[{"status":"public","type":"journal_article","article_type":"original","_id":"9049","title":"Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis","author":[{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465"},{"full_name":"Cottin-Bizonne, Cécile","last_name":"Cottin-Bizonne","first_name":"Cécile"},{"first_name":"Christophe","last_name":"Ybert","full_name":"Ybert, Christophe"},{"full_name":"Bocquet, Lydéric","last_name":"Bocquet","first_name":"Lydéric"}],"article_processing_charge":"No","extern":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_updated":"2023-02-23T13:47:31Z","citation":{"short":"J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Soft Matter 8 (2012) 980–994.","ieee":"J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis,” Soft Matter, vol. 8, no. 4. Royal Society of Chemistry, pp. 980–994, 2012.","apa":"Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2012). Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm06395b","ama":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 2012;8(4):980-994. doi:10.1039/c1sm06395b","mla":"Palacci, Jérémie A., et al. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter, vol. 8, no. 4, Royal Society of Chemistry, 2012, pp. 980–94, doi:10.1039/c1sm06395b.","ista":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2012. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 8(4), 980–994.","chicago":"Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter. Royal Society of Chemistry, 2012. https://doi.org/10.1039/c1sm06395b."},"month":"01","intvolume":" 8","publisher":"Royal Society of Chemistry","quality_controlled":"1","scopus_import":"1","oa_version":"None","abstract":[{"text":"Diffusiophoretic motion of colloids and macromolecules under salt gradients exhibits a logarithmic-sensing, i.e. the particle velocity is proportional to the spatial gradient of the logarithm of the salt concentration, as VDP = DDP∇logc. Here we explore experimentally the implications of this log-sensing behavior, on the basis of a hydrogel microfluidic device allowing to build spatially and temporally controlled gradients. We first demonstrate that the non-linearity of the salt-taxis leads to a trapping of particles under concentration gradient oscillations via a rectification of the motion. As an alternative, we make use of the high sensitivity of diffusiophoretic migration to vanishing salt concentration due to the log-sensing: in a counter-intuitive way, a vanishing gradient can lead to measurable velocity provided that the solute concentration is low enough, thus keeping ∇c/c finite. We show that this leads to a strong segregation of particles in osmotic shock configuration, resulting from a step change of the salt concentration at the boundaries. These various phenomena are rationalized on the basis of a theoretical description for the time-dependent Smoluchowski equation for the colloidal density.","lang":"eng"}],"volume":8,"doi":"10.1039/c1sm06395b","date_published":"2012-01-28T00:00:00Z","issue":"4","date_created":"2021-02-01T13:43:10Z","page":"980-994","day":"28","language":[{"iso":"eng"}],"publication":"Soft Matter","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"year":"2012","publication_status":"published"},{"title":"Mechanical instabilities of biological tubes","external_id":{"arxiv":["1207.1516"]},"article_processing_charge":"No","publist_id":"6519","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"first_name":"Jacques","last_name":"Prost","full_name":"Prost, Jacques"},{"first_name":"Jean","full_name":"Joanny, Jean","last_name":"Joanny"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.018101.","ista":"Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological tubes. Physical Review Letters. 109(1).","mla":"Hannezo, Edouard B., et al. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters, vol. 109, no. 1, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.018101.","ama":"Hannezo EB, Prost J, Joanny J. Mechanical instabilities of biological tubes. Physical Review Letters. 2012;109(1). doi:10.1103/PhysRevLett.109.018101","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2012). Mechanical instabilities of biological tubes. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.018101","short":"E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 109 (2012).","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Mechanical instabilities of biological tubes,” Physical Review Letters, vol. 109, no. 1. American Physical Society, 2012."},"date_updated":"2021-01-12T08:21:56Z","status":"public","type":"journal_article","_id":"922","date_created":"2018-12-11T11:49:13Z","volume":109,"issue":"1","date_published":"2012-07-03T00:00:00Z","doi":"10.1103/PhysRevLett.109.018101","publication":"Physical Review Letters","language":[{"iso":"eng"}],"day":"03","publication_status":"published","year":"2012","intvolume":" 109","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1207.1516"}],"oa":1,"publisher":"American Physical Society","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young's modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation."}]},{"_id":"9499","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-12-14T08:31:14Z","extern":"1","department":[{"_id":"DaZi"}],"abstract":[{"lang":"eng","text":"EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism."}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002512","open_access":"1"}],"scopus_import":"1","intvolume":" 8","month":"03","publication_status":"published","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"language":[{"iso":"eng"}],"volume":8,"issue":"3","article_number":"e1002512","citation":{"ista":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512.","chicago":"Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512.","ieee":"S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS Genetics, vol. 8, no. 3. Public Library of Science, 2012.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012).","apa":"Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512","ama":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3). doi:10.1371/journal.pgen.1002512","mla":"Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002512."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"pmid":["22457632"]},"article_processing_charge":"No","author":[{"last_name":"Kim","full_name":"Kim, Sang Yeol","first_name":"Sang Yeol"},{"full_name":"Lee, Jungeun","last_name":"Lee","first_name":"Jungeun"},{"first_name":"Leor","last_name":"Eshed-Williams","full_name":"Eshed-Williams, Leor"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"},{"first_name":"Z. Renee","last_name":"Sung","full_name":"Sung, Z. Renee"}],"title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","year":"2012","publication":"PLoS Genetics","day":"22","date_created":"2021-06-07T11:07:56Z","date_published":"2012-03-22T00:00:00Z","doi":"10.1371/journal.pgen.1002512"},{"date_published":"2012-10-11T00:00:00Z","doi":"10.1371/journal.pgen.1002988","date_created":"2021-06-07T10:55:27Z","year":"2012","day":"11","publication":"PLoS Genetics","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"author":[{"full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr","first_name":"Devin"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"article_processing_charge":"No","external_id":{"pmid":["23071449"]},"title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes","citation":{"ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.","chicago":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988.","ieee":"D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10. Public Library of Science, 2012.","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).","apa":"Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002988","ama":"Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988","mla":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"e1002988","volume":8,"issue":"10","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002988","open_access":"1"}],"month":"10","intvolume":" 8","abstract":[{"lang":"eng","text":"The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes."}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:29:57Z","extern":"1","type":"journal_article","article_type":"original","status":"public","_id":"9497"},{"author":[{"first_name":"Jason T.","last_name":"Huff","full_name":"Huff, Jason T."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"external_id":{"pmid":["22336527"]},"article_processing_charge":"No","title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","citation":{"mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007.","ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” Current Opinion in Genetics and Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138.","ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007","apa":"Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007","chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007.","ista":"Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"132-138","date_published":"2012-04-01T00:00:00Z","doi":"10.1016/j.gde.2012.01.007","date_created":"2021-06-08T08:58:52Z","year":"2012","publication":"Current Opinion in Genetics and Development","publisher":"Elsevier","quality_controlled":"1","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:32:38Z","extern":"1","article_type":"review","type":"journal_article","status":"public","_id":"9528","issue":"2","volume":22,"publication_identifier":{"issn":["0959-437X"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 22","abstract":[{"text":"Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory.","lang":"eng"}],"pmid":1,"oa_version":"None"},{"extern":1,"date_updated":"2021-01-12T08:22:18Z","citation":{"chicago":"Bieri, Samuel, Maksym Serbyn, Todadri Senthil, and Patrick Lee. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2012. https://doi.org/10.1103/PhysRevB.86.224409.","ista":"Bieri S, Serbyn M, Senthil T, Lee P. 2012. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 86(22).","mla":"Bieri, Samuel, et al. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22, American Physical Society, 2012, doi:10.1103/PhysRevB.86.224409.","ama":"Bieri S, Serbyn M, Senthil T, Lee P. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2012;86(22). doi:10.1103/PhysRevB.86.224409","apa":"Bieri, S., Serbyn, M., Senthil, T., & Lee, P. (2012). Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.86.224409","ieee":"S. Bieri, M. Serbyn, T. Senthil, and P. Lee, “Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22. American Physical Society, 2012.","short":"S. Bieri, M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 86 (2012)."},"title":"Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice","author":[{"first_name":"Samuel","last_name":"Bieri","full_name":"Bieri, Samuel"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn"},{"first_name":"Todadri","last_name":"Senthil","full_name":"Senthil, Todadri S"},{"full_name":"Lee, Patrick","last_name":"Lee","first_name":"Patrick"}],"publist_id":"6431","_id":"966","status":"public","type":"journal_article","day":"13","publication":"Physical Review B - Condensed Matter and Materials Physics","publication_status":"published","year":"2012","issue":"22","date_published":"2012-12-13T00:00:00Z","doi":"10.1103/PhysRevB.86.224409","volume":86,"date_created":"2018-12-11T11:49:27Z","acknowledgement":"We thank Kuang-Ting Chen, Rebecca Flint, Dmitri Ivanov, Z.-X. Liu, Tai-Kai Ng, Lara Thompson, Tamás Tóth, and Fa Wang for helpful discussions. T.S. is supported by NSF DMR 1005434. P.A.L. is supported by NSF DMR 1104498. S.B. acknowledges support from the Swiss National Science Foundation (SNSF).","abstract":[{"lang":"eng","text":"Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario."}],"month":"12","intvolume":" 86","publisher":"American Physical Society","quality_controlled":0,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1208.3231"}],"oa":1},{"quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"acknowledgement":"This work was supported by funding from the UK Natural Environment Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1, NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on earlier versions of the manuscript. ","page":"4605 - 4617","doi":"10.1111/j.1365-294X.2012.05700.x","date_published":"2012-09-01T00:00:00Z","date_created":"2018-12-11T12:00:36Z","has_accepted_license":"1","year":"2012","day":"01","publication":"Molecular Ecology","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publist_id":"3746","author":[{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"George","full_name":"Melika, George","last_name":"Melika"},{"full_name":"Stone, Graham","last_name":"Stone","first_name":"Graham"}],"title":"A likelihood based comparison of population histories in a parasitoid guild","citation":{"mla":"Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x.","ama":"Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617. doi:10.1111/j.1365-294X.2012.05700.x","apa":"Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x","ieee":"K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” Molecular Ecology, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012.","short":"K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617.","chicago":"Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x.","ista":"Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"09","intvolume":" 21","abstract":[{"text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd.","lang":"eng"}],"oa_version":"Submitted Version","related_material":{"record":[{"relation":"research_data","status":"public","id":"13075"}]},"volume":21,"issue":"18","ec_funded":1,"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5304","checksum":"c14ee4cb2a8ba9575bfd8a9bb7a883bb","file_size":235820,"date_updated":"2020-07-14T12:45:57Z","creator":"system","file_name":"IST-2014-296-v1+1_4_wasps_revised3.pdf","date_created":"2018-12-12T10:17:47Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5305","checksum":"f00afc5b887c8222014b57375b8caece","creator":"system","file_size":41975,"date_updated":"2020-07-14T12:45:57Z","file_name":"IST-2014-296-v1+2_4_wasps_Supporting2.pdf","date_created":"2018-12-12T10:17:48Z"}],"language":[{"iso":"eng"}],"type":"journal_article","status":"public","pubrep_id":"296","_id":"2968","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:57Z","date_updated":"2023-05-30T13:07:47Z","ddc":["570","579"]},{"day":"08","year":"2012","date_created":"2023-05-23T17:01:02Z","doi":"10.5061/DRYAD.0G0FS","related_material":{"record":[{"status":"public","id":"2968","relation":"used_in_publication"}]},"date_published":"2012-06-08T00:00:00Z","oa_version":"Published Version","abstract":[{"text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times.","lang":"eng"}],"month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0g0fs"}],"oa":1,"publisher":"Dryad","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"chicago":"Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.","ista":"Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.","mla":"Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.","short":"K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).","ieee":"K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.","ama":"Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS","apa":"Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. https://doi.org/10.5061/DRYAD.0G0FS"},"date_updated":"2023-05-30T13:07:48Z","title":"Data from: A likelihood-based comparison of population histories in a parasitoid guild","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"last_name":"Lohse","full_name":"Lohse, Konrad","first_name":"Konrad"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Graham","last_name":"Stone","full_name":"Stone, Graham"},{"full_name":"Melika, George","last_name":"Melika","first_name":"George"}],"_id":"13075","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference"},{"status":"public","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"article_type":"original","type":"journal_article","_id":"13407","extern":"1","date_updated":"2023-08-08T07:51:10Z","month":"11","intvolume":" 134","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"We show that diamagnetic particles can be remotely manipulated by a magnet by the reversible adsorption of dual-responsive, light-switchable/superparamagnetic nanoparticles down to their surface. Adsorption occurs upon exposure to UV light, and can be reversed thermally or by ambient light. The dynamic self-assembly of thin films of the dual-responsive nanoparticles induces attractive interactions between diamagnetic particles. We demonstrate that catalytic amounts of the dual-responsive nanoparticles are sufficient to magnetically guide and deliver the diamagnetic particles to desired locations, where they can then be released by disassembling the dynamic layers of superparamagnetic nanoparticles with visible light."}],"volume":134,"issue":"48","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"publication_status":"published","title":"Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets","author":[{"first_name":"Olga","last_name":"Chovnik","full_name":"Chovnik, Olga"},{"first_name":"Renata","last_name":"Balgley","full_name":"Balgley, Renata"},{"full_name":"Goldman, Joel R.","last_name":"Goldman","first_name":"Joel R."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"external_id":{"pmid":["23181449"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chovnik, Olga, Renata Balgley, Joel R. Goldman, and Rafal Klajn. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja309633v.","ista":"Chovnik O, Balgley R, Goldman JR, Klajn R. 2012. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 134(48), 19564–19567.","mla":"Chovnik, Olga, et al. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” Journal of the American Chemical Society, vol. 134, no. 48, American Chemical Society, 2012, pp. 19564–67, doi:10.1021/ja309633v.","apa":"Chovnik, O., Balgley, R., Goldman, J. R., & Klajn, R. (2012). Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja309633v","ama":"Chovnik O, Balgley R, Goldman JR, Klajn R. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 2012;134(48):19564-19567. doi:10.1021/ja309633v","ieee":"O. Chovnik, R. Balgley, J. R. Goldman, and R. Klajn, “Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets,” Journal of the American Chemical Society, vol. 134, no. 48. American Chemical Society, pp. 19564–19567, 2012.","short":"O. Chovnik, R. Balgley, J.R. Goldman, R. Klajn, Journal of the American Chemical Society 134 (2012) 19564–19567."},"quality_controlled":"1","publisher":"American Chemical Society","doi":"10.1021/ja309633v","date_published":"2012-11-26T00:00:00Z","date_created":"2023-08-01T09:47:42Z","page":"19564-19567","day":"26","publication":"Journal of the American Chemical Society","year":"2012"},{"type":"journal_article","article_type":"original","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"status":"public","_id":"13408","date_updated":"2023-08-08T07:55:10Z","extern":"1","scopus_import":"1","intvolume":" 8","month":"03","abstract":[{"text":"Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls.","lang":"eng"}],"pmid":1,"oa_version":"None","volume":8,"issue":"5","publication_status":"published","publication_identifier":{"issn":["1613-6810"],"eissn":["1613-6829"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"pmid":["22392681"]},"author":[{"first_name":"Yonatan","full_name":"Ridelman, Yonatan","last_name":"Ridelman"},{"full_name":"Singh, Gurvinder","last_name":"Singh","first_name":"Gurvinder"},{"first_name":"Ronit","full_name":"Popovitz-Biro, Ronit","last_name":"Popovitz-Biro"},{"last_name":"Wolf","full_name":"Wolf, Sharon G.","first_name":"Sharon G."},{"last_name":"Das","full_name":"Das, Sanjib","first_name":"Sanjib"},{"last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"title":"Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles","citation":{"mla":"Ridelman, Yonatan, et al. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small, vol. 8, no. 5, Wiley, 2012, pp. 654–60, doi:10.1002/smll.201101882.","ieee":"Y. Ridelman, G. Singh, R. Popovitz-Biro, S. G. Wolf, S. Das, and R. Klajn, “Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles,” Small, vol. 8, no. 5. Wiley, pp. 654–660, 2012.","short":"Y. Ridelman, G. Singh, R. Popovitz-Biro, S.G. Wolf, S. Das, R. Klajn, Small 8 (2012) 654–660.","apa":"Ridelman, Y., Singh, G., Popovitz-Biro, R., Wolf, S. G., Das, S., & Klajn, R. (2012). Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. Wiley. https://doi.org/10.1002/smll.201101882","ama":"Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 2012;8(5):654-660. doi:10.1002/smll.201101882","chicago":"Ridelman, Yonatan, Gurvinder Singh, Ronit Popovitz-Biro, Sharon G. Wolf, Sanjib Das, and Rafal Klajn. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small. Wiley, 2012. https://doi.org/10.1002/smll.201101882.","ista":"Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. 2012. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 8(5), 654–660."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Wiley","page":"654-660","date_created":"2023-08-01T09:47:55Z","date_published":"2012-03-12T00:00:00Z","doi":"10.1002/smll.201101882","year":"2012","publication":"Small","day":"12"},{"abstract":[{"lang":"eng","text":"We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas."}],"oa_version":"None","alternative_title":["LNCS"],"scopus_import":"1","month":"10","place":"Berlin, Heidelberg","intvolume":" 7561","publication_identifier":{"eisbn":["9783642333866"],"issn":["0302-9743"],"isbn":["9783642333859"],"eissn":["1611-3349"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":7561,"_id":"10903","series_title":"LNCS","type":"conference","conference":{"start_date":"2012-10-03","location":"Thiruvananthapuram, India","end_date":"2012-10-06","name":"ATVA: Automated Technology for Verification and Analysis"},"status":"public","date_updated":"2023-09-05T14:07:24Z","department":[{"_id":"ToHe"}],"acknowledgement":"This work has been partially supported by the French ANR project Veridyc","quality_controlled":"1","publisher":"Springer","year":"2012","day":"15","publication":"Automated Technology for Verification and Analysis","page":"167-182","date_published":"2012-10-15T00:00:00Z","doi":"10.1007/978-3-642-33386-6_14","date_created":"2022-03-21T07:58:39Z","citation":{"apa":"Bouajjani, A., Dragoi, C., Enea, C., & Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In Automated Technology for Verification and Analysis (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-33386-6_14","ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: Automated Technology for Verification and Analysis. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:10.1007/978-3-642-33386-6_14","ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in Automated Technology for Verification and Analysis, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182.","short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182.","mla":"Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” Automated Technology for Verification and Analysis, vol. 7561, Springer, 2012, pp. 167–82, doi:10.1007/978-3-642-33386-6_14.","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182.","chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In Automated Technology for Verification and Analysis, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-33386-6_14."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Ahmed","full_name":"Bouajjani, Ahmed","last_name":"Bouajjani"},{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","full_name":"Dragoi, Cezara","last_name":"Dragoi"},{"first_name":"Constantin","last_name":"Enea","full_name":"Enea, Constantin"},{"first_name":"Mihaela","full_name":"Sighireanu, Mihaela","last_name":"Sighireanu"}],"article_processing_charge":"No","title":"Accurate invariant checking for programs manipulating lists and arrays with infinite data"},{"publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"Supported by the Austrian Science Fund (FWF): P23499-N23, the Austrian Science Fund (FWF): S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award","page":"301-312","doi":"10.1007/978-3-642-33090-2_27","date_published":"2012-10-01T00:00:00Z","date_created":"2022-03-21T08:01:45Z","year":"2012","day":"01","publication":"Algorithms – ESA 2012","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"article_processing_charge":"No","external_id":{"arxiv":["1604.08234"]},"title":"Polynomial-time algorithms for energy games with special weight structures","citation":{"ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2012. Polynomial-time algorithms for energy games with special weight structures. Algorithms – ESA 2012. ESA: European Symposium on Algorithms, LNCS, vol. 7501, 301–312.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” In Algorithms – ESA 2012, 7501:301–12. Springer, 2012. https://doi.org/10.1007/978-3-642-33090-2_27.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2012). Polynomial-time algorithms for energy games with special weight structures. In Algorithms – ESA 2012 (Vol. 7501, pp. 301–312). Ljubljana, Slovenia: Springer. https://doi.org/10.1007/978-3-642-33090-2_27","ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. In: Algorithms – ESA 2012. Vol 7501. Springer; 2012:301-312. doi:10.1007/978-3-642-33090-2_27","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” in Algorithms – ESA 2012, Ljubljana, Slovenia, 2012, vol. 7501, pp. 301–312.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, Algorithms – ESA 2012, Springer, 2012, pp. 301–312.","mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithms – ESA 2012, vol. 7501, Springer, 2012, pp. 301–12, doi:10.1007/978-3-642-33090-2_27."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08234"}],"month":"10","intvolume":" 7501","abstract":[{"lang":"eng","text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP ∩ co−NP, but are not known to be in P. While the existence of polynomial-time algorithms has been a major open problem for decades, there is no algorithm that solves any non-trivial subclass in polynomial time.\r\nIn this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several counter examples that show that many previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting graph structures need not help."}],"oa_version":"Preprint","related_material":{"record":[{"relation":"later_version","id":"535","status":"public"}]},"volume":7501,"ec_funded":1,"publication_identifier":{"issn":["0302-9743"],"isbn":["9783642330896"],"eissn":["1611-3349"],"eisbn":["9783642330902"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"ESA: European Symposium on Algorithms","end_date":"2012-09-12","location":"Ljubljana, Slovenia","start_date":"2012-09-10"},"status":"public","_id":"10905","department":[{"_id":"KrCh"}],"date_updated":"2023-09-05T14:09:30Z"},{"volume":7214,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783642287558"],"eissn":["1611-3349"],"eisbn":["9783642287565"]},"publication_status":"published","month":"04","place":"Berlin, Heidelberg","intvolume":" 7214","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-642-28756-5_46"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"HSF(C) is a tool that automates verification of safety and liveness properties for C programs. This paper describes the verification approach taken by HSF(C) and provides instructions on how to install and use the tool."}],"department":[{"_id":"ToHe"}],"date_updated":"2023-09-05T14:09:54Z","status":"public","type":"conference","conference":{"start_date":"2012-03-24","end_date":"2012-04-01","location":"Tallinn, Estonia","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"series_title":"LNCS","_id":"10906","doi":"10.1007/978-3-642-28756-5_46","date_published":"2012-04-01T00:00:00Z","date_created":"2022-03-21T08:03:30Z","page":"549-551","day":"01","publication":"Tools and Algorithms for the Construction and Analysis of Systems","year":"2012","publisher":"Springer","quality_controlled":"1","oa":1,"editor":[{"first_name":"Cormac","last_name":"Flanagan","full_name":"Flanagan, Cormac"},{"last_name":"König","full_name":"König, Barbara","first_name":"Barbara"}],"title":"HSF(C): A software verifier based on Horn clauses","author":[{"first_name":"Sergey","last_name":"Grebenshchikov","full_name":"Grebenshchikov, Sergey"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta"},{"full_name":"Lopes, Nuno P.","last_name":"Lopes","first_name":"Nuno P."},{"first_name":"Corneliu","last_name":"Popeea","full_name":"Popeea, Corneliu"},{"first_name":"Andrey","last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea, and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In Tools and Algorithms for the Construction and Analysis of Systems, edited by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-28756-5_46.","ista":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C): A software verifier based on Horn clauses. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551.","mla":"Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn Clauses.” Tools and Algorithms for the Construction and Analysis of Systems, edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51, doi:10.1007/978-3-642-28756-5_46.","apa":"Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., & Rybalchenko, A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan & B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-28756-5_46","ama":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software verifier based on Horn clauses. In: Flanagan C, König B, eds. Tools and Algorithms for the Construction and Analysis of Systems. Vol 7214. LNCS. Berlin, Heidelberg: Springer; 2012:549-551. doi:10.1007/978-3-642-28756-5_46","short":"S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:, C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551.","ieee":"S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko, “HSF(C): A software verifier based on Horn clauses,” in Tools and Algorithms for the Construction and Analysis of Systems, Tallinn, Estonia, 2012, vol. 7214, pp. 549–551."}},{"oa_version":"None","place":"Berlin, Heidelberg","intvolume":" 7561","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783642333859","9783642333866"]},"publication_status":"published","file":[{"date_created":"2018-12-18T13:07:35Z","file_name":"2012_ATVA_Gupta.pdf","date_updated":"2020-07-14T12:47:10Z","file_size":465502,"creator":"dernst","file_id":"5746","checksum":"68415837a315de3cc4d120f6019d752c","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":7561,"ec_funded":1,"series_title":"LNCS","_id":"5745","type":"book_chapter","conference":{"end_date":"2012-10-06","location":"Thiruvananthapuram, Kerala, India","start_date":"2012-10-03","name":"ATVA 2012"},"status":"public","pubrep_id":"180","date_updated":"2023-09-05T14:15:29Z","ddc":["005"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:10Z","quality_controlled":"1","publisher":"Springer Berlin Heidelberg","oa":1,"has_accepted_license":"1","year":"2012","publication":"Automated Technology for Verification and Analysis","page":"107-121","doi":"10.1007/978-3-642-33386-6_10","date_published":"2012-01-01T00:00:00Z","date_created":"2018-12-18T13:01:46Z","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"citation":{"short":"A. Gupta, in:, Automated Technology for Verification and Analysis, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 107–121.","ieee":"A. Gupta, “Improved Single Pass Algorithms for Resolution Proof Reduction,” in Automated Technology for Verification and Analysis, vol. 7561, Berlin, Heidelberg: Springer Berlin Heidelberg, 2012, pp. 107–121.","apa":"Gupta, A. (2012). Improved Single Pass Algorithms for Resolution Proof Reduction. In Automated Technology for Verification and Analysis (Vol. 7561, pp. 107–121). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-33386-6_10","ama":"Gupta A. Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. Vol 7561. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012:107-121. doi:10.1007/978-3-642-33386-6_10","mla":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” Automated Technology for Verification and Analysis, vol. 7561, Springer Berlin Heidelberg, 2012, pp. 107–21, doi:10.1007/978-3-642-33386-6_10.","ista":"Gupta A. 2012.Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. vol. 7561, 107–121.","chicago":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” In Automated Technology for Verification and Analysis, 7561:107–21. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. https://doi.org/10.1007/978-3-642-33386-6_10."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta"}],"article_processing_charge":"No","title":"Improved Single Pass Algorithms for Resolution Proof Reduction"},{"file":[{"date_created":"2018-12-12T10:09:35Z","file_name":"IST-2012-100-v1+1_Ideal_abstractions_for_well-structured_transition_systems.pdf","date_updated":"2020-07-14T12:46:05Z","file_size":217104,"creator":"system","file_id":"4759","checksum":"f2f0d55efa32309ad1fe65a5fcaad90c","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":7148,"related_material":{"record":[{"relation":"dissertation_contains","id":"1405","status":"public"}]},"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Many infinite state systems can be seen as well-structured transition systems (WSTS), i.e., systems equipped with a well-quasi-ordering on states that is also a simulation relation. WSTS are an attractive target for formal analysis because there exist generic algorithms that decide interesting verification problems for this class. Among the most popular algorithms are acceleration-based forward analyses for computing the covering set. Termination of these algorithms can only be guaranteed for flattable WSTS. Yet, many WSTS of practical interest are not flattable and the question whether any given WSTS is flattable is itself undecidable. We therefore propose an analysis that computes the covering set and captures the essence of acceleration-based algorithms, but sacrifices precision for guaranteed termination. Our analysis is an abstract interpretation whose abstract domain builds on the ideal completion of the well-quasi-ordered state space, and a widening operator that mimics acceleration and controls the loss of precision of the analysis. We present instances of our framework for various classes of WSTS. Our experience with a prototype implementation indicates that, despite the inherent precision loss, our analysis often computes the precise covering set of the analyzed system."}],"month":"01","intvolume":" 7148","alternative_title":["LNCS"],"ddc":["000","005"],"date_updated":"2023-09-07T11:36:36Z","file_date_updated":"2020-07-14T12:46:05Z","department":[{"_id":"ToHe"}],"_id":"3251","status":"public","pubrep_id":"100","type":"conference","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2012-01-22","location":"Philadelphia, PA, USA","end_date":"2012-01-24"},"day":"01","has_accepted_license":"1","year":"2012","date_published":"2012-01-01T00:00:00Z","doi":"10.1007/978-3-642-27940-9_29","date_created":"2018-12-11T12:02:16Z","page":"445 - 460","acknowledgement":"This research was supported in part by the European Research Council (ERC) Advanced Investigator Grant QUAREM and by the Austrian Science Fund (FWF) project S11402-N23.","publisher":"Springer","quality_controlled":"1","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Zufferey D, Wies T, Henzinger TA. Ideal abstractions for well structured transition systems. In: Vol 7148. Springer; 2012:445-460. doi:10.1007/978-3-642-27940-9_29","apa":"Zufferey, D., Wies, T., & Henzinger, T. A. (2012). Ideal abstractions for well structured transition systems (Vol. 7148, pp. 445–460). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_29","short":"D. Zufferey, T. Wies, T.A. Henzinger, in:, Springer, 2012, pp. 445–460.","ieee":"D. Zufferey, T. Wies, and T. A. Henzinger, “Ideal abstractions for well structured transition systems,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 445–460.","mla":"Zufferey, Damien, et al. Ideal Abstractions for Well Structured Transition Systems. Vol. 7148, Springer, 2012, pp. 445–60, doi:10.1007/978-3-642-27940-9_29.","ista":"Zufferey D, Wies T, Henzinger TA. 2012. Ideal abstractions for well structured transition systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 445–460.","chicago":"Zufferey, Damien, Thomas Wies, and Thomas A Henzinger. “Ideal Abstractions for Well Structured Transition Systems,” 7148:445–60. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_29."},"title":"Ideal abstractions for well structured transition systems","publist_id":"3406","author":[{"full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien"},{"last_name":"Wies","full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}]},{"publist_id":"3537","author":[{"first_name":"Luis","full_name":"Diaz Jr, Luis","last_name":"Diaz Jr"},{"last_name":"Williams","full_name":"Williams, Richard","first_name":"Richard"},{"first_name":"Jian","last_name":"Wu","full_name":"Wu, Jian"},{"first_name":"Isaac","last_name":"Kinde","full_name":"Kinde, Isaac"},{"full_name":"Hecht, Joel","last_name":"Hecht","first_name":"Joel"},{"last_name":"Berlin","full_name":"Berlin, Jordan","first_name":"Jordan"},{"full_name":"Allen, Benjamin","last_name":"Allen","first_name":"Benjamin"},{"full_name":"Božić, Ivana","last_name":"Božić","first_name":"Ivana"},{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"},{"first_name":"Kenneth","last_name":"Kinzler","full_name":"Kinzler, Kenneth"},{"first_name":"Kelly","full_name":"Oliner, Kelly","last_name":"Oliner"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"}],"external_id":{"pmid":["22722843"]},"title":"The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers","citation":{"ieee":"L. Diaz Jr et al., “The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers,” Nature, vol. 486, no. 7404. Nature Publishing Group, pp. 537–540, 2012.","short":"L. Diaz Jr, R. Williams, J. Wu, I. Kinde, J. Hecht, J. Berlin, B. Allen, I. Božić, J. Reiter, M. Nowak, K. Kinzler, K. Oliner, B. Vogelstein, Nature 486 (2012) 537–540.","ama":"Diaz Jr L, Williams R, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012;486(7404):537-540. doi:10.1038/nature11219","apa":"Diaz Jr, L., Williams, R., Wu, J., Kinde, I., Hecht, J., Berlin, J., … Vogelstein, B. (2012). The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11219","mla":"Diaz Jr, Luis, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” Nature, vol. 486, no. 7404, Nature Publishing Group, 2012, pp. 537–40, doi:10.1038/nature11219.","ista":"Diaz Jr L, Williams R, Wu J, Kinde I, Hecht J, Berlin J, Allen B, Božić I, Reiter J, Nowak M, Kinzler K, Oliner K, Vogelstein B. 2012. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 486(7404), 537–540.","chicago":"Diaz Jr, Luis, Richard Williams, Jian Wu, Isaac Kinde, Joel Hecht, Jordan Berlin, Benjamin Allen, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11219."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"page":"537 - 540","date_published":"2012-06-28T00:00:00Z","doi":"10.1038/nature11219","date_created":"2018-12-11T12:01:43Z","year":"2012","day":"28","publication":"Nature","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"department":[{"_id":"KrCh"}],"date_updated":"2023-09-07T11:40:43Z","type":"journal_article","status":"public","_id":"3157","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1400"}]},"volume":486,"issue":"7404","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436069/","open_access":"1"}],"month":"06","intvolume":" 486","abstract":[{"text":"Colorectal tumours that are wild type for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. The simplest hypothesis to account for the development of resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that 9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between 5 and 6months following treatment. Mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. They explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version"},{"publisher":"Academic Press","quality_controlled":"1","oa":1,"day":"01","publication":"Theoretical Population Biology","year":"2012","doi":"10.1016/j.tpb.2011.11.003","date_published":"2012-02-01T00:00:00Z","date_created":"2018-12-11T12:02:19Z","page":"69 - 80","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Reiter J, Nowak M. 2012. Evolutionary dynamics of biological auctions. Theoretical Population Biology. 81(1), 69–80.","chicago":"Chatterjee, Krishnendu, Johannes Reiter, and Martin Nowak. “Evolutionary Dynamics of Biological Auctions.” Theoretical Population Biology. Academic Press, 2012. https://doi.org/10.1016/j.tpb.2011.11.003.","short":"K. Chatterjee, J. Reiter, M. Nowak, Theoretical Population Biology 81 (2012) 69–80.","ieee":"K. Chatterjee, J. Reiter, and M. Nowak, “Evolutionary dynamics of biological auctions,” Theoretical Population Biology, vol. 81, no. 1. Academic Press, pp. 69–80, 2012.","apa":"Chatterjee, K., Reiter, J., & Nowak, M. (2012). Evolutionary dynamics of biological auctions. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2011.11.003","ama":"Chatterjee K, Reiter J, Nowak M. Evolutionary dynamics of biological auctions. Theoretical Population Biology. 2012;81(1):69-80. doi:10.1016/j.tpb.2011.11.003","mla":"Chatterjee, Krishnendu, et al. “Evolutionary Dynamics of Biological Auctions.” Theoretical Population Biology, vol. 81, no. 1, Academic Press, 2012, pp. 69–80, doi:10.1016/j.tpb.2011.11.003."},"title":"Evolutionary dynamics of biological auctions","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"publist_id":"3388","external_id":{"pmid":["22120126"]},"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Many scenarios in the living world, where individual organisms compete for winning positions (or resources), have properties of auctions. Here we study the evolution of bids in biological auctions. For each auction, n individuals are drawn at random from a population of size N. Each individual makes a bid which entails a cost. The winner obtains a benefit of a certain value. Costs and benefits are translated into reproductive success (fitness). Therefore, successful bidding strategies spread in the population. We compare two types of auctions. In “biological all-pay auctions”, the costs are the bid for every participating individual. In “biological second price all-pay auctions”, the cost for everyone other than the winner is the bid, but the cost for the winner is the second highest bid. Second price all-pay auctions are generalizations of the “war of attrition” introduced by Maynard Smith. We study evolutionary dynamics in both types of auctions. We calculate pairwise invasion plots and evolutionarily stable distributions over the continuous strategy space. We find that the average bid in second price all-pay auctions is higher than in all-pay auctions, but the average cost for the winner is similar in both auctions. In both cases, the average bid is a declining function of the number of participants, n. The more individuals participate in an auction the smaller is the chance of winning, and thus expensive bids must be avoided.\r\n","lang":"eng"}],"month":"02","intvolume":" 81","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279759/ ","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"1400","status":"public"}]},"volume":81,"issue":"1","ec_funded":1,"_id":"3260","status":"public","type":"journal_article","date_updated":"2023-09-07T11:40:43Z","department":[{"_id":"KrCh"}]},{"related_material":{"record":[{"relation":"dissertation_contains","id":"2964","status":"public"}]},"volume":15,"issue":"4","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1546-1726"]},"publication_status":"published","month":"04","intvolume":" 15","scopus_import":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617474/","open_access":"1"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. It is generally thought that proximal synapses from the mossy fibers activate these neurons most efficiently, whereas distal inputs from the perforant path have a weaker modulatory influence. We used confocally targeted patch-clamp recording from dendrites and axons to map the activation of rat CA3 pyramidal neurons at the subcellular level. Our results reveal two distinct dendritic domains. In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+ channel–mediated dendritic spikes are efficiently initiated by waveforms mimicking synaptic events. CA3 pyramidal neuron dendrites showed a high Na+-to-K+ conductance density ratio, providing ideal conditions for active backpropagation and dendritic spike initiation. Dendritic spikes may enhance the computational power of CA3 pyramidal neurons in the hippocampal network.","lang":"eng"}],"department":[{"_id":"PeJo"}],"date_updated":"2023-09-07T11:43:52Z","status":"public","type":"journal_article","article_type":"original","_id":"3258","doi":"10.1038/nn.3060","date_published":"2012-04-01T00:00:00Z","date_created":"2018-12-11T12:02:18Z","page":"600 - 606","day":"01","publication":"Nature Neuroscience","year":"2012","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (TR 3/B10) and the European Union (European Research Council Advanced grant to P.J.).","title":"Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons","author":[{"first_name":"Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun","last_name":"Kim"},{"last_name":"Guzmán","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José"},{"id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua","last_name":"Hu","full_name":"Hu, Hua"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"publist_id":"3390","external_id":{"pmid":["22388958"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Kim, S., Guzmán, J., Hu, H., & Jonas, P. M. (2012). Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3060","ama":"Kim S, Guzmán J, Hu H, Jonas PM. Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience. 2012;15(4):600-606. doi:10.1038/nn.3060","short":"S. Kim, J. Guzmán, H. Hu, P.M. Jonas, Nature Neuroscience 15 (2012) 600–606.","ieee":"S. Kim, J. Guzmán, H. Hu, and P. M. Jonas, “Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons,” Nature Neuroscience, vol. 15, no. 4. Nature Publishing Group, pp. 600–606, 2012.","mla":"Kim, Sooyun, et al. “Active Dendrites Support Efficient Initiation of Dendritic Spikes in Hippocampal CA3 Pyramidal Neurons.” Nature Neuroscience, vol. 15, no. 4, Nature Publishing Group, 2012, pp. 600–06, doi:10.1038/nn.3060.","ista":"Kim S, Guzmán J, Hu H, Jonas PM. 2012. Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons. Nature Neuroscience. 15(4), 600–606.","chicago":"Kim, Sooyun, José Guzmán, Hua Hu, and Peter M Jonas. “Active Dendrites Support Efficient Initiation of Dendritic Spikes in Hippocampal CA3 Pyramidal Neurons.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3060."},"project":[{"_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","grant_number":"SFB-TR3-TP10B"}]},{"date_updated":"2023-09-07T11:43:51Z","citation":{"ista":"Kim S. 2012. Active properties of hippocampal CA3 pyramidal neuron dendrites. Institute of Science and Technology Austria.","chicago":"Kim, Sooyun. “Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites.” Institute of Science and Technology Austria, 2012.","ieee":"S. Kim, “Active properties of hippocampal CA3 pyramidal neuron dendrites,” Institute of Science and Technology Austria, 2012.","short":"S. Kim, Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites, Institute of Science and Technology Austria, 2012.","ama":"Kim S. Active properties of hippocampal CA3 pyramidal neuron dendrites. 2012.","apa":"Kim, S. (2012). Active properties of hippocampal CA3 pyramidal neuron dendrites. Institute of Science and Technology Austria.","mla":"Kim, Sooyun. Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites. Institute of Science and Technology Austria, 2012."},"supervisor":[{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"first_name":"Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","full_name":"Kim, Sooyun"}],"publist_id":"3755","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"title":"Active properties of hippocampal CA3 pyramidal neuron dendrites","_id":"2964","type":"dissertation","status":"public","year":"2012","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"day":"01","page":"65","date_created":"2018-12-11T12:00:35Z","date_published":"2012-06-01T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"3258"}]},"abstract":[{"text":"CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. These neurons receive multiple excitatory inputs from numerous sources. Therefore, the rules of spatiotemporal integration of multiple synaptic inputs and propagation of action potentials are important to understand how CA3 neurons contribute to higher brain functions at cellular level. By using confocally targeted patch-clamp recording techniques, we investigated the biophysical properties of rat CA3 pyramidal neuron dendrites. We found two distinct dendritic domains critical for action potential initiation and propagation: In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+-channel mediated dendritic spikes are efficiently evoked by local dendritic depolarization or waveforms mimicking synaptic events. These findings can be explained by a high Na+-to-K+ conductance density ratio of CA3 pyramidal neuron dendrites. The results challenge the prevailing view that proximal mossy fiber inputs activate CA3 pyramidal neurons more efficiently than distal perforant inputs by showing that the distal synapses trigger a different form of activity represented by dendritic spikes. The high probability of dendritic spike initiation in the distal area may enhance the computational power of CA3 pyramidal neurons in the hippocampal network. ","lang":"eng"}],"oa_version":"None","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"month":"06"},{"_id":"3246","type":"journal_article","status":"public","citation":{"ista":"Barone V, Heisenberg C-PJ. 2012. Cell adhesion in embryo morphogenesis. Current Opinion in Cell Biology. 24(1), 148–153.","chicago":"Barone, Vanessa, and Carl-Philipp J Heisenberg. “Cell Adhesion in Embryo Morphogenesis.” Current Opinion in Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ceb.2011.11.006.","ieee":"V. Barone and C.-P. J. Heisenberg, “Cell adhesion in embryo morphogenesis,” Current Opinion in Cell Biology, vol. 24, no. 1. Elsevier, pp. 148–153, 2012.","short":"V. Barone, C.-P.J. Heisenberg, Current Opinion in Cell Biology 24 (2012) 148–153.","apa":"Barone, V., & Heisenberg, C.-P. J. (2012). Cell adhesion in embryo morphogenesis. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2011.11.006","ama":"Barone V, Heisenberg C-PJ. Cell adhesion in embryo morphogenesis. Current Opinion in Cell Biology. 2012;24(1):148-153. doi:10.1016/j.ceb.2011.11.006","mla":"Barone, Vanessa, and Carl-Philipp J. Heisenberg. “Cell Adhesion in Embryo Morphogenesis.” Current Opinion in Cell Biology, vol. 24, no. 1, Elsevier, 2012, pp. 148–53, doi:10.1016/j.ceb.2011.11.006."},"date_updated":"2023-09-07T12:05:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Barone","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"publist_id":"3423","title":"Cell adhesion in embryo morphogenesis","department":[{"_id":"CaHe"}],"abstract":[{"lang":"eng","text":"Visualizing and analyzing shape changes at various scales, ranging from single molecules to whole organisms, are essential for understanding complex morphogenetic processes, such as early embryonic development. Embryo morphogenesis relies on the interplay between different tissues, the properties of which are again determined by the interaction between their constituent cells. Cell interactions, on the other hand, are controlled by various molecules, such as signaling and adhesion molecules, which in order to exert their functions need to be spatiotemporally organized within and between the interacting cells. In this review, we will focus on the role of cell adhesion functioning at different scales to organize cell, tissue and embryo morphogenesis. We will specifically ask how the subcellular distribution of adhesion molecules controls the formation of cell-cell contacts, how cell-cell contacts determine tissue shape, and how tissue interactions regulate embryo morphogenesis."}],"acknowledgement":"This review comes from a themed issue on Cell structure and dynamics Edited by Jason Swedlow and Gaudenz Danuser","oa_version":"None","publisher":"Elsevier","scopus_import":1,"quality_controlled":"1","intvolume":" 24","month":"02","year":"2012","publication_status":"published","language":[{"iso":"eng"}],"publication":"Current Opinion in Cell Biology","day":"01","page":"148 - 153","date_created":"2018-12-11T12:02:14Z","volume":24,"related_material":{"record":[{"relation":"dissertation_contains","id":"961","status":"public"}]},"doi":"10.1016/j.ceb.2011.11.006","date_published":"2012-02-01T00:00:00Z","issue":"1"}]