[{"page":"211-218","quality_controlled":"1","author":[{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"}],"publisher":"ML Research Press","date_published":"2012-06-01T00:00:00Z","year":"2012","publication_status":"published","date_updated":"2023-10-17T11:55:06Z","oa":1,"publist_id":"3572","oa_version":"Preprint","status":"public","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:01:33Z","_id":"3127","article_processing_charge":"No","publication":"Proceedings of the 29th International Conference on Machine Learning","abstract":[{"lang":"eng","text":"When searching for characteristic subpatterns in potentially noisy graph data, it appears self-evident that having multiple observations would be better than having just one. However, it turns out that the inconsistencies introduced when different graph instances have different edge sets pose a serious challenge. In this work we address this challenge for the problem of finding maximum weighted cliques.\r\n We introduce the concept of most persistent soft-clique. This is subset of vertices, that 1) is almost fully or at least densely connected, 2) occurs in all or almost all graph instances, and 3) has the maximum weight. We present a measure of clique-ness, that essentially counts the number of edge missing to make a subset of vertices into a clique. With this measure, we show that the problem of finding the most persistent soft-clique problem can be cast either as: a) a max-min two person game optimization problem, or b) a min-min soft margin optimization problem. Both formulations lead to the same solution when using a partial Lagrangian method to solve the optimization problems. By experiments on synthetic data and on real social network data, we show that the proposed method is able to reliably find soft cliques in graph data, even if that is distorted by random noise or unreliable observations."}],"scopus_import":"1","conference":{"end_date":"2012-07-01","location":"Edinburgh, United Kingdom","name":"ICML: International Conference on Machine Learning","start_date":"2012-06-26"},"citation":{"ista":"Quadrianto N, Lampert C, Chen C. 2012. The most persistent soft-clique in a set of sampled graphs. Proceedings of the 29th International Conference on Machine Learning. ICML: International Conference on Machine Learning, 211–218.","chicago":"Quadrianto, Novi, Christoph Lampert, and Chao Chen. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” In Proceedings of the 29th International Conference on Machine Learning, 211–18. ML Research Press, 2012.","ama":"Quadrianto N, Lampert C, Chen C. The most persistent soft-clique in a set of sampled graphs. In: Proceedings of the 29th International Conference on Machine Learning. ML Research Press; 2012:211-218.","short":"N. Quadrianto, C. Lampert, C. Chen, in:, Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–218.","mla":"Quadrianto, Novi, et al. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–18.","apa":"Quadrianto, N., Lampert, C., & Chen, C. (2012). The most persistent soft-clique in a set of sampled graphs. In Proceedings of the 29th International Conference on Machine Learning (pp. 211–218). Edinburgh, United Kingdom: ML Research Press.","ieee":"N. Quadrianto, C. Lampert, and C. Chen, “The most persistent soft-clique in a set of sampled graphs,” in Proceedings of the 29th International Conference on Machine Learning, Edinburgh, United Kingdom, 2012, pp. 211–218."},"main_file_link":[{"url":"http://arxiv.org/abs/1206.4652","open_access":"1"}],"title":"The most persistent soft-clique in a set of sampled graphs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","type":"conference","department":[{"_id":"ChLa"},{"_id":"HeEd"}],"month":"06"},{"date_updated":"2021-01-12T07:41:15Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"date_created":"2018-12-11T12:01:33Z","_id":"3128","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).","volume":43,"issue":"2","file_date_updated":"2020-07-14T12:46:00Z","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"scopus_import":1,"pubrep_id":"303","citation":{"ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of partial-observation stochastic parity games,” Formal Methods in System Design, vol. 43, no. 2. Springer, pp. 268–284, 2012.","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.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design. Springer, 2012. https://doi.org/10.1007/s10703-012-0164-2.","ama":"Chatterjee K, Doyen L, Henzinger TA. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 2012;43(2):268-284. doi:10.1007/s10703-012-0164-2","mla":"Chatterjee, Krishnendu, et al. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design, vol. 43, no. 2, Springer, 2012, pp. 268–84, doi:10.1007/s10703-012-0164-2.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design 43 (2012) 268–284.","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2012). A survey of partial-observation stochastic parity games. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0164-2"},"month":"10","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"intvolume":" 43","day":"01","date_published":"2012-10-01T00:00:00Z","publication_status":"published","year":"2012","page":"268 - 284","quality_controlled":"1","publisher":"Springer","language":[{"iso":"eng"}],"ec_funded":1,"has_accepted_license":"1","oa":1,"publist_id":"3570","oa_version":"Submitted Version","status":"public","doi":"10.1007/s10703-012-0164-2","publication":"Formal Methods in System Design","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"}],"file":[{"content_type":"application/pdf","creator":"system","access_level":"open_access","checksum":"dd3d590f383bb2ac6cfda1489ac1c42a","relation":"main_file","date_created":"2018-12-12T10:11:27Z","file_size":163983,"file_id":"4882","date_updated":"2020-07-14T12:46:00Z","file_name":"IST-2014-303-v1+1_Survey_Partial-Observation_Stochastic_Parity_Games.pdf"}],"ddc":["005"],"title":"A survey of partial-observation stochastic parity games","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"citation":{"mla":"Busaryev, Oleksiy, et al. Annotating Simplices with a Homology Basis and Its Applications. Vol. 7357, Springer, 2012, pp. 189–200, doi:10.1007/978-3-642-31155-0_17.","short":"O. Busaryev, S. Cabello, C. Chen, T. Dey, Y. Wang, in:, Springer, 2012, pp. 189–200.","apa":"Busaryev, O., Cabello, S., Chen, C., Dey, T., & 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. https://doi.org/10.1007/978-3-642-31155-0_17","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. https://doi.org/10.1007/978-3-642-31155-0_17.","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.","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:10.1007/978-3-642-31155-0_17","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."},"scopus_import":1,"conference":{"end_date":"2012-07-06","location":"Helsinki, Finland","name":"SWAT: Symposium and Workshops on Algorithm Theory","start_date":"2012-07-04"},"external_id":{"arxiv":["1107.3793"]},"month":"06","department":[{"_id":"HeEd"}],"intvolume":" 7357","day":"19","arxiv":1,"date_updated":"2021-01-12T07:41:15Z","author":[{"first_name":"Oleksiy","last_name":"Busaryev","full_name":"Busaryev, Oleksiy"},{"last_name":"Cabello","first_name":"Sergio","full_name":"Cabello, Sergio"},{"full_name":"Chen, Chao","first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dey, Tamal","last_name":"Dey","first_name":"Tamal"},{"full_name":"Wang, Yusu","last_name":"Wang","first_name":"Yusu"}],"date_created":"2018-12-11T12:01:33Z","_id":"3129","volume":7357,"doi":"10.1007/978-3-642-31155-0_17","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 < 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"}],"title":"Annotating simplices with a homology basis and its applications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1107.3793"}],"year":"2012","publication_status":"published","date_published":"2012-06-19T00:00:00Z","quality_controlled":"1","publisher":"Springer","page":"189 - 200","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"oa_version":"Preprint","status":"public","publist_id":"3569","oa":1},{"doi":"10.1371/journal.pgen.1002803","abstract":[{"lang":"eng","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."}],"publication":"PLoS Genetics","ddc":["576"],"file":[{"date_created":"2018-12-12T10:12:52Z","relation":"main_file","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"f8506fb579eda6fc5613ba9bf421b86a","file_id":"4973","file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf","date_updated":"2020-07-14T12:46:01Z","file_size":2674138}],"title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","year":"2012","publication_status":"published","date_published":"2012-06-28T00:00:00Z","quality_controlled":"1","publisher":"Public Library of Science","language":[{"iso":"eng"}],"article_number":"e1002803","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"publist_id":"3567","pubrep_id":"386","citation":{"ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.","chicago":"Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002803.","ama":"Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002803","short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).","apa":"Bergmiller, T., Ackermann, M., & Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002803","mla":"Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002803.","ieee":"T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012."},"scopus_import":1,"department":[{"_id":"CaGu"}],"month":"06","intvolume":" 8","day":"28","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2021-01-12T07:41:16Z","author":[{"first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"},{"full_name":"Silander, Olin","first_name":"Olin","last_name":"Silander"}],"date_created":"2018-12-11T12:01:34Z","_id":"3130","acknowledgement":"We thank Alex Boehm for discussions and comments.","volume":8,"issue":"6","file_date_updated":"2020-07-14T12:46:01Z"},{"quality_controlled":"1","publisher":"Public Library of Science","publication_status":"published","year":"2012","date_published":"2012-06-07T00:00:00Z","oa_version":"Published Version","status":"public","has_accepted_license":"1","publist_id":"3566","oa":1,"language":[{"iso":"eng"}],"article_number":"e1002740","ec_funded":1,"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."}],"publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1002740","title":"Limits to the rate of adaptive substitution in sexual populations","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","file":[{"content_type":"application/pdf","creator":"system","access_level":"open_access","checksum":"729a4becda7d786c4c3db8f9a1f77953","relation":"main_file","date_created":"2018-12-12T10:08:00Z","file_size":1284801,"file_id":"4659","file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf","date_updated":"2020-07-14T12:46:01Z"}],"ddc":["570","576"],"author":[{"first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","full_name":"Weissman, Daniel"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"date_updated":"2021-01-12T07:41:17Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":8,"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.","file_date_updated":"2020-07-14T12:46:01Z","issue":"6","date_created":"2018-12-11T12:01:34Z","_id":"3131","pubrep_id":"114","citation":{"ama":"Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740.","chicago":"Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740.","apa":"Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740","mla":"Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740.","short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).","ieee":"D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012."},"project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"}],"scopus_import":1,"intvolume":" 8","day":"07","department":[{"_id":"NiBa"}],"month":"06"},{"publication_status":"published","year":"2012","date_updated":"2021-01-12T07:41:17Z","date_published":"2012-08-01T00:00:00Z","quality_controlled":"1","author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","first_name":"Matthias"},{"full_name":"Pamminger, Tobias","first_name":"Tobias","last_name":"Pamminger"},{"full_name":"Foitzik, Susanne","last_name":"Foitzik","first_name":"Susanne"}],"publisher":"Springer","page":"627 - 636","date_created":"2018-12-11T12:01:34Z","language":[{"iso":"eng"}],"_id":"3132","oa_version":"None","status":"public","acknowledgement":"We like to thank the editor and three anonymous reviewers for their time and constructive criticism and Inon Scharf, Volker Witte and Andreas Modlmeier for helpful comments on earlier versions of the manuscript. The first and second authors appear in alphabetical order and contributed equally to this paper.","volume":99,"issue":"8","publist_id":"3565","citation":{"ama":"Konrad M, Pamminger T, Foitzik S. Two pathways ensuring social harmony. Naturwissenschaften. 2012;99(8):627-636. doi:10.1007/s00114-012-0943-z","ista":"Konrad M, Pamminger T, Foitzik S. 2012. Two pathways ensuring social harmony. Naturwissenschaften. 99(8), 627–636.","chicago":"Konrad, Matthias, Tobias Pamminger, and Susanne Foitzik. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften. Springer, 2012. https://doi.org/10.1007/s00114-012-0943-z.","apa":"Konrad, M., Pamminger, T., & Foitzik, S. (2012). Two pathways ensuring social harmony. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-012-0943-z","short":"M. Konrad, T. Pamminger, S. Foitzik, Naturwissenschaften 99 (2012) 627–636.","mla":"Konrad, Matthias, et al. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften, vol. 99, no. 8, Springer, 2012, pp. 627–36, doi:10.1007/s00114-012-0943-z.","ieee":"M. Konrad, T. Pamminger, and S. Foitzik, “Two pathways ensuring social harmony,” Naturwissenschaften, vol. 99, no. 8. Springer, pp. 627–636, 2012."},"scopus_import":1,"doi":"10.1007/s00114-012-0943-z","abstract":[{"text":"Reproductive division of labour is a characteristic trait of social insects. The dominant reproductive individual, often the queen, uses chemical communication and/or behaviour to maintain her social status. Queens of many social insects communicate their fertility status via cuticle-bound substances. As these substances usually possess a low volatility, their range in queen–worker communication is potentially limited. Here, we investigate the range and impact of behavioural and chemical queen signals on workers of the ant Temnothorax longispinosus. We compared the behaviour and ovary development of workers subjected to three different treatments: workers with direct chemical and physical contact to the queen, those solely under the influence of volatile queen substances and those entirely separated from the queen. In addition to short-ranged queen signals preventing ovary development in workers, we discovered a novel secondary pathway influencing worker behaviour. Workers with no physical contact to the queen, but exposed to volatile substances, started to develop their ovaries, but did not change their behaviour compared to workers in direct contact to the queen. In contrast, workers in queen-separated groups showed both increased ovary development and aggressive dominance interactions. We conclude that T. longispinosus queens influence worker ovary development and behaviour via two independent signals, both ensuring social harmony within the colony.","lang":"eng"}],"publication":"Naturwissenschaften","department":[{"_id":"SyCr"}],"month":"08","title":"Two pathways ensuring social harmony","intvolume":" 99","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","type":"journal_article"},{"day":"20","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","title":"Alexander duality for functions: The persistent behavior of land and water and shore","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.5052"}],"department":[{"_id":"HeEd"}],"month":"06","abstract":[{"lang":"eng","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. "}],"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","citation":{"mla":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–58, doi:10.1145/2261250.2261287.","short":"H. Edelsbrunner, M. Kerber, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–258.","apa":"Edelsbrunner, H., & Kerber, M. (2012). Alexander duality for functions: The persistent behavior of land and water and shore. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 249–258). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261287","chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 249–58. ACM, 2012. https://doi.org/10.1145/2261250.2261287.","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.","ama":"Edelsbrunner H, Kerber M. Alexander duality for functions: The persistent behavior of land and water and shore. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:249-258. doi:10.1145/2261250.2261287","ieee":"H. Edelsbrunner and M. Kerber, “Alexander duality for functions: The persistent behavior of land and water and shore,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 249–258."},"doi":"10.1145/2261250.2261287","conference":{"end_date":"2012-06-20","start_date":"2012-06-17","name":"SCG: Symposium on Computational Geometry","location":"Chapel Hill, NC, USA"},"scopus_import":1,"status":"public","oa_version":"Preprint","publist_id":"3564","oa":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.","_id":"3133","date_created":"2018-12-11T12:01:35Z","language":[{"iso":"eng"}],"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"}],"publisher":"ACM","quality_controlled":"1","page":"249 - 258","date_updated":"2021-01-12T07:41:17Z","year":"2012","publication_status":"published","date_published":"2012-06-20T00:00:00Z"},{"citation":{"ieee":"H. Edelsbrunner, B. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 91–100.","ama":"Edelsbrunner H, Fasy B, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:91-100. doi:10.1145/2261250.2261265","ista":"Edelsbrunner H, Fasy B, Rote G. 2012. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 91–100.","chicago":"Edelsbrunner, Herbert, Brittany Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 91–100. ACM, 2012. https://doi.org/10.1145/2261250.2261265.","short":"H. Edelsbrunner, B. Fasy, G. Rote, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100.","apa":"Edelsbrunner, H., Fasy, B., & Rote, G. (2012). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 91–100). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261265","mla":"Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100, doi:10.1145/2261250.2261265."},"doi":"10.1145/2261250.2261265","conference":{"location":"Chapel Hill, NC, USA","name":"SCG: Symposium on Computational Geometry","start_date":"2012-06-17","end_date":"2012-06-20"},"scopus_import":1,"abstract":[{"text":"It has been an open question whether the sum of finitely many isotropic Gaussian kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes. We give a detailed analysis of this example, showing that it has exponentially many critical points and that the resilience of the extra mode grows like √n. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. ","lang":"eng"}],"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","month":"06","department":[{"_id":"HeEd"}],"day":"20","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","title":"Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions","date_updated":"2023-02-23T10:59:27Z","publication_status":"published","year":"2012","date_published":"2012-06-20T00:00:00Z","publisher":"ACM","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"last_name":"Fasy","first_name":"Brittany","full_name":"Fasy, Brittany"},{"full_name":"Rote, Günter","first_name":"Günter","last_name":"Rote"}],"quality_controlled":"1","page":"91 - 100","_id":"3134","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:01:35Z","related_material":{"record":[{"id":"2815","status":"public","relation":"later_version"}]},"status":"public","oa_version":"None","publist_id":"3563","acknowledgement":"This research is partially supported by the National Science Foun- dation (NSF) under grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053."},{"project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"scopus_import":1,"conference":{"end_date":"2012-07-13","start_date":"2012-07-07","name":"CAV: Computer Aided Verification","location":"Berkeley, CA, USA"},"citation":{"apa":"Brázdil, B., Chatterjee, K., Kučera, A., & 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. https://doi.org/10.1007/978-3-642-31424-7_8","mla":"Brázdil, Brázdil, et al. Efficient Controller Synthesis for Consumption Games with Multiple Resource Types. Vol. 7358, Springer, 2012, pp. 23–38, doi:10.1007/978-3-642-31424-7_8.","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:10.1007/978-3-642-31424-7_8","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. https://doi.org/10.1007/978-3-642-31424-7_8.","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."},"month":"07","department":[{"_id":"KrCh"}],"intvolume":" 7358","day":"01","date_updated":"2021-01-12T07:41:18Z","author":[{"full_name":"Brázdil, Brázdil","first_name":"Brázdil","last_name":"Brázdil"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"},{"full_name":"Novotny, Petr","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny"}],"date_created":"2018-12-11T12:01:35Z","_id":"3135","volume":7358,"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).","doi":"10.1007/978-3-642-31424-7_8","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"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1202.0796"}],"title":"Efficient controller synthesis for consumption games with multiple resource types","type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2012-07-01T00:00:00Z","publication_status":"published","year":"2012","page":"23 - 38","quality_controlled":"1","publisher":"Springer","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"publist_id":"3562","oa_version":"Preprint","status":"public"},{"_id":"3136","ec_funded":1,"date_created":"2018-12-11T12:01:36Z","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"publist_id":"3561","acknowledgement":"This work was supported by the ERC Advanced Investigator grant on Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation.","volume":"7358 ","status":"public","oa_version":"None","date_published":"2012-07-01T00:00:00Z","date_updated":"2021-01-12T07:41:18Z","year":"2012","publication_status":"published","page":"294 - 309","publisher":"Springer","author":[{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Mateescu","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Mateescu, Maria"},{"full_name":"Sezgin, Ali","first_name":"Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","month":"07","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"type":"conference","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Delayed continuous time Markov chains for genetic regulatory circuits","conference":{"start_date":"2012-07-07","name":"CAV: Computer Aided Verification","location":"Berkeley, CA, USA","end_date":"2012-07-13"},"doi":"10.1007/978-3-642-31424-7_24","scopus_import":1,"project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"citation":{"apa":"Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., & Sezgin, A. (2012). Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358, pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_24","short":"C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer, 2012, pp. 294–309.","mla":"Guet, Calin C., et al. Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits. Vol. 7358, Springer, 2012, pp. 294–309, doi:10.1007/978-3-642-31424-7_24.","ista":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification, LNCS, vol. 7358, 294–309.","ama":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. Delayed continuous time Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309. doi:10.1007/978-3-642-31424-7_24","chicago":"Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,” 7358:294–309. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_24.","ieee":"C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed continuous time Markov chains for genetic regulatory circuits,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309."},"abstract":[{"lang":"eng","text":"Continuous-time Markov chains (CTMC) with their rich theory and efficient simulation algorithms have been successfully used in modeling stochastic processes in diverse areas such as computer science, physics, and biology. However, systems that comprise non-instantaneous events cannot be accurately and efficiently modeled with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that allows for the specification of a lower bound on the time interval between an event's initiation and its completion, and we propose an algorithm for the computation of their behavior. Our algorithm effectively decomposes the computation into two stages: a pure CTMC governs event initiations while a deterministic process guarantees lower bounds on event completion times. Furthermore, from the nature of delayed CTMCs, we obtain a parallelized version of our algorithm. We use our formalism to model genetic regulatory circuits (biological systems where delayed events are common) and report on the results of our numerical algorithm as run on a cluster. We compare performance and accuracy of our results with results obtained by using pure CTMCs. © 2012 Springer-Verlag."}]},{"department":[{"_id":"ToHe"}],"month":"06","intvolume":" 7273","day":"01","scopus_import":1,"conference":{"location":"Stockholm, Sweden","start_date":"2012-06-13","name":"FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems ","end_date":"2012-06-16"},"pubrep_id":"88","citation":{"short":"B. Delahaye, U. Fahrenberg, T.A. Henzinger, A. Legay, D. Nickovic, in:, Springer, 2012, pp. 203–218.","mla":"Delahaye, Benoît, et al. Synchronous Interface Theories and Time Triggered Scheduling. Vol. 7273, Springer, 2012, pp. 203–18, doi:10.1007/978-3-642-30793-5_13.","apa":"Delahaye, B., Fahrenberg, U., Henzinger, T. A., Legay, A., & 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 & FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden: Springer. https://doi.org/10.1007/978-3-642-30793-5_13","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. https://doi.org/10.1007/978-3-642-30793-5_13.","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 & FMOODS: Formal Methods for Open Object-Based Distributed Systems , LNCS, vol. 7273, 203–218.","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:10.1007/978-3-642-30793-5_13","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 & FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden, 2012, vol. 7273, pp. 203–218."},"date_created":"2018-12-11T12:01:43Z","_id":"3155","volume":7273,"acknowledgement":"Research partially supported by the Danish-Chinese Center for Cyber Physical Systems (Grant No.61061130541) and VKR Center of Excellence MT-LAB.","file_date_updated":"2020-07-14T12:46:01Z","date_updated":"2021-01-12T07:41:26Z","author":[{"full_name":"Delahaye, Benoît","first_name":"Benoît","last_name":"Delahaye"},{"full_name":"Fahrenberg, Uli","first_name":"Uli","last_name":"Fahrenberg"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Axel","last_name":"Legay","full_name":"Legay, Axel"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan"}],"file":[{"checksum":"feae2e07f2d9a59843f8ddabf25d179f","content_type":"application/pdf","creator":"system","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:11:25Z","file_size":493198,"date_updated":"2020-07-14T12:46:01Z","file_name":"IST-2012-88-v1+1_Synchronous_interface_theories_and_time_triggered_scheduling.pdf","file_id":"4879"}],"ddc":["004"],"title":"Synchronous interface theories and time triggered scheduling","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","doi":"10.1007/978-3-642-30793-5_13","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"has_accepted_license":"1","oa":1,"publist_id":"3539","oa_version":"Submitted Version","status":"public","date_published":"2012-06-01T00:00:00Z","publication_status":"published","year":"2012","page":"203 - 218","quality_controlled":"1","publisher":"Springer"},{"abstract":[{"lang":"eng","text":"Dispersal is crucial for gene flow and often determines the long-term stability of meta-populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark-recapture observations that are suspected to be poor predictors of long-distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark-recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼ 20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10 km."}],"publication":"Molecular Ecology","citation":{"ieee":"L. V. Ugelvig, A. Andersen, J. Boomsma, and D. Nash, “Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion,” Molecular Ecology, vol. 21, no. 13. Wiley-Blackwell, pp. 3224–3236, 2012.","chicago":"Ugelvig, Line V, Anne Andersen, Jacobus Boomsma, and David Nash. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05592.x.","ista":"Ugelvig LV, Andersen A, Boomsma J, Nash D. 2012. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 21(13), 3224–3236.","ama":"Ugelvig LV, Andersen A, Boomsma J, Nash D. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 2012;21(13):3224-3236. doi:10.1111/j.1365-294X.2012.05592.x","mla":"Ugelvig, Line V., et al. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology, vol. 21, no. 13, Wiley-Blackwell, 2012, pp. 3224–36, doi:10.1111/j.1365-294X.2012.05592.x.","apa":"Ugelvig, L. V., Andersen, A., Boomsma, J., & Nash, D. (2012). Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05592.x","short":"L.V. Ugelvig, A. Andersen, J. Boomsma, D. Nash, Molecular Ecology 21 (2012) 3224–3236."},"doi":"10.1111/j.1365-294X.2012.05592.x","scopus_import":1,"day":"01","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion","intvolume":" 21","month":"07","department":[{"_id":"SyCr"}],"publisher":"Wiley-Blackwell","author":[{"first_name":"Line V","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V"},{"first_name":"Anne","last_name":"Andersen","full_name":"Andersen, Anne"},{"last_name":"Boomsma","first_name":"Jacobus","full_name":"Boomsma, Jacobus"},{"last_name":"Nash","first_name":"David","full_name":"Nash, David"}],"quality_controlled":"1","page":"3224 - 3236","date_updated":"2021-01-12T07:41:27Z","publication_status":"published","year":"2012","date_published":"2012-07-01T00:00:00Z","status":"public","oa_version":"None","issue":"13","publist_id":"3538","volume":21,"acknowledgement":"The work was financed by the Danish National Science Research Foundation via a grant to the Centre for Social Evolution.\r\nWe thank four anonymous reviewers for useful comments on the manuscript, J. Bergsten, P. Bina, B. Carlsson, M. Johannesson and A.E. Lomborg for providing additional wingtip samples, A. Illum for assistance in the field, and in particular P.S. Nielsen for mediating the contact to the collectors and the Swedish authorities. Collection was made possible through a permit by the Åtgärdsprogrammet, supported by the Swedish Environmental Protection Agency.","_id":"3156","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:01:43Z"},{"date_updated":"2023-09-07T11:40:43Z","author":[{"full_name":"Diaz Jr, Luis","first_name":"Luis","last_name":"Diaz Jr"},{"full_name":"Williams, Richard","first_name":"Richard","last_name":"Williams"},{"full_name":"Wu, Jian","first_name":"Jian","last_name":"Wu"},{"last_name":"Kinde","first_name":"Isaac","full_name":"Kinde, Isaac"},{"first_name":"Joel","last_name":"Hecht","full_name":"Hecht, Joel"},{"full_name":"Berlin, Jordan","last_name":"Berlin","first_name":"Jordan"},{"full_name":"Allen, Benjamin","last_name":"Allen","first_name":"Benjamin"},{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"last_name":"Kinzler","first_name":"Kenneth","full_name":"Kinzler, Kenneth"},{"full_name":"Oliner, Kelly","last_name":"Oliner","first_name":"Kelly"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"}],"date_created":"2018-12-11T12:01:43Z","_id":"3157","volume":486,"issue":"7404","scopus_import":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"citation":{"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.","mla":"Diaz Jr, Luis, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” Nature, vol. 486, no. 7404, Nature Publishing Group, 2012, pp. 537–40, doi:10.1038/nature11219.","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. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11219","ama":"Diaz Jr L, Williams R, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012;486(7404):537-540. doi:10.1038/nature11219","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.","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.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11219.","ieee":"L. Diaz Jr et al., “The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers,” Nature, vol. 486, no. 7404. Nature Publishing Group, pp. 537–540, 2012."},"external_id":{"pmid":["22722843"]},"pmid":1,"department":[{"_id":"KrCh"}],"month":"06","intvolume":" 486","day":"28","date_published":"2012-06-28T00:00:00Z","year":"2012","publication_status":"published","page":"537 - 540","quality_controlled":"1","publisher":"Nature Publishing Group","related_material":{"record":[{"id":"1400","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"3537","oa":1,"oa_version":"Submitted Version","status":"public","doi":"10.1038/nature11219","publication":"Nature","abstract":[{"lang":"eng","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."}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436069/"}],"title":"The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article"},{"volume":91,"issue":"11-12","date_created":"2018-12-11T12:01:44Z","_id":"3158","author":[{"full_name":"Schachtner, Hannah","last_name":"Schachtner","first_name":"Hannah"},{"full_name":"Li, Ang","first_name":"Ang","last_name":"Li"},{"last_name":"Stevenson","first_name":"David","full_name":"Stevenson, David"},{"full_name":"Calaminus, Simon","first_name":"Simon","last_name":"Calaminus"},{"full_name":"Thomas, Steven","first_name":"Steven","last_name":"Thomas"},{"first_name":"Steve","last_name":"Watson","full_name":"Watson, Steve"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"first_name":"Roland","last_name":"Wedlich Söldner","full_name":"Wedlich Söldner, Roland"},{"last_name":"Strathdee","first_name":"Douglas","full_name":"Strathdee, Douglas"},{"first_name":"Laura","last_name":"Machesky","full_name":"Machesky, Laura"}],"date_updated":"2021-01-12T07:41:27Z","intvolume":" 91","day":"01","pmid":1,"department":[{"_id":"MiSi"}],"month":"11","external_id":{"pmid":["22658956"]},"citation":{"ieee":"H. Schachtner et al., “Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo,” European Journal of Cell Biology, vol. 91, no. 11–12. Elsevier, pp. 923–929, 2012.","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.","mla":"Schachtner, Hannah, et al. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology, vol. 91, no. 11–12, Elsevier, 2012, pp. 923–29, doi:10.1016/j.ejcb.2012.04.002.","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. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2012.04.002","ama":"Schachtner H, Li A, Stevenson D, et al. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 2012;91(11-12):923-929. doi:10.1016/j.ejcb.2012.04.002","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.","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.” European Journal of Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ejcb.2012.04.002."},"scopus_import":1,"oa_version":"Submitted Version","status":"public","oa":1,"publist_id":"3534","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Elsevier","page":"923 - 929","year":"2012","publication_status":"published","date_published":"2012-11-01T00:00:00Z","title":"Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930012/","open_access":"1"}],"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."}],"publication":"European Journal of Cell Biology","doi":"10.1016/j.ejcb.2012.04.002"},{"scopus_import":1,"pubrep_id":"385","citation":{"chicago":"Mileyko, Yuriy, Herbert Edelsbrunner, Charles Price, and Joshua Weitz. “Hierarchical Ordering of Reticular Networks.” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036715.","ista":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. 2012. Hierarchical ordering of reticular networks. PLoS One. 7(6), e36715.","ama":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. Hierarchical ordering of reticular networks. PLoS One. 2012;7(6). doi:10.1371/journal.pone.0036715","mla":"Mileyko, Yuriy, et al. “Hierarchical Ordering of Reticular Networks.” PLoS One, vol. 7, no. 6, e36715, Public Library of Science, 2012, doi:10.1371/journal.pone.0036715.","short":"Y. Mileyko, H. Edelsbrunner, C. Price, J. Weitz, PLoS One 7 (2012).","apa":"Mileyko, Y., Edelsbrunner, H., Price, C., & Weitz, J. (2012). Hierarchical ordering of reticular networks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036715","ieee":"Y. Mileyko, H. Edelsbrunner, C. Price, and J. Weitz, “Hierarchical ordering of reticular networks,” PLoS One, vol. 7, no. 6. Public Library of Science, 2012."},"department":[{"_id":"HeEd"}],"month":"06","intvolume":" 7","day":"06","date_updated":"2021-01-12T07:41:28Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Mileyko, Yuriy","last_name":"Mileyko","first_name":"Yuriy"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"last_name":"Price","first_name":"Charles","full_name":"Price, Charles"},{"full_name":"Weitz, Joshua","first_name":"Joshua","last_name":"Weitz"}],"date_created":"2018-12-11T12:01:44Z","_id":"3159","volume":7,"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.","issue":"6","file_date_updated":"2020-07-14T12:46:01Z","doi":"10.1371/journal.pone.0036715","publication":"PLoS One","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 "root" 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."}],"ddc":["510"],"file":[{"file_size":541583,"file_id":"5922","date_updated":"2020-07-14T12:46:01Z","file_name":"2012_PLoS_Mileyko.PDF","creator":"kschuh","access_level":"open_access","content_type":"application/pdf","checksum":"515a98ad72e470752f03f13663dcaff8","date_created":"2019-02-05T12:38:43Z","relation":"main_file"}],"title":"Hierarchical ordering of reticular networks","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2012-06-06T00:00:00Z","publication_status":"published","year":"2012","quality_controlled":"1","publisher":"Public Library of Science","language":[{"iso":"eng"}],"article_number":"e36715","has_accepted_license":"1","oa":1,"publist_id":"3530","oa_version":"Published Version","status":"public"},{"date_published":"2012-06-01T00:00:00Z","publication_status":"published","year":"2012","date_updated":"2021-01-12T07:41:28Z","page":"2055 - 2058","quality_controlled":"1","publisher":"Taylor and Francis","author":[{"full_name":"Pantazis, Periklis","last_name":"Pantazis","first_name":"Periklis"},{"first_name":"Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias"}],"date_created":"2018-12-11T12:01:44Z","language":[{"iso":"eng"}],"_id":"3160","volume":11,"publist_id":"3531","issue":"11","oa_version":"None","status":"public","scopus_import":1,"doi":"10.4161/cc.20118","citation":{"ieee":"P. Pantazis and M. T. Bollenbach, “Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo,” Cell Cycle, vol. 11, no. 11. Taylor and Francis, pp. 2055–2058, 2012.","apa":"Pantazis, P., & Bollenbach, M. T. (2012). Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. Taylor and Francis. https://doi.org/10.4161/cc.20118","short":"P. Pantazis, M.T. Bollenbach, Cell Cycle 11 (2012) 2055–2058.","mla":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle, vol. 11, no. 11, Taylor and Francis, 2012, pp. 2055–58, doi:10.4161/cc.20118.","chicago":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle. Taylor and Francis, 2012. https://doi.org/10.4161/cc.20118.","ista":"Pantazis P, Bollenbach MT. 2012. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 11(11), 2055–2058.","ama":"Pantazis P, Bollenbach MT. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 2012;11(11):2055-2058. doi:10.4161/cc.20118"},"publication":"Cell Cycle","abstract":[{"lang":"eng","text":"There is a long-running controversy about how early cell fate decisions are made in the developing mammalian embryo. 1,2 In particular, it is controversial when the first events that can predict the establishment of the pluripotent and extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur. It has long been proposed that the position and polarity of cells at the 16- to 32-cell stage embryo influence their decision to either give rise to the pluripotent cell lineage that eventually contributes to the inner cell mass (ICM), comprising the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm (TE) surrounding the blastocoel. The positioning of cells in the embryo at this developmental stage could largely be the result of random events, making this a stochastic model of cell lineage allocation. Contrary to such a stochastic model, some studies have detected putative differences in the lineage potential of individual blastomeres before compaction, indicating that the first cell fate decisions may occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a key transcription factor (TF) controlling pre-implantation development in the mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications of such molecular heterogeneities in early development and offer potential avenues toward a mechanistic understanding of these observations, contributing to the resolution of the controversy of developmental cell lineage allocation."}],"department":[{"_id":"ToBo"}],"month":"06","title":"Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo","intvolume":" 11","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article"},{"pubrep_id":"97","citation":{"ieee":"M. Vyleta, J. Wong, and B. Magun, “Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome,” PLoS One, 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.","ama":"Vyleta M, Wong J, Magun B. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 2012;7(5). doi:10.1371/journal.pone.0036044","chicago":"Vyleta, Meghan, John Wong, and Bruce Magun. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036044.","apa":"Vyleta, M., Wong, J., & Magun, B. (2012). Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036044","short":"M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012).","mla":"Vyleta, Meghan, et al. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One, vol. 7, no. 5, e36044, Public Library of Science, 2012, doi:10.1371/journal.pone.0036044."},"scopus_import":1,"month":"05","department":[{"_id":"SyCr"}],"intvolume":" 7","day":"14","date_updated":"2021-01-12T07:41:29Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"418901AA-F248-11E8-B48F-1D18A9856A87","last_name":"Vyleta","first_name":"Meghan","full_name":"Vyleta, Meghan"},{"full_name":"Wong, John","first_name":"John","last_name":"Wong"},{"full_name":"Magun, Bruce","last_name":"Magun","first_name":"Bruce"}],"date_created":"2018-12-11T12:01:45Z","_id":"3161","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.","volume":7,"file_date_updated":"2020-07-14T12:46:01Z","issue":"5","doi":"10.1371/journal.pone.0036044","abstract":[{"lang":"eng","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."}],"publication":"PLoS One","ddc":["610"],"file":[{"date_updated":"2020-07-14T12:46:01Z","file_name":"IST-2012-97-v1+1_journal.pone.0036044.pdf","file_id":"5082","file_size":2984012,"relation":"main_file","date_created":"2018-12-12T10:14:30Z","checksum":"30cef37e27eaa467f6571b3640282010","access_level":"open_access","creator":"system","content_type":"application/pdf"}],"title":"Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","publication_status":"published","date_published":"2012-05-14T00:00:00Z","quality_controlled":"1","publisher":"Public Library of Science","language":[{"iso":"eng"}],"article_number":"e36044","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"publist_id":"3526"},{"page":"147 - 160","publisher":"Springer","quality_controlled":"1","date_published":"2012-01-01T00:00:00Z","year":"2012","publication_status":"published","publist_id":"3525","oa":1,"has_accepted_license":"1","status":"public","oa_version":"Submitted Version","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"article_processing_charge":"No","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."}],"doi":"10.1007/978-3-642-29860-8_12","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Parametric identification of temporal properties","ddc":["000"],"file":[{"date_created":"2020-05-15T12:50:15Z","relation":"main_file","checksum":"ba4a75287008fc64b8fbf78a7476ec32","access_level":"open_access","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:46:01Z","file_name":"2012_RV_Asarin.pdf","file_id":"7862","file_size":374726}],"author":[{"full_name":"Asarin, Eugene","last_name":"Asarin","first_name":"Eugene"},{"full_name":"Donzé, Alexandre","last_name":"Donzé","first_name":"Alexandre"},{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"},{"full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan"}],"date_updated":"2021-01-12T07:41:29Z","file_date_updated":"2020-07-14T12:46:01Z","volume":7186,"_id":"3162","date_created":"2018-12-11T12:01:45Z","conference":{"end_date":"2011-09-30","name":"RV: Runtime Verification","start_date":"2011-09-27","location":"San Francisco, CA, United States"},"scopus_import":1,"citation":{"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.","apa":"Asarin, E., Donzé, A., Maler, O., & 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. https://doi.org/10.1007/978-3-642-29860-8_12","mla":"Asarin, Eugene, et al. Parametric Identification of Temporal Properties. Vol. 7186, Springer, 2012, pp. 147–60, doi:10.1007/978-3-642-29860-8_12.","ama":"Asarin E, Donzé A, Maler O, Nickovic D. Parametric identification of temporal properties. In: Vol 7186. Springer; 2012:147-160. doi:10.1007/978-3-642-29860-8_12","ista":"Asarin E, Donzé A, Maler O, Nickovic D. 2012. Parametric identification of temporal properties. RV: Runtime Verification, LNCS, vol. 7186, 147–160.","chicago":"Asarin, Eugene, Alexandre Donzé, Oded Maler, and Dejan Nickovic. “Parametric Identification of Temporal Properties,” 7186:147–60. Springer, 2012. https://doi.org/10.1007/978-3-642-29860-8_12."},"day":"01","intvolume":" 7186","month":"01","department":[{"_id":"ToHe"}]},{"department":[{"_id":"ChLa"}],"month":"09","intvolume":" 99","title":"Guest editorial: Special issue on structured prediction and inference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","type":"journal_article","citation":{"short":"M. Blaschko, C. Lampert, International Journal of Computer Vision 99 (2012) 257–258.","mla":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision, vol. 99, no. 3, Springer, 2012, pp. 257–58, doi:10.1007/s11263-012-0530-y.","apa":"Blaschko, M., & Lampert, C. (2012). Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. Springer. https://doi.org/10.1007/s11263-012-0530-y","ista":"Blaschko M, Lampert C. 2012. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 99(3), 257–258.","chicago":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision. Springer, 2012. https://doi.org/10.1007/s11263-012-0530-y.","ama":"Blaschko M, Lampert C. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 2012;99(3):257-258. doi:10.1007/s11263-012-0530-y","ieee":"M. Blaschko and C. Lampert, “Guest editorial: Special issue on structured prediction and inference,” International Journal of Computer Vision, vol. 99, no. 3. Springer, pp. 257–258, 2012."},"scopus_import":1,"doi":"10.1007/s11263-012-0530-y","abstract":[{"text":"Overview of the Special Issue on structured prediction and inference.","lang":"eng"}],"publication":"International Journal of Computer Vision","date_created":"2018-12-11T12:01:46Z","language":[{"iso":"eng"}],"_id":"3164","oa_version":"None","status":"public","volume":99,"issue":"3","publist_id":"3521","publication_status":"published","year":"2012","date_updated":"2021-01-12T07:41:30Z","date_published":"2012-09-01T00:00:00Z","quality_controlled":"1","author":[{"full_name":"Blaschko, Matthew","last_name":"Blaschko","first_name":"Matthew"},{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"publisher":"Springer","page":"257 - 258"},{"citation":{"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.","chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 1386–99. SIAM, 2012. https://doi.org/10.1137/1.9781611973099.109.","ama":"Chatterjee K, Henzinger MH. An O(n2) time algorithm for alternating Büchi games. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SIAM; 2012:1386-1399. doi:10.1137/1.9781611973099.109","mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2012, pp. 1386–99, doi:10.1137/1.9781611973099.109.","short":"K. Chatterjee, M.H. Henzinger, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2012, pp. 1386–1399.","apa":"Chatterjee, K., & Henzinger, M. H. (2012). An O(n2) time algorithm for alternating Büchi games. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1386–1399). Kyoto, Japan: SIAM. https://doi.org/10.1137/1.9781611973099.109","ieee":"K. Chatterjee and M. H. Henzinger, “An O(n2) time algorithm for alternating Büchi games,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Kyoto, Japan, 2012, pp. 1386–1399."},"pubrep_id":"15","conference":{"location":"Kyoto, Japan","name":"SODA: Symposium on Discrete Algorithms","start_date":"2012-01-17","end_date":"2012-01-19"},"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1109.5018"]},"month":"01","department":[{"_id":"KrCh"}],"day":"01","arxiv":1,"date_updated":"2025-06-02T08:53:48Z","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"_id":"3165","date_created":"2018-12-11T12:01:46Z","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.","doi":"10.1137/1.9781611973099.109","abstract":[{"lang":"eng","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 > 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 > 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."}],"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","title":"An O(n2) time algorithm for alternating Büchi games","main_file_link":[{"url":"https://arxiv.org/abs/1109.5018","open_access":"1"}],"publication_status":"published","year":"2012","date_published":"2012-01-01T00:00:00Z","publisher":"SIAM","quality_controlled":"1","page":"1386 - 1399","article_processing_charge":"No","ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5379"},{"relation":"later_version","id":"2141","status":"public"}]},"language":[{"iso":"eng"}],"status":"public","oa_version":"None","oa":1,"publist_id":"3519"}]