[{"type":"journal_article","date_published":"2009-05-04T00:00:00Z","publication_status":"published","doi":"10.1103/PhysRevE.79.051901","date_created":"2018-12-11T12:04:56Z","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","intvolume":" 79","volume":79,"quality_controlled":0,"citation":{"chicago":"Tkačik, Gašper, and William Bialek. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2009. https://doi.org/10.1103/PhysRevE.79.051901.","apa":"Tkačik, G., & Bialek, W. (2009). Diffusion, dimensionality, and noise in transcriptional regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.79.051901","mla":"Tkačik, Gašper, and William Bialek. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5, American Institute of Physics, 2009, doi:10.1103/PhysRevE.79.051901.","ista":"Tkačik G, Bialek W. 2009. Diffusion, dimensionality, and noise in transcriptional regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 79(5).","ieee":"G. Tkačik and W. Bialek, “Diffusion, dimensionality, and noise in transcriptional regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5. American Institute of Physics, 2009.","ama":"Tkačik G, Bialek W. Diffusion, dimensionality, and noise in transcriptional regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2009;79(5). doi:10.1103/PhysRevE.79.051901","short":"G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 79 (2009)."},"publist_id":"2483","author":[{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik"},{"full_name":"Bialek, William S","last_name":"Bialek","first_name":"William"}],"_id":"3745","date_updated":"2021-01-12T07:51:54Z","abstract":[{"lang":"eng","text":"The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to specific sites on DNA and regulating transcription, the ability of the proteins to diffuse in one dimension by sliding along the length of the DNA, in addition to their diffusion in bulk solution, would seem to generate a larger target for DNA binding, consequently reducing the noise in the occupancy of the regulatory site. Here we show that this effect is largely canceled by the enhanced temporal correlations in one-dimensional diffusion. With realistic parameters, sliding along DNA has surprisingly little effect on the physical limits to the precision of transcriptional regulation."}],"issue":"5","day":"04","extern":1,"year":"2009","month":"05","status":"public","publisher":"American Institute of Physics","title":"Diffusion, dimensionality, and noise in transcriptional regulation"},{"publisher":"Springer","status":"public","title":"Cell Biology: Networks, regulation, pathways","month":"01","date_updated":"2021-01-12T07:51:54Z","extern":1,"year":"2009","day":"01","author":[{"full_name":"Gasper Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William S"}],"_id":"3747","publist_id":"2481","quality_controlled":0,"citation":{"short":"G. Tkačik, W. Bialek, in:, R. Meyers (Ed.), Encyclopedia of Complexity and Systems Science, Springer, 2009, pp. 719–741.","ama":"Tkačik G, Bialek W. Cell Biology: Networks, regulation, pathways. In: Meyers R, ed. Encyclopedia of Complexity and Systems Science. Springer; 2009:719-741. doi:10.1007/978-0-387-30440-3_48","ieee":"G. Tkačik and W. Bialek, “Cell Biology: Networks, regulation, pathways,” in Encyclopedia of Complexity and Systems Science, R. Meyers, Ed. Springer, 2009, pp. 719–741.","ista":"Tkačik G, Bialek W. 2009.Cell Biology: Networks, regulation, pathways. In: Encyclopedia of Complexity and Systems Science. , 719–741.","mla":"Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” Encyclopedia of Complexity and Systems Science, edited by R. Meyers, Springer, 2009, pp. 719–41, doi:10.1007/978-0-387-30440-3_48.","apa":"Tkačik, G., & Bialek, W. (2009). Cell Biology: Networks, regulation, pathways. In R. Meyers (Ed.), Encyclopedia of Complexity and Systems Science (pp. 719–741). Springer. https://doi.org/10.1007/978-0-387-30440-3_48","chicago":"Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” In Encyclopedia of Complexity and Systems Science, edited by R. Meyers, 719–41. Springer, 2009. https://doi.org/10.1007/978-0-387-30440-3_48."},"editor":[{"first_name":"R.","last_name":"Meyers","full_name":"Meyers,R. A."}],"doi":"10.1007/978-0-387-30440-3_48","publication_status":"published","publication":"Encyclopedia of Complexity and Systems Science","page":"719 - 741","date_created":"2018-12-11T12:04:56Z","type":"book_chapter","date_published":"2009-01-01T00:00:00Z"},{"oa_version":"None","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2009-08-01T00:00:00Z","publication_status":"published","doi":"10.1145/1531326.1531382","date_created":"2018-12-11T12:05:02Z","publication":"ACM Transactions on Graphics","volume":28,"intvolume":" 28","citation":{"short":"C. Wojtan, N. Thürey, M. Gross, G. Turk, ACM Transactions on Graphics 28 (2009).","ieee":"C. Wojtan, N. Thürey, M. Gross, and G. Turk, “Deforming meshes that split and merge,” ACM Transactions on Graphics, vol. 28, no. 3. ACM, 2009.","ama":"Wojtan C, Thürey N, Gross M, Turk G. Deforming meshes that split and merge. ACM Transactions on Graphics. 2009;28(3). doi:10.1145/1531326.1531382","ista":"Wojtan C, Thürey N, Gross M, Turk G. 2009. Deforming meshes that split and merge. ACM Transactions on Graphics. 28(3).","mla":"Wojtan, Chris, et al. “Deforming Meshes That Split and Merge.” ACM Transactions on Graphics, vol. 28, no. 3, ACM, 2009, doi:10.1145/1531326.1531382.","apa":"Wojtan, C., Thürey, N., Gross, M., & Turk, G. (2009). Deforming meshes that split and merge. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1531326.1531382","chicago":"Wojtan, Chris, Nils Thürey, Markus Gross, and Greg Turk. “Deforming Meshes That Split and Merge.” ACM Transactions on Graphics. ACM, 2009. https://doi.org/10.1145/1531326.1531382."},"publist_id":"2466","article_processing_charge":"No","author":[{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Thürey","first_name":"Nils","full_name":"Thürey, Nils"},{"first_name":"Markus","last_name":"Gross","full_name":"Gross, Markus"},{"full_name":"Turk, Greg","last_name":"Turk","first_name":"Greg"}],"_id":"3764","date_updated":"2023-02-23T11:41:39Z","abstract":[{"lang":"eng","text":"We present a method for accurately tracking the moving surface of deformable materials in a manner that gracefully handles topological changes. We employ a Lagrangian surface tracking method, and we use a triangle mesh for our surface representation so that fine features can be retained. We make topological changes to the mesh by first identifying merging or splitting events at a particular grid resolution, and then locally creating new pieces of the mesh in the affected cells using a standard isosurface creation method. We stitch the new, topologically simplified portion of the mesh to the rest of the mesh at the cell boundaries. Our method detects and treats topological events with an emphasis on the preservation of detailed features, while simultaneously simplifying those portions of the material that are not visible. Our surface tracker is not tied to a particular method for simulating deformable materials. In particular, we show results from two significantly different simulators: a Lagrangian FEM simulator with tetrahedral elements, and an Eulerian grid-based fluid simulator. Although our surface tracking method is generic, it is particularly well-suited for simulations that exhibit fine surface details and numerous topological events. Highlights of our results include merging of viscoplastic materials with complex geometry, a taffy-pulling animation with many fold and merge events, and stretching and slicing of stiff plastic material."}],"issue":"3","day":"01","extern":"1","year":"2009","month":"08","status":"public","publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Deforming meshes that split and merge"},{"month":"01","title":"Comment on '{A} congruence index for testing topological similarity between trees'.","publisher":"Oxford University Press","status":"public","_id":"3768","author":[{"full_name":"Anne Kupczok","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne"},{"full_name":"von Haeseler,Arndt","last_name":"Von Haeseler","first_name":"Arndt"}],"day":"01","year":"2009","extern":1,"date_updated":"2021-01-12T07:52:03Z","acknowledgement":"10.1093/bioinformatics/btn539","issue":"1","volume":25,"intvolume":" 25","citation":{"ieee":"A. Kupczok and A. Von Haeseler, “Comment on ‘{A} congruence index for testing topological similarity between trees’.,” Bioinformatics, vol. 25, no. 1. Oxford University Press, pp. 147–149, 2009.","ama":"Kupczok A, Von Haeseler A. Comment on “{A} congruence index for testing topological similarity between trees”. Bioinformatics. 2009;25(1):147-149. doi:4199","short":"A. Kupczok, A. Von Haeseler, Bioinformatics 25 (2009) 147–149.","chicago":"Kupczok, Anne, and Arndt Von Haeseler. “Comment on ‘{A} Congruence Index for Testing Topological Similarity between Trees’.” Bioinformatics. Oxford University Press, 2009. https://doi.org/4199.","mla":"Kupczok, Anne, and Arndt Von Haeseler. “Comment on ‘{A} Congruence Index for Testing Topological Similarity between Trees’.” Bioinformatics, vol. 25, no. 1, Oxford University Press, 2009, pp. 147–49, doi:4199.","ista":"Kupczok A, Von Haeseler A. 2009. Comment on ‘{A} congruence index for testing topological similarity between trees’. Bioinformatics. 25(1), 147–149.","apa":"Kupczok, A., & Von Haeseler, A. (2009). Comment on “{A} congruence index for testing topological similarity between trees”. Bioinformatics. Oxford University Press. https://doi.org/4199"},"quality_controlled":0,"publist_id":"2459","date_published":"2009-01-01T00:00:00Z","type":"journal_article","page":"147 - 149","date_created":"2018-12-11T12:05:04Z","publication":"Bioinformatics","publication_status":"published","doi":"4199"},{"scopus_import":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-00554594/document","open_access":"1"}],"intvolume":" 259","citation":{"apa":"Barton, N. H., & Coe, J. (2009). On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2009.03.019","ista":"Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324.","mla":"Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” Journal of Theoretical Biology, vol. 259, no. 2, Elsevier, 2009, pp. 317–24, doi:10.1016/j.jtbi.2009.03.019.","chicago":"Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” Journal of Theoretical Biology. Elsevier, 2009. https://doi.org/10.1016/j.jtbi.2009.03.019.","ama":"Barton NH, Coe J. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 2009;259(2):317-324. doi:10.1016/j.jtbi.2009.03.019","ieee":"N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” Journal of Theoretical Biology, vol. 259, no. 2. Elsevier, pp. 317–324, 2009.","short":"N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324."},"publication_status":"published","doi":"10.1016/j.jtbi.2009.03.019","date_published":"2009-07-21T00:00:00Z","oa_version":"Submitted Version","oa":1,"status":"public","month":"07","year":"2009","date_updated":"2021-01-12T07:52:06Z","issue":"2","abstract":[{"text":"There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits.","lang":"eng"}],"_id":"3775","publist_id":"2452","quality_controlled":"1","volume":259,"page":"317 - 324","date_created":"2018-12-11T12:05:06Z","publication":"Journal of Theoretical Biology","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"type":"journal_article","title":"On the application of statistical physics to evolutionary biology","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"21","acknowledgement":"This work was supported by a Royal Society/Wolfson Award, and by grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates, H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments.","author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Jason","last_name":"Coe","full_name":"Coe, Jason"}]},{"acknowledgement":"We owe a great debt to Jim Murray for his many contributions to the study of Partula, in the field, in the laboratory, in the interpretation of data, and in generating new ideas about evolution. With pleasure and respect we dedicate this paper to him. Jim Murray played a leading role in making the collections used here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis. Comments from an anonymous referee, A. Richard Palmer and the editorial board improved the manuscript. Work in the field was supported by the Royal Society, The Carnegie Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society and the University of Nottingham supported work in the laboratory.","day":"01","author":[{"first_name":"Angus","last_name":"Davison","full_name":"Davison, Angus"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Clarke, Bryan","last_name":"Clarke","first_name":"Bryan"}],"file":[{"file_size":2583812,"content_type":"application/pdf","relation":"main_file","date_created":"2019-02-22T09:21:44Z","date_updated":"2020-07-14T12:46:15Z","file_name":"Davison_JEB_v31_2009.pdf","access_level":"open_access","creator":"dernst","file_id":"6044","checksum":"f70c15c6ab9306121d4153a3be0d2346"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","title":"The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails","has_accepted_license":"1","publication":"Journal of Evolutionary Biology","page":"1624 - 1635","date_created":"2018-12-11T12:05:08Z","type":"journal_article","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"pubrep_id":"553","publist_id":"2447","volume":22,"quality_controlled":"1","abstract":[{"text":"Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (< 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act.","lang":"eng"}],"issue":"8","date_updated":"2021-01-12T07:52:09Z","year":"2009","_id":"3780","status":"public","oa":1,"month":"08","doi":"10.1111/j.1420-9101.2009.01770.x","publication_status":"published","oa_version":"Submitted Version","date_published":"2009-08-01T00:00:00Z","scopus_import":1,"file_date_updated":"2020-07-14T12:46:15Z","ddc":["570"],"citation":{"ieee":"A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails,” Journal of Evolutionary Biology, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.","ama":"Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 2009;22(8):1624-1635. doi:10.1111/j.1420-9101.2009.01770.x","short":"A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009) 1624–1635.","ista":"Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 22(8), 1624–1635.","apa":"Davison, A., Barton, N. H., & Clarke, B. (2009). The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/j.1420-9101.2009.01770.x","mla":"Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology, vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:10.1111/j.1420-9101.2009.01770.x.","chicago":"Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology. Wiley, 2009. https://doi.org/10.1111/j.1420-9101.2009.01770.x."},"intvolume":" 22"},{"publication_status":"published","doi":"10.1126/science.1167852","page":"1313 - 9","date_created":"2018-12-11T12:05:23Z","publication":"Science","type":"journal_article","date_published":"2009-01-01T00:00:00Z","publist_id":"2382","citation":{"chicago":"Schwenk, Jochen, Nadine Harmel, Gerd Zolles, Wolfgang Bildl, Ákos Kulik, Bernd Heimrich, Osamu Chisaka, et al. “Functional Proteomics Identify Cornichon Proteins as Auxiliary Subunits of AMPA Receptors.” Science. American Association for the Advancement of Science, 2009. https://doi.org/10.1126/science.1167852.","mla":"Schwenk, Jochen, et al. “Functional Proteomics Identify Cornichon Proteins as Auxiliary Subunits of AMPA Receptors.” Science, vol. 323, no. 5919, American Association for the Advancement of Science, 2009, pp. 1313–19, doi:10.1126/science.1167852.","ista":"Schwenk J, Harmel N, Zolles G, Bildl W, Kulik Á, Heimrich B, Chisaka O, Jonas PM, Schulte U, Fakler B, Klocker N. 2009. Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors. Science. 323(5919), 1313–9.","apa":"Schwenk, J., Harmel, N., Zolles, G., Bildl, W., Kulik, Á., Heimrich, B., … Klocker, N. (2009). Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1167852","short":"J. Schwenk, N. Harmel, G. Zolles, W. Bildl, Á. Kulik, B. Heimrich, O. Chisaka, P.M. Jonas, U. Schulte, B. Fakler, N. Klocker, Science 323 (2009) 1313–9.","ama":"Schwenk J, Harmel N, Zolles G, et al. Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors. Science. 2009;323(5919):1313-1319. doi:10.1126/science.1167852","ieee":"J. Schwenk et al., “Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors,” Science, vol. 323, no. 5919. American Association for the Advancement of Science, pp. 1313–9, 2009."},"quality_controlled":0,"intvolume":" 323","volume":323,"date_updated":"2021-01-12T07:52:29Z","issue":"5919","abstract":[{"text":"Glutamate receptors of the AMPA-subtype (AMPARs), together with the transmembrane AMPAR regulatory proteins (TARPs), mediate fast excitatory synaptic transmission in the mammalian brain. Here, we show by proteomic analysis that the majority of AMPARs in the rat brain are coassembled with two members of the cornichon family of transmembrane proteins, rather than with the TARPs. Coassembly with cornichon homologs 2 and 3 affects AMPARs in two ways: Cornichons increase surface expression of AMPARs, and they alter channel gating by markedly slowing deactivation and desensitization kinetics. These results demonstrate that cornichons are intrinsic auxiliary subunits of native AMPARs and provide previously unknown molecular determinants for glutamatergic neurotransmission in the central nervous system.","lang":"eng"}],"day":"01","extern":1,"year":"2009","author":[{"last_name":"Schwenk","first_name":"Jochen","full_name":"Schwenk, Jochen"},{"first_name":"Nadine","last_name":"Harmel","full_name":"Harmel, Nadine"},{"first_name":"Gerd","last_name":"Zolles","full_name":"Zolles, Gerd"},{"last_name":"Bildl","first_name":"Wolfgang","full_name":"Bildl, Wolfgang"},{"last_name":"Kulik","first_name":"Ákos","full_name":"Kulik, Ákos"},{"first_name":"Bernd","last_name":"Heimrich","full_name":"Heimrich, Bernd"},{"full_name":"Chisaka, Osamu","first_name":"Osamu","last_name":"Chisaka"},{"full_name":"Peter Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schulte, Uwe","last_name":"Schulte","first_name":"Uwe"},{"last_name":"Fakler","first_name":"Bernd","full_name":"Fakler, Bernd"},{"last_name":"Klocker","first_name":"Nikolaj","full_name":"Klocker, Nikolaj"}],"_id":"3828","status":"public","publisher":"American Association for the Advancement of Science","title":"Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors","month":"01"},{"month":"12","title":"Synthesizing robust systems","publisher":"Springer","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3835","author":[{"last_name":"Bloem","first_name":"Roderick","full_name":"Bloem, Roderick"},{"first_name":"Karin","last_name":"Greimel","full_name":"Greimel, Karin"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"}],"day":"11","year":"2009","extern":"1","date_updated":"2022-03-21T08:25:44Z","abstract":[{"text":"Many specifications include assumptions on the environment. If the environment satisfies the assumptions then a correct system reacts as intended. However, when the environment deviates from its expected behavior, a correct system can behave arbitrarily. We want to synthesize robust systems that degrade gracefully, i.e., a small number of environment failures should induce a small number of system failures. We define ratio games and show that an optimal robust system corresponds to the winning strategy of a ratio game, where the system minimizes the ratio of system errors to environment errors. We show that ratio games can be solved in pseudopolynomial time.","lang":"eng"}],"acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European Combest, Quasimodo, and Gasics projects, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification) funded by the F.R.S.-FNRS.","citation":{"mla":"Bloem, Roderick, et al. Synthesizing Robust Systems. Springer, 2009, pp. 85–92, doi:10.1109/FMCAD.2009.5351139.","apa":"Bloem, R., Greimel, K., Henzinger, T. A., & Jobstmann, B. (2009). Synthesizing robust systems (pp. 85–92). Presented at the FMCAD: Formal Methods in Computer-Aided Design, Springer. https://doi.org/10.1109/FMCAD.2009.5351139","ista":"Bloem R, Greimel K, Henzinger TA, Jobstmann B. 2009. Synthesizing robust systems. FMCAD: Formal Methods in Computer-Aided Design, 85–92.","chicago":"Bloem, Roderick, Karin Greimel, Thomas A Henzinger, and Barbara Jobstmann. “Synthesizing Robust Systems,” 85–92. Springer, 2009. https://doi.org/10.1109/FMCAD.2009.5351139.","ama":"Bloem R, Greimel K, Henzinger TA, Jobstmann B. Synthesizing robust systems. In: Springer; 2009:85-92. doi:10.1109/FMCAD.2009.5351139","ieee":"R. Bloem, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Synthesizing robust systems,” presented at the FMCAD: Formal Methods in Computer-Aided Design, 2009, pp. 85–92.","short":"R. Bloem, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, Springer, 2009, pp. 85–92."},"quality_controlled":"1","scopus_import":"1","publist_id":"2373","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2009-12-11T00:00:00Z","type":"conference","oa_version":"None","page":"85 - 92","date_created":"2018-12-11T12:05:26Z","publication_status":"published","conference":{"name":"FMCAD: Formal Methods in Computer-Aided Design"},"doi":"10.1109/FMCAD.2009.5351139"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","title":"On relational interfaces","author":[{"last_name":"Tripakis","first_name":"Stavros","full_name":"Tripakis, Stavros"},{"last_name":"Lickly","first_name":"Ben","full_name":"Lickly, Ben"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Edward","last_name":"Lee","full_name":"Lee, Edward"}],"project":[{"name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543"},{"name":"Design for Embedded Systems","call_identifier":"FP7","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"file":[{"access_level":"open_access","creator":"system","file_id":"5045","checksum":"3a70e21527dfaad2f198549ae5710786","date_created":"2018-12-12T10:13:57Z","file_name":"IST-2012-70-v1+1_On_Relational_Interfaces.pdf","date_updated":"2020-07-14T12:46:16Z","file_size":310902,"relation":"main_file","content_type":"application/pdf"}],"acknowledgement":"This work is supported by the Center for Hybrid and Embedded Software Systems (CHESS) at UC Berkeley, which receives support from the National Science Foundation (NSF awards #0720882 (CSR-EHS: PRET) and #0720841 (CSR-CPS)), the U.S. Army Research Office (ARO #W911NF-07-2-0019), the U.S. Air Force Office of Scientific Research (MURI #FA9550-06-0312), the Air Force Research Lab (AFRL), the State of California Micro Program, and the following companies: Agilent, Bosch, Lockheed-Martin, National Instruments, Thales and Toyota. This work is also supported by the COMBEST and ArtistDesign projects of the European Union, and the Swiss National Science Foundation. ","day":"01","quality_controlled":"1","pubrep_id":"70","publist_id":"2360","type":"conference","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"EMSOFT '09 Proceedings of the seventh ACM international conference on Embedded software","date_created":"2018-12-11T12:05:26Z","page":"67 - 76","month":"01","ec_funded":1,"status":"public","oa":1,"_id":"3837","abstract":[{"text":"In this paper we extend the work of Alfaro, Henzinger et al. on interface theories for component-based design. Existing interface theories often fail to capture functional relations between the inputs and outputs of an interface. For example, a simple synchronous interface that takes as input a number n ≥ 0 and returns, at the same time, as output n + 1, cannot be expressed in existing theories. In this paper we provide a theory of relational interfaces, where such input-output relations can be captured. Our theory supports synchronous interfaces, both stateless and stateful. It includes explicit notions of environments and pluggability, and satisfies fundamental properties such as preservation of refinement by composition, and characterization of pluggability by refinement. We achieve these properties by making reasonable restrictions on feedback loops in interface compositions.","lang":"eng"}],"date_updated":"2021-01-12T07:52:33Z","year":"2009","citation":{"short":"S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, in:, EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp. 67–76.","ama":"Tripakis S, Lickly B, Henzinger TA, Lee E. On relational interfaces. In: EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software. ACM; 2009:67-76. doi:10.1145/1629335.1629346","ieee":"S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,” in EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software, Grenoble, France, 2009, pp. 67–76.","chicago":"Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On Relational Interfaces.” In EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, 67–76. ACM, 2009. https://doi.org/10.1145/1629335.1629346.","mla":"Tripakis, Stavros, et al. “On Relational Interfaces.” EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp. 67–76, doi:10.1145/1629335.1629346.","ista":"Tripakis S, Lickly B, Henzinger TA, Lee E. 2009. On relational interfaces. EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software. EMSOFT: Embedded Software , 67–76.","apa":"Tripakis, S., Lickly, B., Henzinger, T. A., & Lee, E. (2009). On relational interfaces. In EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software (pp. 67–76). Grenoble, France: ACM. https://doi.org/10.1145/1629335.1629346"},"file_date_updated":"2020-07-14T12:46:16Z","ddc":["004"],"oa_version":"Submitted Version","date_published":"2009-01-01T00:00:00Z","doi":"10.1145/1629335.1629346","publication_status":"published","conference":{"name":"EMSOFT: Embedded Software ","start_date":"2009-10-12","location":"Grenoble, France","end_date":"2009-10-16"}},{"scopus_import":1,"file_date_updated":"2020-07-14T12:46:16Z","ddc":["005"],"citation":{"short":"T.A. Henzinger, B. Jobstmann, V. Wolf, in:, Springer, 2009, pp. 3–23.","ieee":"T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” presented at the RP: Reachability Problems, Palaiseau, France, 2009, vol. 5797, pp. 3–23.","ama":"Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. In: Vol 5797. Springer; 2009:3-23. doi:10.1007/978-3-642-04420-5_2","chicago":"Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models,” 5797:3–23. Springer, 2009. https://doi.org/10.1007/978-3-642-04420-5_2.","mla":"Henzinger, Thomas A., et al. Formalisms for Specifying Markovian Population Models. Vol. 5797, Springer, 2009, pp. 3–23, doi:10.1007/978-3-642-04420-5_2.","apa":"Henzinger, T. A., Jobstmann, B., & Wolf, V. (2009). Formalisms for specifying Markovian population models (Vol. 5797, pp. 3–23). Presented at the RP: Reachability Problems, Palaiseau, France: Springer. https://doi.org/10.1007/978-3-642-04420-5_2","ista":"Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23."},"intvolume":" 5797","doi":"10.1007/978-3-642-04420-5_2","publication_status":"published","conference":{"location":"Palaiseau, France","end_date":"2009-09-25","name":"RP: Reachability Problems","start_date":"2009-09-23"},"oa_version":"Submitted Version","date_published":"2009-09-07T00:00:00Z","status":"public","oa":1,"month":"09","abstract":[{"text":"We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages —matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models— all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model. ","lang":"eng"}],"date_updated":"2023-02-23T11:24:49Z","year":"2009","_id":"3841","pubrep_id":"67","publist_id":"2352","volume":5797,"quality_controlled":"1","related_material":{"record":[{"relation":"later_version","status":"public","id":"3381"}]},"has_accepted_license":"1","date_created":"2018-12-11T12:05:28Z","page":"3 - 23","type":"conference","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"Formalisms for specifying Markovian population models","alternative_title":["LNCS"],"acknowledgement":"This research was supported in part by the Excellence Cluster on Multimodal Computing and Interaction and the Swiss National Science Foundation.","day":"07","author":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"},{"full_name":"Wolf, Verena","last_name":"Wolf","first_name":"Verena"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":222840,"checksum":"df88431872586c773fbcfea37d7b36a2","file_id":"4702","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:46:16Z","file_name":"IST-2012-67-v1+1_Formalisms_for_specifying_Markovian_population_models.pdf","date_created":"2018-12-12T10:08:41Z"}]},{"publist_id":"2348","article_processing_charge":"No","related_material":{"record":[{"id":"3842","relation":"later_version","status":"public"}]},"volume":4,"quality_controlled":"1","page":"118 - 127","date_created":"2018-12-11T12:05:28Z","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"type":"conference","title":"Fast adaptive uniformization of the chemical master equation","publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","acknowledgement":"This research has been partially funded by the Swiss National Science Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal Computing and Interaction at Saarland University.","file":[{"file_size":222890,"content_type":"application/pdf","relation":"main_file","date_created":"2020-05-19T16:33:55Z","date_updated":"2020-07-14T12:46:17Z","file_name":"2009_HIBI_Didier.pdf","access_level":"open_access","checksum":"9a3bde48f43203991a0b3c6a277c2f5b","file_id":"7874","creator":"dernst"}],"author":[{"full_name":"Didier, Frédéric","first_name":"Frédéric","last_name":"Didier"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Mateescu, Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","last_name":"Mateescu","first_name":"Maria"},{"first_name":"Verena","last_name":"Wolf","full_name":"Wolf, Verena"}],"ddc":["000"],"file_date_updated":"2020-07-14T12:46:17Z","scopus_import":1,"citation":{"chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE, 2009. https://doi.org/10.1109/HiBi.2009.23.","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization of the chemical master equation. HIBI: High-Performance Computational Systems Biology vol. 4, 118–127.","mla":"Didier, Frédéric, et al. Fast Adaptive Uniformization of the Chemical Master Equation. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:10.1109/HiBi.2009.23.","apa":"Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2009). Fast adaptive uniformization of the chemical master equation (Vol. 4, pp. 118–127). Presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy: IEEE. https://doi.org/10.1109/HiBi.2009.23","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization of the chemical master equation,” presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of the chemical master equation. In: Vol 4. IEEE; 2009:118-127. doi:10.1109/HiBi.2009.23","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127."},"intvolume":" 4","conference":{"start_date":"2009-10-14","name":"HIBI: High-Performance Computational Systems Biology","end_date":"2009-10-16","location":"Trento, Italy"},"publication_status":"published","doi":"10.1109/HiBi.2009.23","date_published":"2009-10-30T00:00:00Z","oa_version":"Submitted Version","oa":1,"status":"public","month":"10","year":"2009","date_updated":"2023-02-23T11:45:05Z","abstract":[{"text":"Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous- time Markov chain (CTMC).\r\nStandard Uniformization (SU) is an efficient method for the transient analysis of CTMCs. For systems with very different time scales, such as biochemical reaction networks, SU is computationally expensive. In these cases, a variant of SU, called adaptive uniformization (AU), is known to reduce the large number of iterations needed by SU. The additional difficulty of AU is that it requires the solution of a birth process.\r\nIn this paper we present an on-the-fly variant of AU, where we improve the original algorithm for AU at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks.","lang":"eng"}],"issue":"6","_id":"3843"},{"pubrep_id":"65","publist_id":"2346","quality_controlled":"1","page":"171 - 180","date_created":"2018-12-11T12:05:28Z","has_accepted_license":"1","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"type":"conference","title":"Distributed, modular HTL","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","day":"01","acknowledgement":"Supported by the EU ArtistDesign Network of Excellence on Embedded Systems Design, the EU project COMBEST, the Austrian Science Funds P18913-N15 and V00125, and Fundacao para a Ciencia e Tecnologia funds SFRH/BD/29461/2006 and PTDC/EIA/71462/2006","file":[{"relation":"main_file","content_type":"application/pdf","file_size":526458,"file_id":"4655","creator":"system","checksum":"b2b15a5ef71eb50d62eaa5aea7efd8c4","access_level":"open_access","date_updated":"2020-07-14T12:46:17Z","file_name":"IST-2012-65-v1+1_Distributed_modular_Htl.pdf","date_created":"2018-12-12T10:07:56Z"}],"author":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","last_name":"Kirsch","full_name":"Kirsch, Christoph"},{"full_name":"Marques, Eduardo","first_name":"Eduardo","last_name":"Marques"},{"full_name":"Sokolova, Ana","last_name":"Sokolova","first_name":"Ana"}],"project":[{"call_identifier":"FP7","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373"},{"name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"}],"ddc":["000"],"file_date_updated":"2020-07-14T12:46:17Z","citation":{"ama":"Henzinger TA, Kirsch C, Marques E, Sokolova A. Distributed, modular HTL. In: IEEE; 2009:171-180. doi:10.1109/RTSS.2009.9","ieee":"T. A. Henzinger, C. Kirsch, E. Marques, and A. Sokolova, “Distributed, modular HTL,” presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United States, 2009, pp. 171–180.","short":"T.A. Henzinger, C. Kirsch, E. Marques, A. Sokolova, in:, IEEE, 2009, pp. 171–180.","apa":"Henzinger, T. A., Kirsch, C., Marques, E., & Sokolova, A. (2009). Distributed, modular HTL (pp. 171–180). Presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United States: IEEE. https://doi.org/10.1109/RTSS.2009.9","mla":"Henzinger, Thomas A., et al. Distributed, Modular HTL. IEEE, 2009, pp. 171–80, doi:10.1109/RTSS.2009.9.","ista":"Henzinger TA, Kirsch C, Marques E, Sokolova A. 2009. Distributed, modular HTL. RTSS: Real-Time Systems Symposium, 171–180.","chicago":"Henzinger, Thomas A, Christoph Kirsch, Eduardo Marques, and Ana Sokolova. “Distributed, Modular HTL,” 171–80. IEEE, 2009. https://doi.org/10.1109/RTSS.2009.9."},"doi":"10.1109/RTSS.2009.9","conference":{"name":"RTSS: Real-Time Systems Symposium","start_date":"2009-12-01","location":"Washington, DC, United States","end_date":"2009-12-04"},"publication_status":"published","date_published":"2009-01-01T00:00:00Z","oa_version":"Submitted Version","oa":1,"status":"public","ec_funded":1,"month":"01","year":"2009","abstract":[{"text":"The Hierarchical Timing Language (HTL) is a real-time coordination language for distributed control systems. HTL programs must be checked for well-formedness, race freedom, transmission safety (schedulability of inter-host communication), and time safety (schedulability of host computation). We present a modular abstract syntax and semantics for HTL, modular checks of well-formedness, race freedom, and transmission safety, and modular code distribution. Our contributions here complement previous results on HTL time safety and modular code generation. Modularity in HTL can be utilized in easy program composition as well as fast program analysis and code generation, but also in so-called runtime patching, where program components may be modified at runtime.","lang":"eng"}],"date_updated":"2021-01-12T07:52:36Z","_id":"3844"},{"date_published":"2009-05-04T00:00:00Z","type":"journal_article","date_created":"2018-12-11T12:05:37Z","publication":"Logical Methods in Computer Science","publication_status":"published","doi":"10.2168/LMCS-5(2:7)2009","citation":{"ista":"Chatterjee K, De Alfaro L, Faella M, Legay A. 2009. Qualitative logics and equivalences for probabilistic systems. Logical Methods in Computer Science. 5(2).","mla":"Chatterjee, Krishnendu, et al. “Qualitative Logics and Equivalences for Probabilistic Systems.” Logical Methods in Computer Science, vol. 5, no. 2, International Federation of Computational Logic, 2009, doi:10.2168/LMCS-5(2:7)2009.","apa":"Chatterjee, K., De Alfaro, L., Faella, M., & Legay, A. (2009). Qualitative logics and equivalences for probabilistic systems. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-5(2:7)2009","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, and Axel Legay. “Qualitative Logics and Equivalences for Probabilistic Systems.” Logical Methods in Computer Science. International Federation of Computational Logic, 2009. https://doi.org/10.2168/LMCS-5(2:7)2009.","short":"K. Chatterjee, L. De Alfaro, M. Faella, A. Legay, Logical Methods in Computer Science 5 (2009).","ama":"Chatterjee K, De Alfaro L, Faella M, Legay A. Qualitative logics and equivalences for probabilistic systems. Logical Methods in Computer Science. 2009;5(2). doi:10.2168/LMCS-5(2:7)2009","ieee":"K. Chatterjee, L. De Alfaro, M. Faella, and A. Legay, “Qualitative logics and equivalences for probabilistic systems,” Logical Methods in Computer Science, vol. 5, no. 2. International Federation of Computational Logic, 2009."},"quality_controlled":0,"intvolume":" 5","volume":5,"publist_id":"2308","_id":"3869","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Krishnendu Chatterjee"},{"full_name":"de Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"first_name":"Marco","last_name":"Faella","full_name":"Faella, Marco"},{"first_name":"Axel","last_name":"Legay","full_name":"Legay, Axel"}],"day":"04","extern":1,"year":"2009","date_updated":"2021-01-12T07:52:49Z","acknowledgement":"A preliminary version of this paper appeared in the proceedings of the 4th International Conference on the Quantitative Evaluation of Systems (QEST 2007).","issue":"2","abstract":[{"lang":"eng","text":"We investigate logics and equivalence relations that capture the qualitative behavior of Markov Decision Processes (MDPs). We present Qualitative Randomized CTL (QRCTL): formulas of this logic can express the fact that certain temporal properties hold over all paths, or with probability 0 or 1, but they do not distinguish among intermediate probability values. We present a symbolic, polynomial time model-checking algorithm for QRCTL on MDPs. The logic QRCTL induces an equivalence relation over states of an MDP that we call qualitative equivalence: informally, two states are qualitatively equivalent if the sets of formulas that hold with probability 0 or 1 at the two states are the same. We show that for finite alternating MDPs, where nondeterministic and probabilistic choices occur in different states, qualitative equivalence coincides with alternating bisimulation, and can thus be computed via efficient partition-refinement algorithms. On the other hand, in non-alternating MDPs the equivalence relations cannot be computed via partition-refinement algorithms, but rather, they require non-local computation. Finally, we consider QRCTL*, that extends QRCTL with nested temporal operators in the same manner in which CTL* extends CTL. We show that QRCTL and QRCTL* induce the same qualitative equivalence on alternating MDPs, while on non-alternating MDPs, the equivalence arising from QRCTL* can be strictly finer. We also provide a full characterization of the relation between qualitative equivalence, bisimulation, and alternating bisimulation, according to whether the MDPs are finite, and to whether their transition relations are finitely-branching."}],"month":"05","title":"Qualitative logics and equivalences for probabilistic systems","status":"public","publisher":"International Federation of Computational Logic"},{"has_accepted_license":"1","publication":"ACM Transactions on Computational Logic (TOCL)","date_created":"2018-12-11T12:05:37Z","type":"journal_article","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"pubrep_id":"53","publist_id":"2309","volume":11,"quality_controlled":"1","acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, the NSF grants CCR-0132780, CNS-0720884, and CCR- 225610, by the Swiss National Science Foundation, by the COMBEST project of the European Union, and EU-TMR network Games.\r\nWe thank anonymous reviewers for useful comments.","day":"01","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Florian","id":"37327ACE-F248-11E8-B48F-1D18A9856A87","last_name":"Horn","full_name":"Horn, Florian"}],"project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7"}],"file":[{"file_id":"5125","creator":"system","checksum":"139c4586d24f11e5da31fb3a0cf96ef4","access_level":"open_access","file_name":"IST-2012-53-v1+1_Finitary_winning_in_omega-regular_games.pdf","date_updated":"2020-07-14T12:46:20Z","date_created":"2018-12-12T10:15:08Z","content_type":"application/pdf","relation":"main_file","file_size":180082}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","title":"Finitary winning in omega-regular games","doi":"10.1145/1614431.1614432","publication_status":"published","oa_version":"Submitted Version","date_published":"2009-10-01T00:00:00Z","scopus_import":1,"file_date_updated":"2020-07-14T12:46:20Z","ddc":["004"],"intvolume":" 11","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Finitary Winning in Omega-Regular Games.” ACM Transactions on Computational Logic (TOCL). ACM, 2009. https://doi.org/10.1145/1614431.1614432.","mla":"Chatterjee, Krishnendu, et al. “Finitary Winning in Omega-Regular Games.” ACM Transactions on Computational Logic (TOCL), vol. 11, no. 1, 1, ACM, 2009, doi:10.1145/1614431.1614432.","apa":"Chatterjee, K., Henzinger, T. A., & Horn, F. (2009). Finitary winning in omega-regular games. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/1614431.1614432","ista":"Chatterjee K, Henzinger TA, Horn F. 2009. Finitary winning in omega-regular games. ACM Transactions on Computational Logic (TOCL). 11(1), 1.","ama":"Chatterjee K, Henzinger TA, Horn F. Finitary winning in omega-regular games. ACM Transactions on Computational Logic (TOCL). 2009;11(1). doi:10.1145/1614431.1614432","ieee":"K. Chatterjee, T. A. Henzinger, and F. Horn, “Finitary winning in omega-regular games,” ACM Transactions on Computational Logic (TOCL), vol. 11, no. 1. ACM, 2009.","short":"K. Chatterjee, T.A. Henzinger, F. Horn, ACM Transactions on Computational Logic (TOCL) 11 (2009)."},"issue":"1","abstract":[{"text":"Games on graphs with omega-regular objectives provide a model for the control and synthesis of reactive systems. Every omega-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Buchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. We show that finitary parity games can be solved in polynomial time, which is not known for infinitary parity games. For finitary Streett games, we give an EXPTIME algorithm and show that the problem is NP-hard. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound.","lang":"eng"}],"date_updated":"2021-01-12T07:52:50Z","year":"2009","article_number":"1","_id":"3870","status":"public","oa":1,"month":"10","ec_funded":1},{"oa":1,"status":"public","ec_funded":1,"month":"09","year":"2009","date_updated":"2021-01-12T07:52:50Z","abstract":[{"text":"Nondeterministic weighted automata are finite automata with numerical weights oil transitions. They define quantitative languages 1, that assign to each word v; a real number L(w). The value of ail infinite word w is computed as the maximal value of all runs over w, and the value of a run as the supremum, limsup liminf, limit average, or discounted sum of the transition weights. We introduce probabilistic weighted antomata, in which the transitions are chosen in a randomized (rather than nondeterministic) fashion. Under almost-sure semantics (resp. positive semantics), the value of a word v) is the largest real v such that the runs over w have value at least v with probability I (resp. positive probability). We study the classical questions of automata theory for probabilistic weighted automata: emptiness and universality, expressiveness, and closure under various operations oil languages. For quantitative languages, emptiness university axe defined as whether the value of some (resp. every) word exceeds a given threshold. We prove some, of these questions to he decidable, and others undecidable. Regarding expressive power, we show that probabilities allow its to define a wide variety of new classes of quantitative languages except for discounted-sum automata, where probabilistic choice is no more expressive than nondeterminism. Finally we live ail almost complete picture of the closure of various classes of probabilistic weighted automata for the following, provide, is operations oil quantitative languages: maximum, sum. and numerical complement.","lang":"eng"}],"_id":"3871","ddc":["000","005"],"file_date_updated":"2020-07-14T12:46:20Z","scopus_import":1,"citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Probabilistic Weighted Automata,” 5710:244–58. Springer, 2009. https://doi.org/10.1007/978-3-642-04081-8_17.","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2009). Probabilistic weighted automata (Vol. 5710, pp. 244–258). Presented at the CONCUR: Concurrency Theory, Bologna, Italy: Springer. https://doi.org/10.1007/978-3-642-04081-8_17","ista":"Chatterjee K, Doyen L, Henzinger TA. 2009. Probabilistic weighted automata. CONCUR: Concurrency Theory, LNCS, vol. 5710, 244–258.","mla":"Chatterjee, Krishnendu, et al. Probabilistic Weighted Automata. Vol. 5710, Springer, 2009, pp. 244–58, doi:10.1007/978-3-642-04081-8_17.","ama":"Chatterjee K, Doyen L, Henzinger TA. Probabilistic weighted automata. In: Vol 5710. Springer; 2009:244-258. doi:10.1007/978-3-642-04081-8_17","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “Probabilistic weighted automata,” presented at the CONCUR: Concurrency Theory, Bologna, Italy, 2009, vol. 5710, pp. 244–258.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 244–258."},"intvolume":" 5710","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2009-09-01","location":"Bologna, Italy","end_date":"2009-09-04"},"publication_status":"published","doi":"10.1007/978-3-642-04081-8_17","date_published":"2009-09-01T00:00:00Z","oa_version":"Submitted Version","title":"Probabilistic weighted automata","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"day":"01","acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European projects Combest, Quasimodo, and Gasics, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification ) funded by the F.R.S.-FNRS.","file":[{"relation":"main_file","content_type":"application/pdf","file_size":200161,"file_name":"IST-2012-52-v1+1_Probabilistic_Weighted_Automata.pdf","date_updated":"2020-07-14T12:46:20Z","date_created":"2018-12-12T10:09:46Z","creator":"system","file_id":"4771","checksum":"af973ddbcf131b8810c6bff2c055ff56","access_level":"open_access"}],"project":[{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373","call_identifier":"FP7","name":"Design for Embedded Systems"},{"grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques"}],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"2304","pubrep_id":"52","quality_controlled":"1","volume":5710,"date_created":"2018-12-11T12:05:37Z","page":"244 - 258","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"type":"conference"},{"volume":364,"citation":{"mla":"Cremer, Sylvia, and Michael K. Sixt. “Analogies in the Evolution of Individual and Social Immunity.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 364, no. 1513, Royal Society, The, 2009, pp. 129–42, doi:10.1098/rstb.2008.0166.","ista":"Cremer S, Sixt MK. 2009. Analogies in the evolution of individual and social immunity. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 364(1513), 129–142.","apa":"Cremer, S., & Sixt, M. K. (2009). Analogies in the evolution of individual and social immunity. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2008.0166","chicago":"Cremer, Sylvia, and Michael K Sixt. “Analogies in the Evolution of Individual and Social Immunity.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2009. https://doi.org/10.1098/rstb.2008.0166.","ieee":"S. Cremer and M. K. Sixt, “Analogies in the evolution of individual and social immunity,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 364, no. 1513. Royal Society, The, pp. 129–142, 2009.","ama":"Cremer S, Sixt MK. Analogies in the evolution of individual and social immunity. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2009;364(1513):129-142. doi:10.1098/rstb.2008.0166","short":"S. Cremer, M.K. Sixt, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 364 (2009) 129–142."},"intvolume":" 364","publist_id":"2181","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666697/"}],"type":"journal_article","oa_version":"None","date_published":"2009-01-12T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1098/rstb.2008.0166","publication_status":"published","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","page":"129 - 142","date_created":"2018-12-11T12:06:02Z","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society, The","status":"public","oa":1,"title":"Analogies in the evolution of individual and social immunity","author":[{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"_id":"3946","issue":"1513","abstract":[{"text":"We compare anti-parasite defences at the level of multicellular organisms and insect societies, and find that selection by parasites at these two organisational levels is often very similar and has created a number of parallel evolutionary solutions in the host's immune response. The defence mechanisms of both individuals and insect colonies start with border defences to prevent parasite intake and are followed by soma defences that prevent the establishment and spread of the parasite between the body's cells or the social insect workers. Lastly, germ line defences are employed to inhibit infection of the reproductive tissue of organisms or the reproductive individuals in colonies. We further find sophisticated self/non-self-recognition systems operating at both levels, which appear to be vital in maintaining the integrity of the body or colony as a reproductive entity. We then expand on the regulation of immune responses and end with a contemplation of how evolution may shape the different immune components, both within and between levels. The aim of this review is to highlight common evolutionary principles acting in disease defence at the level of both individual organisms and societies, thereby linking the fields of physiological and ecological immunology.","lang":"eng"}],"date_updated":"2021-01-12T07:53:23Z","year":"2009","extern":"1","day":"12"},{"status":"public","publisher":"American Society of Hematology","title":"Cdc42-dependent leading edge coordination is essential for interstitial dendritic cell migration (Plenary Paper)","month":"06","abstract":[{"text":"Mature dendritic cells (DCs) moving from the skin to the lymph node are a prototypic example of rapidly migrating amoeboid leukocytes. Interstitial DC migration is directionally guided by chemokines, but independent of specific adhesive interactions with the tissue as well as pericellular proteolysis. Instead, the protrusive flow of the actin cytoskeleton directly drives a basal mode of locomotion that is occasionally supported by actomyosin contractions at the trailing edge to propel the cell's rigid nucleus. We here delete the small GTPase Cdc42 in DCs and find that actin flow and actomyosin contraction are still initiated in response to chemotactic cues. Accordingly, the cells are able to polarize and form protrusions. However, in the absence of Cdc42 the protrusions are temporally and spatially dysregulated, which leads to impaired leading edge coordination. Although this defect still allows the cells to move on 2-dimensional surfaces, their in vivo motility is completely abrogated. We show that this difference is entirely caused by the geometric complexity of the environment, as multiple competing protrusions lead to instantaneous entanglement within 3-dimensional extracellular matrix scaffolds. This demonstrates that the decisive factor for migrating DCs is not specific interaction with the extracellular environment, but adequate coordination of cytoskeletal flow.","lang":"eng"}],"acknowledgement":"We thank Sylvia Cremer for help with statistics and critical reading of the paper and Reinhard Fässler for continuous support.\n\nThis work was supported by the German Research Foundation (Bonn, Germany), the Peter Hans Hofschneider Foundation for Experimental Biomedicine (Zürich, Switzerland), and the Max Planck Society (Munich, Germany).","issue":"23","date_updated":"2021-01-12T07:53:23Z","year":"2009","extern":1,"day":"04","author":[{"first_name":"Tim","last_name":"Lämmermann","full_name":"Lämmermann, Tim"},{"full_name":"Jörg Renkawitz","first_name":"Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wu, Xunwei","last_name":"Wu","first_name":"Xunwei"},{"last_name":"Hirsch","first_name":"Karin","full_name":"Hirsch, Karin"},{"full_name":"Brakebusch, Cord","last_name":"Brakebusch","first_name":"Cord"},{"full_name":"Michael Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"_id":"3947","publist_id":"2179","volume":113,"intvolume":" 113","quality_controlled":0,"citation":{"short":"T. Lämmermann, J. Renkawitz, X. Wu, K. Hirsch, C. Brakebusch, M.K. Sixt, Blood 113 (2009) 5703–5710.","ama":"Lämmermann T, Renkawitz J, Wu X, Hirsch K, Brakebusch C, Sixt MK. Cdc42-dependent leading edge coordination is essential for interstitial dendritic cell migration (Plenary Paper). Blood. 2009;113(23):5703-5710. doi:10.1182/blood-2008-11-191882","ieee":"T. Lämmermann, J. Renkawitz, X. Wu, K. Hirsch, C. Brakebusch, and M. K. Sixt, “Cdc42-dependent leading edge coordination is essential for interstitial dendritic cell migration (Plenary Paper),” Blood, vol. 113, no. 23. American Society of Hematology, pp. 5703–5710, 2009.","mla":"Lämmermann, Tim, et al. “Cdc42-Dependent Leading Edge Coordination Is Essential for Interstitial Dendritic Cell Migration (Plenary Paper).” Blood, vol. 113, no. 23, American Society of Hematology, 2009, pp. 5703–10, doi:10.1182/blood-2008-11-191882.","ista":"Lämmermann T, Renkawitz J, Wu X, Hirsch K, Brakebusch C, Sixt MK. 2009. Cdc42-dependent leading edge coordination is essential for interstitial dendritic cell migration (Plenary Paper). Blood. 113(23), 5703–5710.","apa":"Lämmermann, T., Renkawitz, J., Wu, X., Hirsch, K., Brakebusch, C., & Sixt, M. K. (2009). Cdc42-dependent leading edge coordination is essential for interstitial dendritic cell migration (Plenary Paper). Blood. American Society of Hematology. https://doi.org/10.1182/blood-2008-11-191882","chicago":"Lämmermann, Tim, Jörg Renkawitz, Xunwei Wu, Karin Hirsch, Cord Brakebusch, and Michael K Sixt. “Cdc42-Dependent Leading Edge Coordination Is Essential for Interstitial Dendritic Cell Migration (Plenary Paper).” Blood. American Society of Hematology, 2009. https://doi.org/10.1182/blood-2008-11-191882."},"doi":"10.1182/blood-2008-11-191882","publication_status":"published","publication":"Blood","page":"5703 - 5710","date_created":"2018-12-11T12:06:03Z","type":"journal_article","date_published":"2009-06-04T00:00:00Z"},{"publisher":"National Academy of Sciences","status":"public","title":"β1 integrins differentially control extravasation of inflammatory cell subsets into the CNS during autoimmunity","month":"02","date_updated":"2021-01-12T07:53:24Z","abstract":[{"text":"Inhibiting the alpha(4) subunit of the integrin heterodimers alpha(4)beta(1) and alpha(4)beta(7) with the monoclonal antibody natalizumab is an effective treatment for multiple sclerosis (MS). However, the pharmacological action of natalizumab is not understood conclusively. Previous studies suggested that natalizumab inhibits activation, proliferation, or extravasation of inflammatory cells. To specify which mechanisms, cell types, and alpha(4) heterodimers are affected by the antibody treatment, we studied MS-like experimental autoimmune encephalomyelitis (EAE) in mice lacking the beta(1)-integrin gene either in all hematopoietic cells or selectively in T lymphocytes. Our results show that T cells critically rely on beta(1) integrins to accumulate in the central nervous system (CNS) during EAE, whereas CNS infiltration of beta(1)-deficient myeloid cells remains unaffected, suggesting that T cells are the main target of anti-alpha(4)-antibody blockade. We demonstrate that beta(1)-integrin expression on encephalitogenic T cells is critical for EAE development, and we therefore exclude alpha(4)beta(7) as a target integrin of the antibody treatment. T cells lacking beta(1) integrin are unable to firmly adhere to CNS endothelium in vivo, whereas their priming and expansion remain unaffected. Collectively, these results suggest that the primary action of natalizumab is interference with T cell extravasation via inhibition of alpha(4)beta(1) integrins.","lang":"eng"}],"issue":"6","day":"10","extern":1,"year":"2009","author":[{"full_name":"Bauer, Martina","last_name":"Bauer","first_name":"Martina"},{"first_name":"Cord","last_name":"Brakebusch","full_name":"Brakebusch, Cord"},{"full_name":"Coisne, Caroline","first_name":"Caroline","last_name":"Coisne"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Michael Sixt"},{"first_name":"Hartmut","last_name":"Wekerle","full_name":"Wekerle, Hartmut"},{"full_name":"Engelhardt, Britta","last_name":"Engelhardt","first_name":"Britta"},{"last_name":"Fässler","first_name":"Reinhard","full_name":"Fässler, Reinhard"}],"_id":"3948","publist_id":"2180","citation":{"chicago":"Bauer, Martina, Cord Brakebusch, Caroline Coisne, Michael K Sixt, Hartmut Wekerle, Britta Engelhardt, and Reinhard Fässler. “Β1 Integrins Differentially Control Extravasation of Inflammatory Cell Subsets into the CNS during Autoimmunity.” PNAS. National Academy of Sciences, 2009. https://doi.org/10.1073/pnas.0808909106.","apa":"Bauer, M., Brakebusch, C., Coisne, C., Sixt, M. K., Wekerle, H., Engelhardt, B., & Fässler, R. (2009). β1 integrins differentially control extravasation of inflammatory cell subsets into the CNS during autoimmunity. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0808909106","mla":"Bauer, Martina, et al. “Β1 Integrins Differentially Control Extravasation of Inflammatory Cell Subsets into the CNS during Autoimmunity.” PNAS, vol. 106, no. 6, National Academy of Sciences, 2009, pp. 1920–25, doi:10.1073/pnas.0808909106.","ista":"Bauer M, Brakebusch C, Coisne C, Sixt MK, Wekerle H, Engelhardt B, Fässler R. 2009. β1 integrins differentially control extravasation of inflammatory cell subsets into the CNS during autoimmunity. PNAS. 106(6), 1920–1925.","short":"M. Bauer, C. Brakebusch, C. Coisne, M.K. Sixt, H. Wekerle, B. Engelhardt, R. Fässler, PNAS 106 (2009) 1920–1925.","ieee":"M. Bauer et al., “β1 integrins differentially control extravasation of inflammatory cell subsets into the CNS during autoimmunity,” PNAS, vol. 106, no. 6. National Academy of Sciences, pp. 1920–1925, 2009.","ama":"Bauer M, Brakebusch C, Coisne C, et al. β1 integrins differentially control extravasation of inflammatory cell subsets into the CNS during autoimmunity. PNAS. 2009;106(6):1920-1925. doi:10.1073/pnas.0808909106"},"volume":106,"quality_controlled":0,"intvolume":" 106","publication_status":"published","doi":"10.1073/pnas.0808909106","date_created":"2018-12-11T12:06:03Z","page":"1920 - 1925","publication":"PNAS","type":"journal_article","date_published":"2009-02-10T00:00:00Z"},{"author":[{"first_name":"Thomas","last_name":"Quast","full_name":"Quast, Thomas"},{"first_name":"Barbara","last_name":"Tappertzhofen","full_name":"Tappertzhofen, Barbara"},{"full_name":"Schild, Cora","last_name":"Schild","first_name":"Cora"},{"full_name":"Grell, Jessica","first_name":"Jessica","last_name":"Grell"},{"full_name":"Czeloth, Niklas","last_name":"Czeloth","first_name":"Niklas"},{"full_name":"Förster, Reinhold","last_name":"Förster","first_name":"Reinhold"},{"first_name":"Ronen","last_name":"Alon","full_name":"Alon, Ronen"},{"full_name":"Fraemohs, Line","last_name":"Fraemohs","first_name":"Line"},{"full_name":"Dreck, Katrin","first_name":"Katrin","last_name":"Dreck"},{"last_name":"Weber","first_name":"Christian","full_name":"Weber, Christian"},{"full_name":"Lämmermann, Tim","last_name":"Lämmermann","first_name":"Tim"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Michael Sixt"},{"full_name":"Kolanus, Waldemar","first_name":"Waldemar","last_name":"Kolanus"}],"_id":"3949","date_updated":"2021-01-12T07:53:24Z","issue":"23","abstract":[{"text":"Adhesion and motility of mammalian leukocytes are essential requirements for innate and adaptive immune defense mechanisms. We show here that the guanine nucleotide exchange factor cytohesin-1, which had previously been demonstrated to be an important component of beta-2 integrin activation in lymphocytes, regulates the activation of the small GTPase RhoA in primary dendritic cells (DCs). Cytohesin-1 and RhoA are both required for the induction of chemokine-dependent conformational changes of the integrin beta-2 subunit of DCs during adhesion under physiological flow conditions. Furthermore, use of RNAi in murine bone marrow DCs (BM-DCs) revealed that interference with cytohesin-1 signaling impairs migration of wild-type dendritic cells in complex 3D environments and in vivo. This phenotype was not observed in the complete absence of integrins. We thus demonstrate an essential role of cytohesin-1/RhoA during ameboid migration in the presence of integrins and further suggest that DCs without integrins switch to a different migration mode.","lang":"eng"}],"day":"04","year":"2009","extern":1,"month":"06","publisher":"American Society of Hematology","status":"public","title":"Cytohesin-1 controls the activation of RhoA and modulates integrin-dependent adhesion and migration of dendritic cells","type":"journal_article","date_published":"2009-06-04T00:00:00Z","publication_status":"published","doi":"10.1182/blood-2008-08-176123","page":"5801 - 5810","date_created":"2018-12-11T12:06:03Z","publication":"Blood","citation":{"ista":"Quast T, Tappertzhofen B, Schild C, Grell J, Czeloth N, Förster R, Alon R, Fraemohs L, Dreck K, Weber C, Lämmermann T, Sixt MK, Kolanus W. 2009. Cytohesin-1 controls the activation of RhoA and modulates integrin-dependent adhesion and migration of dendritic cells. Blood. 113(23), 5801–5810.","apa":"Quast, T., Tappertzhofen, B., Schild, C., Grell, J., Czeloth, N., Förster, R., … Kolanus, W. (2009). Cytohesin-1 controls the activation of RhoA and modulates integrin-dependent adhesion and migration of dendritic cells. Blood. American Society of Hematology. https://doi.org/10.1182/blood-2008-08-176123","mla":"Quast, Thomas, et al. “Cytohesin-1 Controls the Activation of RhoA and Modulates Integrin-Dependent Adhesion and Migration of Dendritic Cells.” Blood, vol. 113, no. 23, American Society of Hematology, 2009, pp. 5801–10, doi:10.1182/blood-2008-08-176123.","chicago":"Quast, Thomas, Barbara Tappertzhofen, Cora Schild, Jessica Grell, Niklas Czeloth, Reinhold Förster, Ronen Alon, et al. “Cytohesin-1 Controls the Activation of RhoA and Modulates Integrin-Dependent Adhesion and Migration of Dendritic Cells.” Blood. American Society of Hematology, 2009. https://doi.org/10.1182/blood-2008-08-176123.","ieee":"T. Quast et al., “Cytohesin-1 controls the activation of RhoA and modulates integrin-dependent adhesion and migration of dendritic cells,” Blood, vol. 113, no. 23. American Society of Hematology, pp. 5801–5810, 2009.","ama":"Quast T, Tappertzhofen B, Schild C, et al. Cytohesin-1 controls the activation of RhoA and modulates integrin-dependent adhesion and migration of dendritic cells. Blood. 2009;113(23):5801-5810. doi:10.1182/blood-2008-08-176123","short":"T. Quast, B. Tappertzhofen, C. Schild, J. Grell, N. Czeloth, R. Förster, R. Alon, L. Fraemohs, K. Dreck, C. Weber, T. Lämmermann, M.K. Sixt, W. Kolanus, Blood 113 (2009) 5801–5810."},"volume":113,"quality_controlled":0,"intvolume":" 113","publist_id":"2177"},{"month":"02","title":"Kindlin-3 is required for β2 integrin-mediated leukocyte adhesion to endothelial cells","publisher":"Nature Publishing Group","status":"public","_id":"3950","author":[{"last_name":"Moser","first_name":"Markus","full_name":"Moser, Markus"},{"first_name":"Martina","last_name":"Bauer","full_name":"Bauer, Martina"},{"last_name":"Schmid","first_name":"Stephan","full_name":"Schmid, Stephan"},{"last_name":"Ruppert","first_name":"Raphael","full_name":"Ruppert, Raphael"},{"first_name":"Sarah","last_name":"Schmidt","full_name":"Schmidt, Sarah"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Michael Sixt"},{"full_name":"Wang, Hao-Ven","last_name":"Wang","first_name":"Hao"},{"first_name":"Markus","last_name":"Sperandio","full_name":"Sperandio, Markus"},{"full_name":"Fässler, Reinhard","first_name":"Reinhard","last_name":"Fässler"}],"year":"2009","extern":1,"day":"22","issue":"3","abstract":[{"text":"Integrin activation is essential for the function of all blood cells, including platelets and leukocytes. The blood cell-specific FERM domain protein Kindlin-3 is required for the activation of the beta1 and beta3 integrins on platelets. Impaired activation of beta1, beta2 and beta3 integrins on platelets and leukocytes is the hallmark of a rare autosomal recessive leukocyte adhesion deficiency syndrome in humans called LAD-III, characterized by severe bleeding and impaired adhesion of leukocytes to inflamed endothelia. Here we show that Kindlin-3 also binds the beta2 integrin cytoplasmic domain and is essential for neutrophil binding and spreading on beta2 integrin-dependent ligands such as intercellular adhesion molecule-1 and the complement C3 activation product iC3b. Moreover, loss of Kindlin-3 expression abolished firm adhesion and arrest of neutrophils on activated endothelial cells in vitro and in vivo, whereas selectin-mediated rolling was unaffected. Thus, Kindlin-3 is essential to activate the beta1, beta2 and beta3 integrin classes, and loss of Kindlin-3 function is sufficient to cause a LAD-III-like phenotype in mice.","lang":"eng"}],"date_updated":"2021-01-12T07:53:25Z","intvolume":" 15","volume":15,"quality_controlled":0,"citation":{"short":"M. Moser, M. Bauer, S. Schmid, R. Ruppert, S. Schmidt, M.K. Sixt, H. Wang, M. Sperandio, R. Fässler, Nature Medicine 15 (2009) 300–305.","ama":"Moser M, Bauer M, Schmid S, et al. Kindlin-3 is required for β2 integrin-mediated leukocyte adhesion to endothelial cells. Nature Medicine. 2009;15(3):300-305. doi:10.1038/nm.1921","ieee":"M. Moser et al., “Kindlin-3 is required for β2 integrin-mediated leukocyte adhesion to endothelial cells,” Nature Medicine, vol. 15, no. 3. Nature Publishing Group, pp. 300–305, 2009.","ista":"Moser M, Bauer M, Schmid S, Ruppert R, Schmidt S, Sixt MK, Wang H, Sperandio M, Fässler R. 2009. Kindlin-3 is required for β2 integrin-mediated leukocyte adhesion to endothelial cells. Nature Medicine. 15(3), 300–305.","apa":"Moser, M., Bauer, M., Schmid, S., Ruppert, R., Schmidt, S., Sixt, M. K., … Fässler, R. (2009). Kindlin-3 is required for β2 integrin-mediated leukocyte adhesion to endothelial cells. Nature Medicine. Nature Publishing Group. https://doi.org/10.1038/nm.1921","mla":"Moser, Markus, et al. “Kindlin-3 Is Required for Β2 Integrin-Mediated Leukocyte Adhesion to Endothelial Cells.” Nature Medicine, vol. 15, no. 3, Nature Publishing Group, 2009, pp. 300–05, doi:10.1038/nm.1921.","chicago":"Moser, Markus, Martina Bauer, Stephan Schmid, Raphael Ruppert, Sarah Schmidt, Michael K Sixt, Hao Wang, Markus Sperandio, and Reinhard Fässler. “Kindlin-3 Is Required for Β2 Integrin-Mediated Leukocyte Adhesion to Endothelial Cells.” Nature Medicine. Nature Publishing Group, 2009. https://doi.org/10.1038/nm.1921."},"publist_id":"2178","date_published":"2009-02-22T00:00:00Z","type":"journal_article","publication":"Nature Medicine","date_created":"2018-12-11T12:06:04Z","page":"300 - 305","doi":"10.1038/nm.1921","publication_status":"published"}]