.2261287\">10.1145/2261250.2261287</a>","apa":"Edelsbrunner, H., &#38; Kerber, M. (2012). Alexander duality for functions: The persistent behavior of land and water and shore. In <i>Proceedings of the twenty-eighth annual symposium on Computational geometry </i> (pp. 249–258). Chapel Hill, NC, USA: ACM. <a href=\"https://doi.org/10.1145/2261250.2261287\">https://doi.org/10.1145/2261250.2261287</a>","mla":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” <i>Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry </i>, ACM, 2012, pp. 249–58, doi:<a href=\"https://doi.org/10.1145/2261250.2261287\">10.1145/2261250.2261287</a>.","ista":"Edelsbrunner H, Kerber M. 2012. Alexander duality for functions: The persistent behavior of land and water and shore. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 249–258.","ieee":"H. Edelsbrunner and M. Kerber, “Alexander duality for functions: The persistent behavior of land and water and shore,” in <i>Proceedings of the twenty-eighth annual symposium on Computational geometry </i>, Chapel Hill, NC, USA, 2012, pp. 249–258."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.5052"}],"publisher":"ACM","title":"Alexander duality for functions: The persistent behavior of land and water and shore","scopus_import":1,"type":"conference","status":"public"},{"date_updated":"2021-01-12T07:41:18Z","oa":1,"publication_status":"published","conference":{"location":"Berkeley, CA, USA","name":"CAV: Computer Aided Verification","start_date":"2012-07-07","end_date":"2012-07-13"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3562","oa_version":"Preprint","month":"07","alternative_title":["LNCS"],"department":[{"_id":"KrCh"}],"acknowledgement":"Tomas Brazdil, Antonin Kucera, and Petr Novotny are supported by the Czech Science Foundation, grant No. P202/10/1469. Krishnendu Chatterjee is supported by the FWF (Austrian Science Fund) NFN Grant No S11407-N23 (RiSE) and ERC Start grant (279307: Graph Games).","quality_controlled":"1","page":"23 - 38","_id":"3135","intvolume":"      7358","doi":"10.1007/978-3-642-31424-7_8","status":"public","type":"conference","title":"Efficient controller synthesis for consumption games with multiple resource types","citation":{"mla":"Brázdil, Brázdil, et al. <i>Efficient Controller Synthesis for Consumption Games with Multiple Resource Types</i>. Vol. 7358, Springer, 2012, pp. 23–38, doi:<a href=\"https://doi.org/10.1007/978-3-642-31424-7_8\">10.1007/978-3-642-31424-7_8</a>.","apa":"Brázdil, B., Chatterjee, K., Kučera, A., &#38; Novotný, P. (2012). Efficient controller synthesis for consumption games with multiple resource types (Vol. 7358, pp. 23–38). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-31424-7_8\">https://doi.org/10.1007/978-3-642-31424-7_8</a>","chicago":"Brázdil, Brázdil, Krishnendu Chatterjee, Antonín Kučera, and Petr Novotný. “Efficient Controller Synthesis for Consumption Games with Multiple Resource Types,” 7358:23–38. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-31424-7_8\">https://doi.org/10.1007/978-3-642-31424-7_8</a>.","short":"B. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, in:, Springer, 2012, pp. 23–38.","ama":"Brázdil B, Chatterjee K, Kučera A, Novotný P. Efficient controller synthesis for consumption games with multiple resource types. In: Vol 7358. Springer; 2012:23-38. doi:<a href=\"https://doi.org/10.1007/978-3-642-31424-7_8\">10.1007/978-3-642-31424-7_8</a>","ista":"Brázdil B, Chatterjee K, Kučera A, Novotný P. 2012. Efficient controller synthesis for consumption games with multiple resource types. CAV: Computer Aided Verification, LNCS, vol. 7358, 23–38.","ieee":"B. Brázdil, K. Chatterjee, A. Kučera, and P. Novotný, “Efficient controller synthesis for consumption games with multiple resource types,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 23–38."},"ec_funded":1,"day":"01","year":"2012","language":[{"iso":"eng"}],"abstract":[{"text":"We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or ω. The ω updates model the reloading of a given resource. Each vertex belongs either to player □ or player ◇, where the aim of player □ is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors) and bounded resource updates. ","lang":"eng"}],"volume":7358,"date_published":"2012-07-01T00:00:00Z","author":[{"first_name":"Brázdil","last_name":"Brázdil","full_name":"Brázdil, Brázdil"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kučera, Antonín","first_name":"Antonín","last_name":"Kučera"},{"full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","first_name":"Petr"}],"date_created":"2018-12-11T12:01:35Z","project":[{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"scopus_import":1,"publisher":"Springer","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1202.0796"}]},{"file_date_updated":"2020-07-14T12:46:01Z","author":[{"full_name":"Delahaye, Benoît","first_name":"Benoît","last_name":"Delahaye"},{"first_name":"Uli","last_name":"Fahrenberg","full_name":"Fahrenberg, Uli"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Legay, Axel","first_name":"Axel","last_name":"Legay"},{"last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"}],"volume":7273,"abstract":[{"text":"We propose synchronous interfaces, a new interface theory for discrete-time systems. We use an application to time-triggered scheduling to drive the design choices for our formalism; in particular, additionally to deriving useful mathematical properties, we focus on providing a syntax which is adapted to natural high-level system modeling. As a result, we develop an interface model that relies on a guarded-command based language and is equipped with shared variables and explicit discrete-time clocks. We define all standard interface operations: compatibility checking, composition, refinement, and shared refinement. Apart from the synchronous interface model, the contribution of this paper is the establishment of a formal relation between interface theories and real-time scheduling, where we demonstrate a fully automatic framework for the incremental computation of time-triggered schedules.","lang":"eng"}],"date_published":"2012-06-01T00:00:00Z","day":"01","year":"2012","language":[{"iso":"eng"}],"file":[{"creator":"system","date_created":"2018-12-12T10:11:25Z","relation":"main_file","checksum":"feae2e07f2d9a59843f8ddabf25d179f","file_id":"4879","file_name":"IST-2012-88-v1+1_Synchronous_interface_theories_and_time_triggered_scheduling.pdf","file_size":493198,"access_level":"open_access","date_updated":"2020-07-14T12:46:01Z","content_type":"application/pdf"}],"publisher":"Springer","scopus_import":1,"date_created":"2018-12-11T12:01:43Z","has_accepted_license":"1","alternative_title":["LNCS"],"oa_version":"Submitted Version","month":"06","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3539","publication_status":"published","oa":1,"conference":{"location":"Stockholm, Sweden","end_date":"2012-06-16","start_date":"2012-06-13","name":"FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems "},"ddc":["004"],"date_updated":"2021-01-12T07:41:26Z","citation":{"mla":"Delahaye, Benoît, et al. <i>Synchronous Interface Theories and Time Triggered Scheduling</i>. Vol. 7273, Springer, 2012, pp. 203–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-30793-5_13\">10.1007/978-3-642-30793-5_13</a>.","apa":"Delahaye, B., Fahrenberg, U., Henzinger, T. A., Legay, A., &#38; Nickovic, D. (2012). Synchronous interface theories and time triggered scheduling (Vol. 7273, pp. 203–218). Presented at the FORTE: Formal Techniques for Networked and Distributed Systems &#38; FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-642-30793-5_13\">https://doi.org/10.1007/978-3-642-30793-5_13</a>","ama":"Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. Synchronous interface theories and time triggered scheduling. In: Vol 7273. Springer; 2012:203-218. doi:<a href=\"https://doi.org/10.1007/978-3-642-30793-5_13\">10.1007/978-3-642-30793-5_13</a>","short":"B. Delahaye, U. Fahrenberg, T.A. Henzinger, A. Legay, D. Nickovic, in:, Springer, 2012, pp. 203–218.","chicago":"Delahaye, Benoît, Uli Fahrenberg, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Synchronous Interface Theories and Time Triggered Scheduling,” 7273:203–18. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-30793-5_13\">https://doi.org/10.1007/978-3-642-30793-5_13</a>.","ieee":"B. Delahaye, U. Fahrenberg, T. A. Henzinger, A. Legay, and D. Nickovic, “Synchronous interface theories and time triggered scheduling,” presented at the FORTE: Formal Techniques for Networked and Distributed Systems &#38; FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden, 2012, vol. 7273, pp. 203–218.","ista":"Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. 2012. Synchronous interface theories and time triggered scheduling. FORTE: Formal Techniques for Networked and Distributed Systems &#38; FMOODS: Formal Methods for Open Object-Based Distributed Systems , LNCS, vol. 7273, 203–218."},"title":"Synchronous interface theories and time triggered scheduling","status":"public","type":"conference","pubrep_id":"88","doi":"10.1007/978-3-642-30793-5_13","page":"203 - 218","_id":"3155","intvolume":"      7273","acknowledgement":"Research partially supported by the Danish-Chinese Center for Cyber Physical Systems (Grant No.61061130541) and VKR Center of Excellence MT-LAB.","quality_controlled":"1","department":[{"_id":"ToHe"}]},{"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"date_created":"2018-12-11T12:01:43Z","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436069/","open_access":"1"}],"pmid":1,"publisher":"Nature Publishing Group","ec_funded":1,"year":"2012","language":[{"iso":"eng"}],"day":"28","publication":"Nature","date_published":"2012-06-28T00:00:00Z","abstract":[{"text":"Colorectal tumours that are wild type for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. The simplest hypothesis to account for the development of resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that 9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between 5 and 6months following treatment. Mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. They explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion.","lang":"eng"}],"volume":486,"author":[{"full_name":"Diaz Jr, Luis","last_name":"Diaz Jr","first_name":"Luis"},{"full_name":"Williams, Richard","last_name":"Williams","first_name":"Richard"},{"last_name":"Wu","first_name":"Jian","full_name":"Wu, Jian"},{"first_name":"Isaac","last_name":"Kinde","full_name":"Kinde, Isaac"},{"last_name":"Hecht","first_name":"Joel","full_name":"Hecht, Joel"},{"last_name":"Berlin","first_name":"Jordan","full_name":"Berlin, Jordan"},{"full_name":"Allen, Benjamin","first_name":"Benjamin","last_name":"Allen"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"orcid":"0000-0002-0170-7353","first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"full_name":"Kinzler, Kenneth","first_name":"Kenneth","last_name":"Kinzler"},{"first_name":"Kelly","last_name":"Oliner","full_name":"Oliner, Kelly"},{"full_name":"Vogelstein, Bert","first_name":"Bert","last_name":"Vogelstein"}],"issue":"7404","department":[{"_id":"KrCh"}],"quality_controlled":"1","intvolume":"       486","page":"537 - 540","_id":"3157","external_id":{"pmid":["22722843"]},"doi":"10.1038/nature11219","type":"journal_article","status":"public","title":"The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers","citation":{"ieee":"L. Diaz Jr <i>et al.</i>, “The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers,” <i>Nature</i>, vol. 486, no. 7404. Nature Publishing Group, pp. 537–540, 2012.","ista":"Diaz Jr L, Williams R, Wu J, Kinde I, Hecht J, Berlin J, Allen B, Božić I, Reiter J, Nowak M, Kinzler K, Oliner K, Vogelstein B. 2012. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 486(7404), 537–540.","short":"L. Diaz Jr, R. Williams, J. Wu, I. Kinde, J. Hecht, J. Berlin, B. Allen, I. Božić, J. Reiter, M. Nowak, K. Kinzler, K. Oliner, B. Vogelstein, Nature 486 (2012) 537–540.","ama":"Diaz Jr L, Williams R, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. <i>Nature</i>. 2012;486(7404):537-540. doi:<a href=\"https://doi.org/10.1038/nature11219\">10.1038/nature11219</a>","chicago":"Diaz Jr, Luis, Richard Williams, Jian Wu, Isaac Kinde, Joel Hecht, Jordan Berlin, Benjamin Allen, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” <i>Nature</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nature11219\">https://doi.org/10.1038/nature11219</a>.","mla":"Diaz Jr, Luis, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” <i>Nature</i>, vol. 486, no. 7404, Nature Publishing Group, 2012, pp. 537–40, doi:<a href=\"https://doi.org/10.1038/nature11219\">10.1038/nature11219</a>.","apa":"Diaz Jr, L., Williams, R., Wu, J., Kinde, I., Hecht, J., Berlin, J., … Vogelstein, B. (2012). The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature11219\">https://doi.org/10.1038/nature11219</a>"},"date_updated":"2023-09-07T11:40:43Z","oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3537","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1400"}]},"month":"06","oa_version":"Submitted Version"},{"abstract":[{"lang":"eng","text":"We describe here the development and characterization of a conditionally inducible mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous actin. We have used this model to study platelets, megakaryocytes and melanoblasts and we provide evidence that Lifeact-GFP is a useful reporter in these cell types ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable by traditional methods, so conditional activation of Lifeact allows the study of actin dynamics in these cells live. We studied melanoblasts in native skin explants from embryos, allowing the visualization of live actin dynamics during cytokinesis and migration. Our study revealed that melanoblasts lacking the small GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis that accounts for the previously reported cytokinesis delay in these cells. Thus, through use of this mouse model, we were able to gain insights into the actin dynamics of cells that could only previously be studied using fixed specimens or following isolation from their native tissue environment."}],"volume":91,"date_published":"2012-11-01T00:00:00Z","author":[{"full_name":"Schachtner, Hannah","first_name":"Hannah","last_name":"Schachtner"},{"last_name":"Li","first_name":"Ang","full_name":"Li, Ang"},{"first_name":"David","last_name":"Stevenson","full_name":"Stevenson, David"},{"first_name":"Simon","last_name":"Calaminus","full_name":"Calaminus, Simon"},{"first_name":"Steven","last_name":"Thomas","full_name":"Thomas, Steven"},{"full_name":"Watson, Steve","last_name":"Watson","first_name":"Steve"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"first_name":"Roland","last_name":"Wedlich Söldner","full_name":"Wedlich Söldner, Roland"},{"first_name":"Douglas","last_name":"Strathdee","full_name":"Strathdee, Douglas"},{"full_name":"Machesky, Laura","last_name":"Machesky","first_name":"Laura"}],"issue":"11-12","day":"01","language":[{"iso":"eng"}],"year":"2012","publication":"European Journal of Cell Biology","scopus_import":1,"publisher":"Elsevier","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930012/","open_access":"1"}],"pmid":1,"date_created":"2018-12-11T12:01:44Z","date_updated":"2021-01-12T07:41:27Z","oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3534","oa_version":"Submitted Version","month":"11","status":"public","type":"journal_article","title":"Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo","citation":{"ieee":"H. Schachtner <i>et al.</i>, “Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo,” <i>European Journal of Cell Biology</i>, vol. 91, no. 11–12. Elsevier, pp. 923–929, 2012.","ista":"Schachtner H, Li A, Stevenson D, Calaminus S, Thomas S, Watson S, Sixt MK, Wedlich Söldner R, Strathdee D, Machesky L. 2012. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 91(11–12), 923–929.","short":"H. Schachtner, A. Li, D. Stevenson, S. Calaminus, S. Thomas, S. Watson, M.K. Sixt, R. Wedlich Söldner, D. Strathdee, L. Machesky, European Journal of Cell Biology 91 (2012) 923–929.","chicago":"Schachtner, Hannah, Ang Li, David Stevenson, Simon Calaminus, Steven Thomas, Steve Watson, Michael K Sixt, Roland Wedlich Söldner, Douglas Strathdee, and Laura Machesky. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” <i>European Journal of Cell Biology</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.ejcb.2012.04.002\">https://doi.org/10.1016/j.ejcb.2012.04.002</a>.","ama":"Schachtner H, Li A, Stevenson D, et al. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. <i>European Journal of Cell Biology</i>. 2012;91(11-12):923-929. doi:<a href=\"https://doi.org/10.1016/j.ejcb.2012.04.002\">10.1016/j.ejcb.2012.04.002</a>","mla":"Schachtner, Hannah, et al. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” <i>European Journal of Cell Biology</i>, vol. 91, no. 11–12, Elsevier, 2012, pp. 923–29, doi:<a href=\"https://doi.org/10.1016/j.ejcb.2012.04.002\">10.1016/j.ejcb.2012.04.002</a>.","apa":"Schachtner, H., Li, A., Stevenson, D., Calaminus, S., Thomas, S., Watson, S., … Machesky, L. (2012). Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. <i>European Journal of Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejcb.2012.04.002\">https://doi.org/10.1016/j.ejcb.2012.04.002</a>"},"department":[{"_id":"MiSi"}],"quality_controlled":"1","page":"923 - 929","_id":"3158","intvolume":"        91","doi":"10.1016/j.ejcb.2012.04.002","external_id":{"pmid":["22658956"]}},{"citation":{"mla":"Mileyko, Yuriy, et al. “Hierarchical Ordering of Reticular Networks.” <i>PLoS One</i>, vol. 7, no. 6, e36715, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pone.0036715\">10.1371/journal.pone.0036715</a>.","apa":"Mileyko, Y., Edelsbrunner, H., Price, C., &#38; Weitz, J. (2012). Hierarchical ordering of reticular networks. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0036715\">https://doi.org/10.1371/journal.pone.0036715</a>","chicago":"Mileyko, Yuriy, Herbert Edelsbrunner, Charles Price, and Joshua Weitz. “Hierarchical Ordering of Reticular Networks.” <i>PLoS One</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pone.0036715\">https://doi.org/10.1371/journal.pone.0036715</a>.","short":"Y. Mileyko, H. Edelsbrunner, C. Price, J. Weitz, PLoS One 7 (2012).","ama":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. Hierarchical ordering of reticular networks. <i>PLoS One</i>. 2012;7(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0036715\">10.1371/journal.pone.0036715</a>","ista":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. 2012. Hierarchical ordering of reticular networks. PLoS One. 7(6), e36715.","ieee":"Y. Mileyko, H. Edelsbrunner, C. Price, and J. Weitz, “Hierarchical ordering of reticular networks,” <i>PLoS One</i>, vol. 7, no. 6. Public Library of Science, 2012."},"pubrep_id":"385","status":"public","type":"journal_article","title":"Hierarchical ordering of reticular networks","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"         7","_id":"3159","doi":"10.1371/journal.pone.0036715","department":[{"_id":"HeEd"}],"quality_controlled":"1","acknowledgement":"his work was supported by the National Science Foundation Plant Genome Research Program (grant 0820624 to H.E. and J.S.W.), the Defense Advanced Projects Research Agency (grant HR0011-09-1-0055 to H.E. and J.S.W.), and the European Science Foundation (under the Research Networking Programme on “Applied and Computational Algebraic Topology” run by H.E.). Joshua S. Weitz, Ph.D., holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.\r\n\r\n\r\n\r\nDuring preparation of this manuscript the authors became aware of a related work by Katifori and Magnasco (arXiv:1110.1412v1), concurrently submitted and accepted for publication in PLoS ONE.","has_accepted_license":"1","article_number":"e36715","publist_id":"3530","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"06","oa_version":"Published Version","ddc":["510"],"date_updated":"2021-01-12T07:41:28Z","publication_status":"published","oa":1,"file":[{"relation":"main_file","checksum":"515a98ad72e470752f03f13663dcaff8","date_created":"2019-02-05T12:38:43Z","creator":"kschuh","file_id":"5922","file_size":541583,"access_level":"open_access","file_name":"2012_PLoS_Mileyko.PDF","content_type":"application/pdf","date_updated":"2020-07-14T12:46:01Z"}],"publisher":"Public Library of Science","scopus_import":1,"date_created":"2018-12-11T12:01:44Z","issue":"6","file_date_updated":"2020-07-14T12:46:01Z","date_published":"2012-06-06T00:00:00Z","volume":7,"abstract":[{"lang":"eng","text":"The structure of hierarchical networks in biological and physical systems has long been characterized using the Horton-Strahler ordering scheme. The scheme assigns an integer order to each edge in the network based on the topology of branching such that the order increases from distal parts of the network (e.g., mountain streams or capillaries) to the &quot;root&quot; of the network (e.g., the river outlet or the aorta). However, Horton-Strahler ordering cannot be applied to networks with loops because they they create a contradiction in the edge ordering in terms of which edge precedes another in the hierarchy. Here, we present a generalization of the Horton-Strahler order to weighted planar reticular networks, where weights are assumed to correlate with the importance of network edges, e.g., weights estimated from edge widths may correlate to flow capacity. Our method assigns hierarchical levels not only to edges of the network, but also to its loops, and classifies the edges into reticular edges, which are responsible for loop formation, and tree edges. In addition, we perform a detailed and rigorous theoretical analysis of the sensitivity of the hierarchical levels to weight perturbations. In doing so, we show that the ordering of the reticular edges is more robust to noise in weight estimation than is the ordering of the tree edges. We discuss applications of this generalized Horton-Strahler ordering to the study of leaf venation and other biological networks."}],"author":[{"first_name":"Yuriy","last_name":"Mileyko","full_name":"Mileyko, Yuriy"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"last_name":"Price","first_name":"Charles","full_name":"Price, Charles"},{"last_name":"Weitz","first_name":"Joshua","full_name":"Weitz, Joshua"}],"year":"2012","language":[{"iso":"eng"}],"day":"06","publication":"PLoS One"},{"title":"Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pubrep_id":"97","type":"journal_article","status":"public","citation":{"apa":"Vyleta, M., Wong, J., &#38; Magun, B. (2012). Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0036044\">https://doi.org/10.1371/journal.pone.0036044</a>","mla":"Vyleta, Meghan, et al. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” <i>PLoS One</i>, vol. 7, no. 5, e36044, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pone.0036044\">10.1371/journal.pone.0036044</a>.","chicago":"Vyleta, Meghan, John Wong, and Bruce Magun. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” <i>PLoS One</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pone.0036044\">https://doi.org/10.1371/journal.pone.0036044</a>.","short":"M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012).","ama":"Vyleta M, Wong J, Magun B. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. <i>PLoS One</i>. 2012;7(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0036044\">10.1371/journal.pone.0036044</a>","ieee":"M. Vyleta, J. Wong, and B. Magun, “Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome,” <i>PLoS One</i>, vol. 7, no. 5. Public Library of Science, 2012.","ista":"Vyleta M, Wong J, Magun B. 2012. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 7(5), e36044."},"quality_controlled":"1","acknowledgement":"Supported by National Institutes of Health grants GM071338 (ML) and AI059355 (BM).\r\nWe acknowledge the expertise of Dr. Martina Ralle in Department of Biochemistry and Molecular Biology at OHSU for measurements of potassium using inductively coupled plasma mass spectrometry.","department":[{"_id":"SyCr"}],"doi":"10.1371/journal.pone.0036044","intvolume":"         7","_id":"3161","article_number":"e36044","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["610"],"date_updated":"2021-01-12T07:41:29Z","oa_version":"Published Version","month":"05","publist_id":"3526","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publisher":"Public Library of Science","file":[{"creator":"system","date_created":"2018-12-12T10:14:30Z","relation":"main_file","checksum":"30cef37e27eaa467f6571b3640282010","file_id":"5082","file_name":"IST-2012-97-v1+1_journal.pone.0036044.pdf","access_level":"open_access","file_size":2984012,"date_updated":"2020-07-14T12:46:01Z","content_type":"application/pdf"}],"date_created":"2018-12-11T12:01:45Z","author":[{"last_name":"Vyleta","first_name":"Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Meghan"},{"first_name":"John","last_name":"Wong","full_name":"Wong, John"},{"last_name":"Magun","first_name":"Bruce","full_name":"Magun, Bruce"}],"date_published":"2012-05-14T00:00:00Z","abstract":[{"text":"Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by inducing efflux of cellular potassium. Loss of cellular potassium is known to potently suppress protein synthesis, leading us to test whether the inhibition of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome. Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide, puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin, ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of IL-1ß from cells in response to these agents was detected by immunoblotting and ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition of translation by each of the tested translation inhibitors led to processing of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger efflux of intracellular potassium, the addition of high extracellular potassium suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA, which are known to activate the NLRP3 inflammasome, also substantially inhibited protein translation, supporting a close association between inhibition of translation and inflammasome activation. These data demonstrate that translational inhibition itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent inflammatory signaling and that other physical, chemical, or pathogen-associated agents that impair translation may lead to IL-1ß-dependent inflammation through activation of the NLRP3 inflammasome. For agents that inhibit translation through decreased cellular potassium, the application of high extracellular potassium restores protein translation and suppresses activation of the NLRP inflammasome. For agents that inhibit translation through mechanisms that do not involve loss of potassium, high extracellular potassium suppresses IL-1ß processing through a mechanism that remains undefined.","lang":"eng"}],"volume":7,"file_date_updated":"2020-07-14T12:46:01Z","issue":"5","publication":"PLoS One","year":"2012","language":[{"iso":"eng"}],"day":"14"},{"file":[{"creator":"dernst","date_created":"2020-05-15T12:50:15Z","checksum":"ba4a75287008fc64b8fbf78a7476ec32","relation":"main_file","file_id":"7862","file_name":"2012_RV_Asarin.pdf","access_level":"open_access","file_size":374726,"date_updated":"2020-07-14T12:46:01Z","content_type":"application/pdf"}],"publisher":"Springer","scopus_import":1,"date_created":"2018-12-11T12:01:45Z","file_date_updated":"2020-07-14T12:46:01Z","date_published":"2012-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"Given a dense-time real-valued signal and a parameterized temporal logic formula with both magnitude and timing parameters, we compute the subset of the parameter space that renders the formula satisfied by the trace. We provide two preliminary implementations, one which follows the exact semantics and attempts to compute the validity domain by quantifier elimination in linear arithmetics and one which conducts adaptive search in the parameter space."}],"volume":7186,"author":[{"full_name":"Asarin, Eugene","first_name":"Eugene","last_name":"Asarin"},{"first_name":"Alexandre","last_name":"Donzé","full_name":"Donzé, Alexandre"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"}],"year":"2012","language":[{"iso":"eng"}],"day":"01","citation":{"ista":"Asarin E, Donzé A, Maler O, Nickovic D. 2012. Parametric identification of temporal properties. RV: Runtime Verification, LNCS, vol. 7186, 147–160.","ieee":"E. Asarin, A. Donzé, O. Maler, and D. Nickovic, “Parametric identification of temporal properties,” presented at the RV: Runtime Verification, San Francisco, CA, United States, 2012, vol. 7186, pp. 147–160.","short":"E. Asarin, A. Donzé, O. Maler, D. Nickovic, in:, Springer, 2012, pp. 147–160.","ama":"Asarin E, Donzé A, Maler O, Nickovic D. Parametric identification of temporal properties. In: Vol 7186. Springer; 2012:147-160. doi:<a href=\"https://doi.org/10.1007/978-3-642-29860-8_12\">10.1007/978-3-642-29860-8_12</a>","chicago":"Asarin, Eugene, Alexandre Donzé, Oded Maler, and Dejan Nickovic. “Parametric Identification of Temporal Properties,” 7186:147–60. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-29860-8_12\">https://doi.org/10.1007/978-3-642-29860-8_12</a>.","apa":"Asarin, E., Donzé, A., Maler, O., &#38; Nickovic, D. (2012). Parametric identification of temporal properties (Vol. 7186, pp. 147–160). Presented at the RV: Runtime Verification, San Francisco, CA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-642-29860-8_12\">https://doi.org/10.1007/978-3-642-29860-8_12</a>","mla":"Asarin, Eugene, et al. <i>Parametric Identification of Temporal Properties</i>. Vol. 7186, Springer, 2012, pp. 147–60, doi:<a href=\"https://doi.org/10.1007/978-3-642-29860-8_12\">10.1007/978-3-642-29860-8_12</a>."},"article_processing_charge":"No","status":"public","type":"conference","title":"Parametric identification of temporal properties","intvolume":"      7186","page":"147 - 160","_id":"3162","doi":"10.1007/978-3-642-29860-8_12","department":[{"_id":"ToHe"}],"quality_controlled":"1","alternative_title":["LNCS"],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3525","month":"01","oa_version":"Submitted Version","date_updated":"2021-01-12T07:41:29Z","ddc":["000"],"conference":{"location":"San Francisco, CA, United States","start_date":"2011-09-27","name":"RV: Runtime Verification","end_date":"2011-09-30"},"oa":1,"publication_status":"published"},{"arxiv":1,"related_material":{"record":[{"status":"public","id":"5379","relation":"earlier_version"},{"id":"2141","relation":"later_version","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3519","oa_version":"None","month":"01","date_updated":"2025-06-02T08:53:48Z","publication_status":"published","oa":1,"conference":{"location":"Kyoto, Japan","start_date":"2012-01-17","name":"SODA: Symposium on Discrete Algorithms","end_date":"2012-01-19"},"article_processing_charge":"No","citation":{"apa":"Chatterjee, K., &#38; Henzinger, M. H. (2012). An O(n2) time algorithm for alternating Büchi games. In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 1386–1399). Kyoto, Japan: SIAM. <a href=\"https://doi.org/10.1137/1.9781611973099.109\">https://doi.org/10.1137/1.9781611973099.109</a>","mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, SIAM, 2012, pp. 1386–99, doi:<a href=\"https://doi.org/10.1137/1.9781611973099.109\">10.1137/1.9781611973099.109</a>.","chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 1386–99. SIAM, 2012. <a href=\"https://doi.org/10.1137/1.9781611973099.109\">https://doi.org/10.1137/1.9781611973099.109</a>.","short":"K. Chatterjee, M.H. Henzinger, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2012, pp. 1386–1399.","ama":"Chatterjee K, Henzinger MH. An O(n2) time algorithm for alternating Büchi games. In: <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>. SIAM; 2012:1386-1399. doi:<a href=\"https://doi.org/10.1137/1.9781611973099.109\">10.1137/1.9781611973099.109</a>","ieee":"K. Chatterjee and M. H. Henzinger, “An O(n2) time algorithm for alternating Büchi games,” in <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Kyoto, Japan, 2012, pp. 1386–1399.","ista":"Chatterjee K, Henzinger MH. 2012. An O(n2) time algorithm for alternating Büchi games. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1386–1399."},"type":"conference","status":"public","pubrep_id":"15","title":"An O(n2) time algorithm for alternating Büchi games","_id":"3165","page":"1386 - 1399","doi":"10.1137/1.9781611973099.109","external_id":{"arxiv":["1109.5018"]},"department":[{"_id":"KrCh"}],"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, Vienna Science and Technology Fund (WWTF) Grant ICT10-002, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","quality_controlled":"1","abstract":[{"text":"Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is Õ(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n·m) boundary by presenting a new technique that reduces the running time to O(n 2). This bound also leads to O(n 2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n 3)), and (3) in Markov decision processes (improving for m &gt; n 4/3 an earlier bound of O(min(m 1.5, m·n 2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n 2), which is an improvement over earlier bounds for m &gt; n 4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem.","lang":"eng"}],"date_published":"2012-01-01T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H"}],"day":"01","year":"2012","language":[{"iso":"eng"}],"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","ec_funded":1,"publisher":"SIAM","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1109.5018"}],"date_created":"2018-12-11T12:01:46Z","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}]},{"file_date_updated":"2020-07-14T12:46:02Z","author":[{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","last_name":"Vladar","first_name":"Harold"}],"date_published":"2012-02-10T00:00:00Z","abstract":[{"text":"There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)","lang":"eng"}],"volume":7,"publication":"Biology Direct","year":"2012","language":[{"iso":"eng"}],"day":"10","ec_funded":1,"publisher":"BioMed Central","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:46:02Z","file_size":4099536,"access_level":"open_access","file_name":"IST-2012-99-v1+1_1745-6150-7-6.pdf","file_id":"5166","relation":"main_file","checksum":"e511e401e239ef608a7fd79b21a06d78","date_created":"2018-12-12T10:15:44Z","creator":"system"}],"date_created":"2018-12-11T12:01:46Z","project":[{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","article_number":"6","oa_version":"Published Version","month":"02","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3518","publication_status":"published","oa":1,"date_updated":"2021-01-12T07:41:31Z","ddc":["570","576"],"citation":{"ama":"de Vladar H. Amino acid fermentation at the origin of the genetic code. <i>Biology Direct</i>. 2012;7. doi:<a href=\"https://doi.org/10.1186/1745-6150-7-6\">10.1186/1745-6150-7-6</a>","short":"H. de Vladar, Biology Direct 7 (2012).","chicago":"Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” <i>Biology Direct</i>. BioMed Central, 2012. <a href=\"https://doi.org/10.1186/1745-6150-7-6\">https://doi.org/10.1186/1745-6150-7-6</a>.","apa":"de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-7-6\">https://doi.org/10.1186/1745-6150-7-6</a>","mla":"de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” <i>Biology Direct</i>, vol. 7, 6, BioMed Central, 2012, doi:<a href=\"https://doi.org/10.1186/1745-6150-7-6\">10.1186/1745-6150-7-6</a>.","ista":"de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6.","ieee":"H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” <i>Biology Direct</i>, vol. 7. BioMed Central, 2012."},"title":"Amino acid fermentation at the origin of the genetic code","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pubrep_id":"99","status":"public","type":"journal_article","doi":"10.1186/1745-6150-7-6","intvolume":"         7","_id":"3166","quality_controlled":"1","acknowledgement":"The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ","department":[{"_id":"NiBa"}]},{"ec_funded":1,"publication":"PLoS Biology","day":"03","language":[{"iso":"eng"}],"year":"2012","author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias","first_name":"Matthias","last_name":"Konrad"},{"id":"418901AA-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Meghan","last_name":"Vyleta","first_name":"Meghan"},{"full_name":"Theis, Fabian","last_name":"Theis","first_name":"Fabian"},{"first_name":"Miriam","last_name":"Stock","full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Klatt","first_name":"Martina","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38","full_name":"Klatt, Martina"},{"last_name":"Drescher","first_name":"Verena","full_name":"Drescher, Verena"},{"full_name":"Marr, Carsten","last_name":"Marr","first_name":"Carsten"},{"last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"volume":10,"abstract":[{"text":"Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”).","lang":"eng"}],"date_published":"2012-04-03T00:00:00Z","file_date_updated":"2020-07-14T12:46:04Z","issue":"4","project":[{"name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1"},{"call_identifier":"FP7","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"name":"Antnet","_id":"25E0E184-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T12:02:13Z","scopus_import":1,"publisher":"Public Library of Science","file":[{"file_id":"4689","date_created":"2018-12-12T10:08:28Z","creator":"system","checksum":"4ebacefd9fbab5c68adf829124115fd1","relation":"main_file","date_updated":"2020-07-14T12:46:04Z","content_type":"application/pdf","file_name":"IST-2012-96-v1+1_journal.pbio.1001300.pdf","access_level":"open_access","file_size":674228}],"oa":1,"publication_status":"published","date_updated":"2023-02-23T14:07:11Z","ddc":["570","579"],"month":"04","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"9755","relation":"research_data"}]},"publist_id":"3434","article_number":"e1001300","has_accepted_license":"1","acknowledgement":"Funding for this project was obtained by the German Research Foundation DFG (http://www.dfg.de/en/index.jsp) as an Individual Research Grant (CR118/2-1 to SC) and the European Research Council (http://erc.europa.eu/) in form of two ERC Starting Grants (ERC-2009-StG240371-SocialVaccines to SC and ERC-2010-StG259294-LatentCauses to FJT). In addition, the Junge Akademie (Young Academy of the Berlin-Brandenburg Academy of Sciences and Humanities and the National Academy of Sciences Leopoldina (http://www.diejungeakademie.de/english/i​ndex.html) funded this joint Antnet project of SC and FJT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","quality_controlled":"1","department":[{"_id":"SyCr"}],"doi":"10.1371/journal.pbio.1001300","_id":"3242","intvolume":"        10","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Social transfer of pathogenic fungus promotes active immunisation in ant colonies","status":"public","type":"journal_article","pubrep_id":"96","citation":{"apa":"Konrad, M., Vyleta, M., Theis, F., Stock, M., Tragust, S., Klatt, M., … Cremer, S. (2012). Social transfer of pathogenic fungus promotes active immunisation in ant colonies. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001300\">https://doi.org/10.1371/journal.pbio.1001300</a>","mla":"Konrad, Matthias, et al. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” <i>PLoS Biology</i>, vol. 10, no. 4, e1001300, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001300\">10.1371/journal.pbio.1001300</a>.","ama":"Konrad M, Vyleta M, Theis F, et al. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. <i>PLoS Biology</i>. 2012;10(4). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001300\">10.1371/journal.pbio.1001300</a>","chicago":"Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Simon Tragust, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” <i>PLoS Biology</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pbio.1001300\">https://doi.org/10.1371/journal.pbio.1001300</a>.","short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, S. Tragust, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, PLoS Biology 10 (2012).","ista":"Konrad M, Vyleta M, Theis F, Stock M, Tragust S, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 10(4), e1001300.","ieee":"M. Konrad <i>et al.</i>, “Social transfer of pathogenic fungus promotes active immunisation in ant colonies,” <i>PLoS Biology</i>, vol. 10, no. 4. Public Library of Science, 2012."}},{"publication":"Büchereiperspektiven","language":[{"iso":"ger"}],"year":"2012","day":"01","issue":"1","author":[{"full_name":"Danowski, Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick","last_name":"Danowski","orcid":"0000-0002-6026-4409"}],"date_published":"2012-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"Wie wandelt sich das Berufsbild in Wissenschaftlichen Bibliotheken? Patrick Danowski gibt seine Einschätzung ab. "}],"volume":2012,"article_type":"letter_note","date_created":"2018-12-11T12:02:13Z","main_file_link":[{"open_access":"1","url":"https://www.bvoe.at/sites/default/files/2022-07/BP_1_12.pdf"}],"publisher":"Büchereiverband Österreichs","oa_version":"Published Version","month":"03","publist_id":"3433","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"publication_identifier":{"issn":["1607-7172"]},"date_updated":"2023-10-16T10:40:18Z","intvolume":"      2012","page":"11","_id":"3243","department":[{"_id":"E-Lib"}],"citation":{"ista":"Danowski P. 2012. Zwischen Technologie und Information. Büchereiperspektiven. 2012(1), 11.","ieee":"P. Danowski, “Zwischen Technologie und Information,” <i>Büchereiperspektiven</i>, vol. 2012, no. 1. Büchereiverband Österreichs, p. 11, 2012.","chicago":"Danowski, Patrick. “Zwischen Technologie und Information.” <i>Büchereiperspektiven</i>. Büchereiverband Österreichs, 2012.","ama":"Danowski P. Zwischen Technologie und Information. <i>Büchereiperspektiven</i>. 2012;2012(1):11.","short":"P. Danowski, Büchereiperspektiven 2012 (2012) 11.","mla":"Danowski, Patrick. “Zwischen Technologie und Information.” <i>Büchereiperspektiven</i>, vol. 2012, no. 1, Büchereiverband Österreichs, 2012, p. 11.","apa":"Danowski, P. (2012). Zwischen Technologie und Information. <i>Büchereiperspektiven</i>. Büchereiverband Österreichs."},"article_processing_charge":"No","title":"Zwischen Technologie und Information","type":"journal_article","popular_science":"1","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3432","month":"04","oa_version":"Published Version","publication_identifier":{"issn":["1869 -1137"]},"date_updated":"2023-10-16T10:19:14Z","publication_status":"published","oa":1,"intvolume":"        64","page":"284","_id":"3244","department":[{"_id":"E-Lib"}],"article_processing_charge":"No","citation":{"short":"P. Danowski, BuB - Forum Bibliothek und Information 64 (2012) 284.","chicago":"Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” <i>BuB - Forum Bibliothek und Information</i>. Fachzeitschrift des BIB – Berufsverband Information Bibliothek, 2012.","ama":"Danowski P. Die Zeit des Abwartens ist vorbei! <i>BuB - Forum Bibliothek und Information</i>. 2012;64(4):284.","apa":"Danowski, P. (2012). Die Zeit des Abwartens ist vorbei! <i>BuB - Forum Bibliothek und Information</i>. Fachzeitschrift des BIB – Berufsverband Information Bibliothek.","mla":"Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” <i>BuB - Forum Bibliothek und Information</i>, vol. 64, no. 4, Fachzeitschrift des BIB – Berufsverband Information Bibliothek, 2012, p. 284.","ista":"Danowski P. 2012. Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek und Information. 64(4), 284.","ieee":"P. Danowski, “Die Zeit des Abwartens ist vorbei!,” <i>BuB - Forum Bibliothek und Information</i>, vol. 64, no. 4. Fachzeitschrift des BIB – Berufsverband Information Bibliothek, p. 284, 2012."},"type":"journal_article","popular_science":"1","status":"public","title":"Die Zeit des Abwartens ist vorbei!","year":"2012","language":[{"iso":"ger"}],"day":"15","publication":"BuB - Forum Bibliothek und Information","issue":"4","date_published":"2012-04-15T00:00:00Z","abstract":[{"text":"Bibliothekare haben die Aufgabe, sich mit neuen Medienformen auseinanderzusetzen.\r\n","lang":"eng"}],"volume":64,"author":[{"orcid":"0000-0002-6026-4409","first_name":"Patrick","last_name":"Danowski","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick"}],"article_type":"letter_note","date_created":"2018-12-11T12:02:13Z","main_file_link":[{"open_access":"1","url":"https://www.b-u-b.de/fileadmin/archiv/imports/pdf_files/2012/bub_2012_04_284.pdf"}],"publisher":"Fachzeitschrift des BIB – Berufsverband Information Bibliothek"},{"publication_status":"published","oa":1,"date_updated":"2022-05-24T08:05:40Z","ddc":["000"],"publication_identifier":{"eissn":["1861-8219"],"issn":["1861-8200"]},"oa_version":"Submitted Version","month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3417","has_accepted_license":"1","quality_controlled":"1","department":[{"_id":"ChLa"}],"doi":"10.1007/s11554-010-0168-3","_id":"3248","page":"31 - 41","intvolume":"         7","title":"Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"ieee":"C. Lampert and J. Peters, “Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components,” <i>Journal of Real-Time Image Processing</i>, vol. 7, no. 1. Springer, pp. 31–41, 2012.","ista":"Lampert C, Peters J. 2012. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 7(1), 31–41.","chicago":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” <i>Journal of Real-Time Image Processing</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s11554-010-0168-3\">https://doi.org/10.1007/s11554-010-0168-3</a>.","ama":"Lampert C, Peters J. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. <i>Journal of Real-Time Image Processing</i>. 2012;7(1):31-41. doi:<a href=\"https://doi.org/10.1007/s11554-010-0168-3\">10.1007/s11554-010-0168-3</a>","short":"C. Lampert, J. Peters, Journal of Real-Time Image Processing 7 (2012) 31–41.","apa":"Lampert, C., &#38; Peters, J. (2012). Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. <i>Journal of Real-Time Image Processing</i>. Springer. <a href=\"https://doi.org/10.1007/s11554-010-0168-3\">https://doi.org/10.1007/s11554-010-0168-3</a>","mla":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” <i>Journal of Real-Time Image Processing</i>, vol. 7, no. 1, Springer, 2012, pp. 31–41, doi:<a href=\"https://doi.org/10.1007/s11554-010-0168-3\">10.1007/s11554-010-0168-3</a>."},"publication":"Journal of Real-Time Image Processing","day":"01","year":"2012","language":[{"iso":"eng"}],"author":[{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887"},{"full_name":"Peters, Jan","first_name":"Jan","last_name":"Peters"}],"abstract":[{"text":"We describe RTblob, a high speed vision system that detects objects in cluttered scenes based on their color and shape at a speed of over 800 frames/s. Because the system is available as open-source software and relies only on off-the-shelf PC hardware components, it can provide the basis for multiple application scenarios. As an illustrative example, we show how RTblob can be used in a robotic table tennis scenario to estimate ball trajectories through 3D space simultaneously from four cameras images at a speed of 200 Hz.","lang":"eng"}],"volume":7,"date_published":"2012-03-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:04Z","issue":"1","article_type":"original","date_created":"2018-12-11T12:02:15Z","scopus_import":"1","publisher":"Springer","file":[{"date_updated":"2020-07-14T12:46:04Z","content_type":"application/pdf","file_name":"2012_Springer_Lampert.pdf","access_level":"open_access","file_size":2933187,"file_id":"5958","creator":"kschuh","date_created":"2019-02-12T10:52:25Z","relation":"main_file","checksum":"241be47ea50e81a283bcf4c45b07e8cc"}]},{"publisher":"Springer","file":[{"file_id":"4759","relation":"main_file","checksum":"f2f0d55efa32309ad1fe65a5fcaad90c","creator":"system","date_created":"2018-12-12T10:09:35Z","content_type":"application/pdf","date_updated":"2020-07-14T12:46:05Z","file_size":217104,"access_level":"open_access","file_name":"IST-2012-100-v1+1_Ideal_abstractions_for_well-structured_transition_systems.pdf"}],"project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"date_created":"2018-12-11T12:02:16Z","file_date_updated":"2020-07-14T12:46:05Z","date_published":"2012-01-01T00:00:00Z","volume":7148,"abstract":[{"text":"Many infinite state systems can be seen as well-structured transition systems (WSTS), i.e., systems equipped with a well-quasi-ordering on states that is also a simulation relation. WSTS are an attractive target for formal analysis because there exist generic algorithms that decide interesting verification problems for this class. Among the most popular algorithms are acceleration-based forward analyses for computing the covering set. Termination of these algorithms can only be guaranteed for flattable WSTS. Yet, many WSTS of practical interest are not flattable and the question whether any given WSTS is flattable is itself undecidable. We therefore propose an analysis that computes the covering set and captures the essence of acceleration-based algorithms, but sacrifices precision for guaranteed termination. Our analysis is an abstract interpretation whose abstract domain builds on the ideal completion of the well-quasi-ordered state space, and a widening operator that mimics acceleration and controls the loss of precision of the analysis. We present instances of our framework for various classes of WSTS. Our experience with a prototype implementation indicates that, despite the inherent precision loss, our analysis often computes the precise covering set of the analyzed system.","lang":"eng"}],"author":[{"orcid":"0000-0002-3197-8736","first_name":"Damien","last_name":"Zufferey","full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Wies, Thomas"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"}],"language":[{"iso":"eng"}],"year":"2012","day":"01","ec_funded":1,"citation":{"ama":"Zufferey D, Wies T, Henzinger TA. Ideal abstractions for well structured transition systems. In: Vol 7148. Springer; 2012:445-460. doi:<a href=\"https://doi.org/10.1007/978-3-642-27940-9_29\">10.1007/978-3-642-27940-9_29</a>","short":"D. Zufferey, T. Wies, T.A. Henzinger, in:, Springer, 2012, pp. 445–460.","chicago":"Zufferey, Damien, Thomas Wies, and Thomas A Henzinger. “Ideal Abstractions for Well Structured Transition Systems,” 7148:445–60. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-27940-9_29\">https://doi.org/10.1007/978-3-642-27940-9_29</a>.","mla":"Zufferey, Damien, et al. <i>Ideal Abstractions for Well Structured Transition Systems</i>. Vol. 7148, Springer, 2012, pp. 445–60, doi:<a href=\"https://doi.org/10.1007/978-3-642-27940-9_29\">10.1007/978-3-642-27940-9_29</a>.","apa":"Zufferey, D., Wies, T., &#38; Henzinger, T. A. (2012). Ideal abstractions for well structured transition systems (Vol. 7148, pp. 445–460). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-27940-9_29\">https://doi.org/10.1007/978-3-642-27940-9_29</a>","ista":"Zufferey D, Wies T, Henzinger TA. 2012. Ideal abstractions for well structured transition systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 445–460.","ieee":"D. Zufferey, T. Wies, and T. A. Henzinger, “Ideal abstractions for well structured transition systems,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 445–460."},"pubrep_id":"100","type":"conference","status":"public","title":"Ideal abstractions for well structured transition systems","intvolume":"      7148","page":"445 - 460","_id":"3251","doi":"10.1007/978-3-642-27940-9_29","department":[{"_id":"ToHe"}],"quality_controlled":"1","acknowledgement":"This research was supported in part by the European Research Council (ERC) Advanced Investigator Grant QUAREM and by the Austrian Science Fund (FWF) project S11402-N23.","alternative_title":["LNCS"],"has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1405"}]},"publist_id":"3406","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"01","oa_version":"Submitted Version","ddc":["000","005"],"date_updated":"2023-09-07T11:36:36Z","conference":{"location":"Philadelphia, PA, USA","name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2012-01-22","end_date":"2012-01-24"},"oa":1,"publication_status":"published"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3405","oa_version":"Preprint","month":"01","date_updated":"2021-01-12T07:42:08Z","conference":{"location":"Philadelphia, PA, USA","start_date":"2012-01-22","end_date":"2012-01-24","name":"VMCAI: Verification, Model Checking and Abstract Interpretation"},"oa":1,"publication_status":"published","alternative_title":["LNCS"],"intvolume":"      7148","_id":"3252","page":"152 - 168","doi":"10.1007/978-3-642-27940-9_11","department":[{"_id":"KrCh"}],"quality_controlled":"1","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 (Modern Graph Algorithmic Techniques in Formal Verification), FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.\r\nThe authors would like to thank Avik Chaudhuri for his invaluable help and feedback.","citation":{"ieee":"K. Chatterjee and V. Raman, “Synthesizing protocols for digital contract signing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 152–168.","ista":"Chatterjee K, Raman V. 2012. Synthesizing protocols for digital contract signing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 152–168.","ama":"Chatterjee K, Raman V. Synthesizing protocols for digital contract signing. In: Vol 7148. Springer; 2012:152-168. doi:<a href=\"https://doi.org/10.1007/978-3-642-27940-9_11\">10.1007/978-3-642-27940-9_11</a>","short":"K. Chatterjee, V. Raman, in:, Springer, 2012, pp. 152–168.","chicago":"Chatterjee, Krishnendu, and Vishwanath Raman. “Synthesizing Protocols for Digital Contract Signing,” 7148:152–68. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-27940-9_11\">https://doi.org/10.1007/978-3-642-27940-9_11</a>.","apa":"Chatterjee, K., &#38; Raman, V. (2012). Synthesizing protocols for digital contract signing (Vol. 7148, pp. 152–168). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-27940-9_11\">https://doi.org/10.1007/978-3-642-27940-9_11</a>","mla":"Chatterjee, Krishnendu, and Vishwanath Raman. <i>Synthesizing Protocols for Digital Contract Signing</i>. Vol. 7148, Springer, 2012, pp. 152–68, doi:<a href=\"https://doi.org/10.1007/978-3-642-27940-9_11\">10.1007/978-3-642-27940-9_11</a>."},"status":"public","type":"conference","title":"Synthesizing protocols for digital contract signing","year":"2012","language":[{"iso":"eng"}],"day":"20","ec_funded":1,"date_published":"2012-01-20T00:00:00Z","abstract":[{"lang":"eng","text":"We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents, the trusted third party (TTP) and the protocols as path formulas in Linear Temporal Logic (LTL) and prove that the satisfaction of the objectives of the agents and the TTP imply satisfaction of the protocol objectives. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail in synthesizing these protocols, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of assume-guarantee synthesis as follows: (a) any solution of assume-guarantee synthesis is attack-free; no subset of participants can violate the objectives of the other participants without violating their own objectives; (b) the Asokan-Shoup-Waidner (ASW) certified mail protocol that has known vulnerabilities is not a solution of AGS; and (c) the Kremer-Markowitch (KM) non-repudiation protocol is a solution of AGS. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can generate correct protocols and automatically discover vulnerabilities. The solution to assume-guarantee synthesis can be computed efficiently as the secure equilibrium solution of three-player graph games. © 2012 Springer-Verlag."}],"volume":7148,"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Raman, Vishwanath","first_name":"Vishwanath","last_name":"Raman"}],"date_created":"2018-12-11T12:02:16Z","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.2697"}],"publisher":"Springer","scopus_import":1}]