[{"publication":"Molecular Ecology","citation":{"ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","apa":"Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x","chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x.","mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643."},"quality_controlled":"1","page":"3640 - 3643","date_published":"2012-08-01T00:00:00Z","doi":"10.1111/j.1365-294X.2012.05643.x","language":[{"iso":"eng"}],"scopus_import":1,"month":"08","day":"01","year":"2012","_id":"3122","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"intvolume":" 21","author":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"last_name":"Barrett","first_name":"Spencer","full_name":"Barrett, Spencer"}],"date_created":"2018-12-11T12:01:31Z","date_updated":"2021-01-12T07:41:13Z","volume":21,"oa_version":"None","type":"journal_article","abstract":[{"text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ","lang":"eng"}],"publist_id":"3577","issue":"15"},{"date_published":"2012-09-01T00:00:00Z","page":"1195 - 1197","citation":{"chicago":"Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta, and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3162.","mla":"Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience, vol. 15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:10.1038/nn.3162.","short":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience 15 (2012) 1195–1197.","ista":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 15(9), 1195–1197.","apa":"Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., & Smith, S. (2012). Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3162","ieee":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA,” Nature Neuroscience, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197, 2012.","ama":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 2012;15(9):1195-1197. doi:10.1038/nn.3162"},"publication":"Nature Neuroscience","day":"01","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 15","status":"public","title":"Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3121","issue":"9","abstract":[{"text":"Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/nn.3162","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/"}],"oa":1,"external_id":{"pmid":["22842148"]},"month":"09","volume":15,"date_updated":"2021-01-12T07:41:12Z","date_created":"2018-12-11T12:01:30Z","author":[{"full_name":"Williams, Courtney","last_name":"Williams","first_name":"Courtney"},{"full_name":"Chen, Wenyan","first_name":"Wenyan","last_name":"Chen"},{"full_name":"Lee, Chia","last_name":"Lee","first_name":"Chia"},{"last_name":"Yaeger","first_name":"Daniel","full_name":"Yaeger, Daniel"},{"full_name":"Vyleta, Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas","last_name":"Vyleta"},{"full_name":"Smith, Stephen","first_name":"Stephen","last_name":"Smith"}],"publisher":"Nature Publishing Group","department":[{"_id":"PeJo"}],"publication_status":"published","pmid":1,"year":"2012","acknowledgement":"The work was supported by the US National Institutes of Health (DA027110 and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah for helpful comments. ","publist_id":"3578"},{"type":"journal_article","abstract":[{"text":"We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica.","lang":"eng"}],"issue":"4","status":"public","title":"Fano 3 folds in codimension 4 Tom and Jerry Part I","intvolume":" 148","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3120","oa_version":"Preprint","scopus_import":1,"day":"01","page":"1171 - 1194","publication":"Compositio Mathematica","citation":{"ama":"Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 2012;148(4):1171-1194. doi:10.1112/S0010437X11007226","ista":"Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 148(4), 1171–1194.","apa":"Brown, G., Kerber, M., & Reid, M. (2012). Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X11007226","ieee":"G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry Part I,” Compositio Mathematica, vol. 148, no. 4. Cambridge University Press, pp. 1171–1194, 2012.","mla":"Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica, vol. 148, no. 4, Cambridge University Press, 2012, pp. 1171–94, doi:10.1112/S0010437X11007226.","short":"G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194.","chicago":"Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica. Cambridge University Press, 2012. https://doi.org/10.1112/S0010437X11007226."},"date_published":"2012-07-01T00:00:00Z","publist_id":"3579","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Cambridge University Press","acknowledgement":"This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0.","year":"2012","date_updated":"2021-01-12T07:41:12Z","date_created":"2018-12-11T12:01:30Z","volume":148,"author":[{"first_name":"Gavin","last_name":"Brown","full_name":"Brown, Gavin"},{"first_name":"Michael","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"},{"last_name":"Reid","first_name":"Miles","full_name":"Reid, Miles"}],"month":"07","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1009.4313"}],"language":[{"iso":"eng"}],"doi":"10.1112/S0010437X11007226"},{"doi":"10.1016/j.dam.2012.05.025","date_published":"2012-10-01T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1006.1990","open_access":"1"}],"citation":{"chicago":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2012.05.025.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258.","mla":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:10.1016/j.dam.2012.05.025.","apa":"Kolmogorov, V. (2012). Minimizing a sum of submodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2012.05.025","ieee":"V. Kolmogorov, “Minimizing a sum of submodular functions,” Discrete Applied Mathematics, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.","ista":"Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 160(15), 2246–2258.","ama":"Kolmogorov V. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 2012;160(15):2246-2258. doi:10.1016/j.dam.2012.05.025"},"publication":"Discrete Applied Mathematics","page":"2246 - 2258","quality_controlled":"1","day":"01","month":"10","scopus_import":1,"author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","volume":160,"date_created":"2018-12-11T12:01:29Z","date_updated":"2021-01-12T07:41:11Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3117","year":"2012","department":[{"_id":"VlKo"}],"intvolume":" 160","publisher":"Elsevier","title":"Minimizing a sum of submodular functions","publication_status":"published","status":"public","publist_id":"3582","issue":"15","abstract":[{"text":"We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms.","lang":"eng"}],"type":"journal_article"},{"date_published":"2012-06-07T00:00:00Z","publication":"PLoS Genetics","citation":{"short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).","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.","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.","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","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.","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","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740."},"day":"07","has_accepted_license":"1","scopus_import":1,"pubrep_id":"114","file":[{"creator":"system","file_size":1284801,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf","checksum":"729a4becda7d786c4c3db8f9a1f77953","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:08:00Z","file_id":"4659","relation":"main_file"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3131","title":"Limits to the rate of adaptive substitution in sexual populations","ddc":["570","576"],"status":"public","intvolume":" 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."}],"issue":"6","type":"journal_article","doi":"10.1371/journal.pgen.1002740","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"month":"06","author":[{"first_name":"Daniel","last_name":"Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"date_created":"2018-12-11T12:01:34Z","date_updated":"2021-01-12T07:41:17Z","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.","year":"2012","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:46:01Z","ec_funded":1,"publist_id":"3566","article_number":"e1002740"},{"article_number":"e1002803","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"3567","publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","acknowledgement":"We thank Alex Boehm for discussions and comments.","year":"2012","date_updated":"2021-01-12T07:41:16Z","date_created":"2018-12-11T12:01:34Z","volume":8,"author":[{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"},{"first_name":"Olin","last_name":"Silander","full_name":"Silander, Olin"}],"month":"06","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1002803","type":"journal_article","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."}],"issue":"6","ddc":["576"],"title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","status":"public","intvolume":" 8","_id":"3130","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"4973","relation":"main_file","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:12:52Z","checksum":"f8506fb579eda6fc5613ba9bf421b86a","file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":2674138}],"pubrep_id":"386","scopus_import":1,"day":"28","has_accepted_license":"1","publication":"PLoS Genetics","citation":{"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","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.","ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.","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","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.","short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).","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."},"date_published":"2012-06-28T00:00:00Z"},{"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."}],"publist_id":"3561","ec_funded":1,"type":"conference","alternative_title":["LNCS"],"author":[{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"Mateescu","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","full_name":"Mateescu, Maria"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","last_name":"Sezgin","full_name":"Sezgin, Ali"}],"date_updated":"2021-01-12T07:41:18Z","date_created":"2018-12-11T12:01:36Z","volume":"7358 ","oa_version":"None","_id":"3136","acknowledgement":"This work was supported by the ERC Advanced Investigator grant on Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation.","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Delayed continuous time Markov chains for genetic regulatory circuits","status":"public","publication_status":"published","publisher":"Springer","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"day":"01","month":"07","scopus_import":1,"conference":{"location":"Berkeley, CA, USA","start_date":"2012-07-07","end_date":"2012-07-13","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-642-31424-7_24","date_published":"2012-07-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"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","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.","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","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.","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.","short":"C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer, 2012, pp. 294–309.","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."},"quality_controlled":"1","page":"294 - 309","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}]},{"scopus_import":1,"day":"01","citation":{"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","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.","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","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.","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.","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."},"page":"23 - 38","date_published":"2012-07-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","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. "}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3135","intvolume":" 7358","title":"Efficient controller synthesis for consumption games with multiple resource types","status":"public","oa_version":"Preprint","month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1202.0796"}],"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/978-3-642-31424-7_8","conference":{"start_date":"2012-07-07","location":"Berkeley, CA, USA","end_date":"2012-07-13","name":"CAV: Computer Aided Verification"},"language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"3562","year":"2012","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).","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","author":[{"full_name":"Brázdil, Brázdil","last_name":"Brázdil","first_name":"Brázdil"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","first_name":"Petr","full_name":"Novotny, Petr"}],"volume":7358,"date_updated":"2021-01-12T07:41:18Z","date_created":"2018-12-11T12:01:35Z"},{"title":"Alexander duality for functions: The persistent behavior of land and water and shore","status":"public","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"ACM","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3133","year":"2012","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.","date_created":"2018-12-11T12:01:35Z","date_updated":"2021-01-12T07:41:17Z","oa_version":"Preprint","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"first_name":"Michael","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"}],"type":"conference","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. "}],"publist_id":"3564","quality_controlled":"1","page":"249 - 258","publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","citation":{"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","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.","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","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.","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.","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."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.5052"}],"language":[{"iso":"eng"}],"conference":{"location":"Chapel Hill, NC, USA","start_date":"2012-06-17","end_date":"2012-06-20","name":"SCG: Symposium on Computational Geometry"},"date_published":"2012-06-20T00:00:00Z","doi":"10.1145/2261250.2261287","scopus_import":1,"day":"20","month":"06"},{"type":"conference","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"}],"publist_id":"3563","_id":"3134","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.","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions","status":"public","publisher":"ACM","department":[{"_id":"HeEd"}],"author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Fasy, Brittany","last_name":"Fasy","first_name":"Brittany"},{"last_name":"Rote","first_name":"Günter","full_name":"Rote, Günter"}],"related_material":{"record":[{"id":"2815","status":"public","relation":"later_version"}]},"date_updated":"2023-02-23T10:59:27Z","date_created":"2018-12-11T12:01:35Z","oa_version":"None","scopus_import":1,"month":"06","day":"20","publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","citation":{"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.","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.","short":"H. Edelsbrunner, B. Fasy, G. Rote, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100.","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.","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","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"},"quality_controlled":"1","page":"91 - 100","conference":{"name":"SCG: Symposium on Computational Geometry","location":"Chapel Hill, NC, USA","start_date":"2012-06-17","end_date":"2012-06-20"},"doi":"10.1145/2261250.2261265","date_published":"2012-06-20T00:00:00Z","language":[{"iso":"eng"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3132","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.","year":"2012","status":"public","publication_status":"published","title":"Two pathways ensuring social harmony","department":[{"_id":"SyCr"}],"intvolume":" 99","publisher":"Springer","author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Konrad"},{"first_name":"Tobias","last_name":"Pamminger","full_name":"Pamminger, Tobias"},{"full_name":"Foitzik, Susanne","last_name":"Foitzik","first_name":"Susanne"}],"date_updated":"2021-01-12T07:41:17Z","date_created":"2018-12-11T12:01:34Z","oa_version":"None","volume":99,"type":"journal_article","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"}],"publist_id":"3565","issue":"8","publication":"Naturwissenschaften","citation":{"ieee":"M. Konrad, T. Pamminger, and S. Foitzik, “Two pathways ensuring social harmony,” Naturwissenschaften, vol. 99, no. 8. Springer, pp. 627–636, 2012.","apa":"Konrad, M., Pamminger, T., & Foitzik, S. (2012). Two pathways ensuring social harmony. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-012-0943-z","ista":"Konrad M, Pamminger T, Foitzik S. 2012. Two pathways ensuring social harmony. Naturwissenschaften. 99(8), 627–636.","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","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.","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."},"quality_controlled":"1","page":"627 - 636","doi":"10.1007/s00114-012-0943-z","date_published":"2012-08-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"08"},{"date_published":"2012-05-14T00:00:00Z","publication":"PLoS One","citation":{"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","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.","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."},"day":"14","has_accepted_license":"1","scopus_import":1,"file":[{"access_level":"open_access","file_name":"IST-2012-97-v1+1_journal.pone.0036044.pdf","content_type":"application/pdf","file_size":2984012,"creator":"system","relation":"main_file","file_id":"5082","checksum":"30cef37e27eaa467f6571b3640282010","date_created":"2018-12-12T10:14:30Z","date_updated":"2020-07-14T12:46:01Z"}],"oa_version":"Published Version","pubrep_id":"97","status":"public","title":"Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome","ddc":["610"],"intvolume":" 7","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3161","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"}],"issue":"5","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0036044","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"05","date_updated":"2021-01-12T07:41:29Z","date_created":"2018-12-11T12:01:45Z","volume":7,"author":[{"full_name":"Vyleta, Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87","first_name":"Meghan","last_name":"Vyleta"},{"full_name":"Wong, John","first_name":"John","last_name":"Wong"},{"full_name":"Magun, Bruce","last_name":"Magun","first_name":"Bruce"}],"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"SyCr"}],"year":"2012","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.","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"3526","article_number":"e36044"},{"month":"01","conference":{"end_date":"2011-09-30","start_date":"2011-09-27","location":"San Francisco, CA, United States","name":"RV: Runtime Verification"},"doi":"10.1007/978-3-642-29860-8_12","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"3525","author":[{"first_name":"Eugene","last_name":"Asarin","full_name":"Asarin, Eugene"},{"last_name":"Donzé","first_name":"Alexandre","full_name":"Donzé, Alexandre"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T12:01:45Z","date_updated":"2021-01-12T07:41:29Z","volume":7186,"year":"2012","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"date_published":"2012-01-01T00:00:00Z","citation":{"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.","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.","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.","short":"E. Asarin, A. Donzé, O. Maler, D. Nickovic, in:, Springer, 2012, pp. 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."},"page":"147 - 160","abstract":[{"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.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","file":[{"checksum":"ba4a75287008fc64b8fbf78a7476ec32","date_created":"2020-05-15T12:50:15Z","date_updated":"2020-07-14T12:46:01Z","file_id":"7862","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":374726,"access_level":"open_access","file_name":"2012_RV_Asarin.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3162","ddc":["000"],"status":"public","title":"Parametric identification of temporal properties","intvolume":" 7186"},{"_id":"3160","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","publication_status":"published","title":"Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo","status":"public","intvolume":" 11","department":[{"_id":"ToBo"}],"publisher":"Taylor and Francis","author":[{"last_name":"Pantazis","first_name":"Periklis","full_name":"Pantazis, Periklis"},{"full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias"}],"date_created":"2018-12-11T12:01:44Z","date_updated":"2021-01-12T07:41:28Z","volume":11,"oa_version":"None","type":"journal_article","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."}],"publist_id":"3531","issue":"11","publication":"Cell Cycle","citation":{"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.","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.","short":"P. Pantazis, M.T. Bollenbach, Cell Cycle 11 (2012) 2055–2058.","ista":"Pantazis P, Bollenbach MT. 2012. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 11(11), 2055–2058.","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","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.","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"},"quality_controlled":"1","page":"2055 - 2058","date_published":"2012-06-01T00:00:00Z","doi":"10.4161/cc.20118","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"06"},{"page":"257 - 258","quality_controlled":"1","citation":{"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","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","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.","ista":"Blaschko M, Lampert C. 2012. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 99(3), 257–258.","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.","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."},"publication":"International Journal of Computer Vision","language":[{"iso":"eng"}],"date_published":"2012-09-01T00:00:00Z","doi":"10.1007/s11263-012-0530-y","scopus_import":1,"month":"09","day":"01","department":[{"_id":"ChLa"}],"intvolume":" 99","publisher":"Springer","status":"public","publication_status":"published","title":"Guest editorial: Special issue on structured prediction and inference","_id":"3164","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","volume":99,"oa_version":"None","date_updated":"2021-01-12T07:41:30Z","date_created":"2018-12-11T12:01:46Z","author":[{"full_name":"Blaschko, Matthew","last_name":"Blaschko","first_name":"Matthew"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"type":"journal_article","issue":"3","publist_id":"3521","abstract":[{"text":"Overview of the Special Issue on structured prediction and inference.","lang":"eng"}]},{"abstract":[{"lang":"eng","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)"}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":4099536,"creator":"system","access_level":"open_access","file_name":"IST-2012-99-v1+1_1745-6150-7-6.pdf","checksum":"e511e401e239ef608a7fd79b21a06d78","date_created":"2018-12-12T10:15:44Z","date_updated":"2020-07-14T12:46:02Z","relation":"main_file","file_id":"5166"}],"oa_version":"Published Version","pubrep_id":"99","intvolume":" 7","status":"public","ddc":["570","576"],"title":"Amino acid fermentation at the origin of the genetic code","_id":"3166","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"10","date_published":"2012-02-10T00:00:00Z","citation":{"chicago":"Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6.","mla":"de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6.","short":"H. de Vladar, Biology Direct 7 (2012).","ista":"de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6.","apa":"de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6","ieee":"H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” Biology Direct, vol. 7. BioMed Central, 2012.","ama":"de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-6"},"publication":"Biology Direct","publist_id":"3518","ec_funded":1,"file_date_updated":"2020-07-14T12:46:02Z","article_number":"6","volume":7,"date_created":"2018-12-11T12:01:46Z","date_updated":"2021-01-12T07:41:31Z","author":[{"full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","first_name":"Harold"}],"publisher":"BioMed Central","department":[{"_id":"NiBa"}],"publication_status":"published","acknowledgement":"The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ","year":"2012","month":"02","language":[{"iso":"eng"}],"doi":"10.1186/1745-6150-7-6","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"language":[{"iso":"eng"}],"date_published":"2012-04-06T00:00:00Z","doi":"10.1126/science.336.6077.32","page":"32-34","article_type":"letter_note","external_id":{"pmid":["22491839"]},"citation":{"short":"M. Weber, Science 336 (2012) 32–34.","mla":"Weber, Michele. “NextGen Speaks 13 .” Science, vol. 336, no. 6077, American Association for the Advancement of Science, 2012, pp. 32–34, doi:10.1126/science.336.6077.32.","chicago":"Weber, Michele. “NextGen Speaks 13 .” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.336.6077.32.","ama":"Weber M. NextGen speaks 13 . Science. 2012;336(6077):32-34. doi:10.1126/science.336.6077.32","ieee":"M. Weber, “NextGen speaks 13 ,” Science, vol. 336, no. 6077. American Association for the Advancement of Science, pp. 32–34, 2012.","apa":"Weber, M. (2012). NextGen speaks 13 . Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.336.6077.32","ista":"Weber M. 2012. NextGen speaks 13 . Science. 336(6077), 32–34."},"publication":"Science","day":"06","month":"04","oa_version":"None","volume":336,"date_updated":"2021-01-12T07:41:32Z","date_created":"2018-12-11T12:01:47Z","popular_science":"1","author":[{"id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Weber","full_name":"Weber, Michele"}],"intvolume":" 336","publisher":"American Association for the Advancement of Science","department":[{"_id":"MiSi"}],"title":"NextGen speaks 13 ","status":"public","publication_status":"published","pmid":1,"_id":"3167","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6077","publist_id":"3516","type":"journal_article"},{"quality_controlled":0,"page":"116 - 135","publication":"Journal of Cryptology","citation":{"ista":"Pietrzak KZ, Wikström D. 2012. Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. 25(1), 116–135.","ieee":"K. Z. Pietrzak and D. Wikström, “Parallel repetition of computationally sound protocols revisited,” Journal of Cryptology, vol. 25, no. 1. Springer, pp. 116–135, 2012.","apa":"Pietrzak, K. Z., & Wikström, D. (2012). Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-010-9090-x","ama":"Pietrzak KZ, Wikström D. Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. 2012;25(1):116-135. doi:10.1007/s00145-010-9090-x","chicago":"Pietrzak, Krzysztof Z, and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited.” Journal of Cryptology. Springer, 2012. https://doi.org/10.1007/s00145-010-9090-x.","mla":"Pietrzak, Krzysztof Z., and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited.” Journal of Cryptology, vol. 25, no. 1, Springer, 2012, pp. 116–35, doi:10.1007/s00145-010-9090-x.","short":"K.Z. Pietrzak, D. Wikström, Journal of Cryptology 25 (2012) 116–135."},"date_published":"2012-11-01T00:00:00Z","doi":"10.1007/s00145-010-9090-x","month":"11","day":"01","title":"Parallel repetition of computationally sound protocols revisited","publication_status":"published","status":"public","publisher":"Springer","intvolume":" 25","year":"2012","_id":"3241","date_created":"2018-12-11T12:02:12Z","date_updated":"2021-01-12T07:42:03Z","volume":25,"author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Krzysztof Pietrzak"},{"first_name":"Douglas","last_name":"Wikström","full_name":"Wikström, Douglas"}],"type":"journal_article","extern":1,"abstract":[{"text":"We prove a negative result concerning error reduction by parallel repetition for computationally sound protocols, e.g., interactive arguments. Our main result is a complete and computationally sound eight round interactive argument for which k-fold parallel repetition does not reduce the error below a constant for any polynomial k. The starting point for our construction is the work of Bellare, Impagliazzo and Naor (FOCS'97). For any fixed k, they construct a four round protocol for which k-fold parallel repetition does not lower the soundness error. The communication complexity of this protocol is linear in k. By using universal arguments due to Barak and Goldreich (CCC 2002), we turn this protocol into an eight-round protocol whose complexity is basically independent of k. ","lang":"eng"}],"issue":"1","publist_id":"3439"},{"day":"20","scopus_import":1,"date_published":"2012-01-20T00:00:00Z","page":"152 - 168","citation":{"short":"K. Chatterjee, V. Raman, in:, Springer, 2012, pp. 152–168.","mla":"Chatterjee, Krishnendu, and Vishwanath Raman. Synthesizing Protocols for Digital Contract Signing. Vol. 7148, Springer, 2012, pp. 152–68, doi:10.1007/978-3-642-27940-9_11.","chicago":"Chatterjee, Krishnendu, and Vishwanath Raman. “Synthesizing Protocols for Digital Contract Signing,” 7148:152–68. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_11.","ama":"Chatterjee K, Raman V. Synthesizing protocols for digital contract signing. In: Vol 7148. Springer; 2012:152-168. doi:10.1007/978-3-642-27940-9_11","apa":"Chatterjee, K., & 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. https://doi.org/10.1007/978-3-642-27940-9_11","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."},"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."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 7148","title":"Synthesizing protocols for digital contract signing","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3252","month":"01","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-27940-9_11","conference":{"location":"Philadelphia, PA, USA","start_date":"2012-01-22","end_date":"2012-01-24","name":"VMCAI: Verification, Model Checking and Abstract Interpretation"},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1004.2697","open_access":"1"}],"oa":1,"publist_id":"3405","ec_funded":1,"volume":7148,"date_updated":"2021-01-12T07:42:08Z","date_created":"2018-12-11T12:02:16Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Raman, Vishwanath","last_name":"Raman","first_name":"Vishwanath"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2012","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."},{"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"date_created":"2018-12-11T12:02:17Z","date_updated":"2021-01-12T07:42:10Z","volume":7119,"acknowledgement":"This work was partially supported by FWF NFN Grant S11407-N23 (RiSE) and a Microsoft faculty fellowship.","year":"2012","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:05Z","publist_id":"3400","conference":{"start_date":"2011-10-14","location":"Lednice, Czech Republic","end_date":"2011-10-16","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"doi":"10.1007/978-3-642-25929-6_3","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"month":"01","oa_version":"Submitted Version","file":[{"creator":"dernst","file_size":114060,"content_type":"application/pdf","file_name":"2012_MEMICS_Chatterjee.pdf","access_level":"open_access","date_created":"2020-05-15T12:53:12Z","date_updated":"2020-07-14T12:46:05Z","checksum":"eed2cc1e76b160418c977e76e8899a60","file_id":"7863","relation":"main_file"}],"_id":"3255","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"status":"public","title":"Games and Markov decision processes with mean payoff parity and energy parity objectives","intvolume":" 7119","abstract":[{"text":"In this paper we survey results of two-player games on graphs and Markov decision processes with parity, mean-payoff and energy objectives, and the combination of mean-payoff and energy objectives with parity objectives. These problems have applications in verification and synthesis of reactive systems in resource-constrained environments.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2012-01-01T00:00:00Z","citation":{"ama":"Chatterjee K, Doyen L. Games and Markov decision processes with mean payoff parity and energy parity objectives. In: Vol 7119. Springer; 2012:37-46. doi:10.1007/978-3-642-25929-6_3","ista":"Chatterjee K, Doyen L. 2012. Games and Markov decision processes with mean payoff parity and energy parity objectives. MEMICS: Mathematical and Engineering Methods in Computer Science, LNCS, vol. 7119, 37–46.","apa":"Chatterjee, K., & Doyen, L. (2012). Games and Markov decision processes with mean payoff parity and energy parity objectives (Vol. 7119, pp. 37–46). Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-25929-6_3","ieee":"K. Chatterjee and L. Doyen, “Games and Markov decision processes with mean payoff parity and energy parity objectives,” presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic, 2012, vol. 7119, pp. 37–46.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives. Vol. 7119, Springer, 2012, pp. 37–46, doi:10.1007/978-3-642-25929-6_3.","short":"K. Chatterjee, L. Doyen, in:, Springer, 2012, pp. 37–46.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives,” 7119:37–46. Springer, 2012. https://doi.org/10.1007/978-3-642-25929-6_3."},"page":"37 - 46","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1}]